cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mb0sh
title: Data from: Biodiversity in agricultural landscapes: the effect of apple cultivar on epiphyte diversity

description: In natural systems, extended phenotypes of trees can be important in
 determining the species composition and diversity of associated
 communities. Orchards are productive systems where trees dominate, and can
 be highly biodiverse, but few studies have considered the importance of
 tree genetic background in promoting associated biodiversity. We tested
 the effect of apple cultivar (plant genetic background) on the diversity
 and composition of the associated epiphytic bryophyte community across a
 total of seven cultivars in five productive East Anglian orchards where
 each orchard contained two cultivars. Data were collected from 617
 individual trees, over 5 years. Species richness and community composition
 were significantly influenced by both orchard and cultivar. Differences
 among orchards explained 16% of the variation in bryophyte community data,
 while cultivar explained 4%. For 13 of the 41 bryophyte species recorded,
 apple cultivar was an important factor in explaining their distribution.
 While the effects of cultivar were small, we were able to detect them at
 multiple levels of analysis. We provide evidence that extended phenotypes
 act in productive as well as natural systems. With issues of food security
 ranking high on the international agenda, it is important to understand
 the impact of production regimes on associated biodiversity. Our results
 can inform mitigation of this potential conflict.
description: Epiphyte community data
 from East Anglian productive orchardsThe file contains
 presence and absence data for epiphytic bryophytes surveyed from five
 productive East Anglian orchards between 2005-2009New_moss.csv
DOI: 10.5061/dryad.83576bv
title: Data from: Single-dose oral ciprofloxacin prophylaxis as a response to a meningococcal meningitis epidemic in the African meningitis belt: a three-arm, open-label, cluster-randomized trial

description: Background: Antibiotic prophylaxis for contacts of meningitis cases is not
 recommended during outbreaks in the African meningitis belt. We assessed
 the effectiveness of single-dose oral ciprofloxacin administered to
 household contacts and in village-wide distributions on the overall attack
 rate (AR) in an outbreak of meningococcal meningitis. Methods and
 findings: In this 3-arm, open-label, cluster-randomized trial during a
 meningococcal meningitis outbreak in Madarounfa District, Niger, villages
 notifying a suspected case were randomly assigned (1:1:1) to standard care
 (the control arm), single-dose oral ciprofloxacin for household contacts
 within 24 hours of case notification, or village-wide distribution of
 ciprofloxacin within 72 hours of first case notification. The primary
 outcome was the overall AR of suspected meningitis after inclusion. A
 random sample of 20 participating villages was enrolled to document any
 changes in fecal carriage prevalence of ciprofloxacin-resistant and
 extended-spectrum beta-lactamase (ESBL)–producing Enterobacteriaceae
 before and after the intervention. Between April 22 and May 18, 2017, 49
 villages were included: 17 to the control arm, 17 to household
 prophylaxis, and 15 to village-wide prophylaxis. A total of 248 cases were
 notified in the study after the index cases. The AR was 451 per 100,000
 persons in the control arm, 386 per 100,000 persons in the household
 prophylaxis arm (t test versus control p = 0.68), and 190 per 100,000
 persons in the village-wide prophylaxis arm (t test versus control p =
 0.032). The adjusted AR ratio between the household prophylaxis arm and
 the control arm was 0.94 (95% CI 0.52–1.73, p = 0.85), and the adjusted AR
 ratio between the village-wide prophylaxis arm and the control arm was
 0.40 (95% CI 0.19‒0.87, p = 0.022). No adverse events were notified.
 Baseline carriage prevalence of ciprofloxacin-resistant Enterobacteriaceae
 was 95% and of ESBL-producing Enterobacteriaceae was &gt;90%, and did
 not change post-intervention. One limitation of the study was the small
 number of cerebrospinal fluid samples sent for confirmatory testing.
 Conclusions: Village-wide distribution of single-dose oral ciprofloxacin
 within 72 hours of case notification reduced overall meningitis AR.
 Distributions of ciprofloxacin could be an effective tool in future
 meningitis outbreak responses, but further studies investigating length of
 protection, effectiveness in urban settings, and potential impact on
 antimicrobial resistance patterns should be carried out.
description: NCT02724046 Main trial
 databaseData from
 NCT02724046NCT02724046 Trial
 database.xlsx
DOI: 10.5061/dryad.v01kb
title: Data from: Context-dependence of maternal effects: testing assumptions of optimal egg size, differential- and sex-allocation models

description: If offspring develop in adverse conditions, the maternal component of
 their phenotypic variation might increase due to the stronger dependence
 of offspring traits on parental investment. This should result in
 increased parental investment to individual offspring, as assumed by the
 model of optimal egg size. The opposite pattern, i.e., stronger dependence
 of offspring fitness on parental investment and consequently larger
 parental investment under good conditions is assumed by both the theory of
 differential allocation if attractive males provide material benefits, and
 reproductive compensation if they invest less into paternal care. Another
 influential idea is the Trivers-Willard model, which assumes sex-specific
 dependence of offspring fitness on parental investment. Here we tested
 these ideas by examining the effects of egg size on offspring fitness
 across many postnatal contexts in the Collared Flycatcher Ficedula
 albicollis. We employed a cross-fostering design that generated variation
 in egg size within nests and used brood means of fledgling mass as a
 functional measure of the quality of rearing conditions. Effects of egg
 size on three offspring traits, including lifetime reproductive success of
 recruits, were more pronounced in low-quality broods. These results
 support the assumption of the model of optimal egg size. Based on female
 preference for males providing material benefits, this pattern could
 support differential allocation, if attractive males invest less in
 paternal care, or reproductive compensation, if they invest more. By
 comparison, we did not find any evidence for sex specificity of fitness
 returns that might explain sex monomorphism of egg size in this species.
 The challenge for future studies will be the integration of components of
 parental investment and offspring fitness into their global measures and
 testing how the former affects the latter across gradients of postnatal
 conditions.
description: dataset
DOI: 10.5061/dryad.tj1jk
title: Data from: Postglacial recolonizations, watershed crossings and human translocations shape the distribution of chub lineages around the Swiss Alps

description: Background: Distributions of European fish species were shaped by
 glaciations and the geological history of river networks until human
 activities partially abrogated the restrictions of biogeographical
 regions. The nearby origins of the Rhine, Rhone, Danube and Po rivers in
 the Swiss Alps allow the examination of historical and human-influenced
 patterns in fish genetic structure over a small geographic scale. We
 investigated these patterns in the widespread European chub (Squalius
 cephalus) from the Rhone, Rhine and Danube catchments and its proposed
 southern sister species Italian chub (Squalius squalus) from the Po
 catchment. Results: A phylogenetic tree constructed from mitochondrial
 Cytochrome b and COI sequences was consistent with earlier work in that it
 showed a separation of European chub and Italian chub, which was also
 reflected in microsatellite allele frequencies, morphological traits and
 shape differences quantified by geometric morphometrics. A new finding was
 that the predominant mitochondrial haplotype of European chub from the
 Rhine and Rhone catchments was also discovered in some individuals from
 Swiss populations of the Italian chub, presumably as a result of human
 translocation. Consistent with postglacial recolonizations from multiple
 refugia along the major rivers, the nuclear genetic structure of the
 European chub largely reflected drainage structure, but it was modified by
 watershed crossings between Rhine and Rhone near Lake Geneva as well as
 between Danube and Rhine near Lake Constance. Conclusion: Our study adds
 new insights into the cyprinid colonization history of central Europe by
 showing that multiple processes shaped the distribution of different chub
 lineages around the Swiss Alps. Interestingly, we find evidence that
 cross-catchment migration has been mediated by unusual geological events
 such as drainage captures or watershed crossings facilitated by retreating
 glaciers, as well as evidence that human transport has interfered with the
 historical distribution of these fish (European chub haplotypes present in
 the Italian chub). The desirable preservation of evolutionarily distinct
 lineages will thus require the prevention of further translocations.
description: dryad_microsatellite_dataMicrosatellite genotypes of all chub analyzed in the study.dryad_traditional_morphmetric_dataTraditional morphometric data of all chub analyzed in the study.dryad_geometric_morphometric_dataRaw data used for geometric morphometric analyses (landmark coordinates in .tps format for import into geometric morphometrics software packages such as MorphoJ).
DOI: 10.5061/dryad.3qv3p
title: Data from: Ontogenetic and interspecific metabolic scaling in insects

description: Design constraints imposed by increasing size cause metabolic rate in
 animals to increase more slowly than mass. This ubiquitous biological
 phenomenon is referred to as metabolic scaling. However, mechanistic
 explanations for interspecific metabolic scaling do not apply to
 ontogenetic size changes within a species, implying different mechanisms
 for scaling phenomena. Here, we show that the dynamic energy budget theory
 approach of compartmentalizing biomass into reserve and structural
 components provides a unified framework for understanding ontogenetic and
 interspecific metabolic scaling. We formulate the theory for insects and
 show that it can account for ontogenetic metabolic scaling during the
 embryonic and larval phases, as well as the U-shaped respiration curve
 during pupation. After correcting for the predicted ontogenetic scaling
 effects, which we show to follow universal curves, the scaling of
 respiration between species is approximated by a three-quarters power law,
 supporting past empirical studies on insect metabolic scaling and our
 theoretical predictions. The ability to explain ontogenetic and
 interspecific metabolic scaling effects under one consistent framework
 suggests that the partitioning of biomass into reserve and structure is a
 necessary foundation to a general metabolic theory.
description: Insect ontogenetic
 respirationThis data set includes
 respiration measurements on 50 insects across various stages of
 ontogenetic development (embryonic, immature, and pupal respiration). The
 data were compiled from the literature with references and comments given
 in the document.Dataset_1.xlsx
DOI: 10.5061/dryad.128jr
title: Data from: Evidence for two sympatric sirenian species (Mammalia, Tethytheria) in the early Oligocene of Central Europe

description: The early Oligocene (Rupelian) sirenian Halitherium schinzii Kaup, 1838,
 which represents the type species of the genus Halitherium Kaup, 1838, is
 revised herein based on a morphological re-evaluation of skeletal material
 originally assigned to this taxon. This study provides new and
 comprehensive information on the cranial and postcranial anatomy and
 allows the distinction of two sympatric species. Following a recent
 approach on the invalidity and subsequent rejection of H. schinzii Kaup,
 1838, Kaupitherium gruelli new genus new species is established on the
 basis of a nearly complete holotype. The second taxon resembles K. gruelli
 n. sp. in a number of skeletal features, such as reduced nasals and
 absence of the canines, but can be clearly distinguished mainly by the
 post-canine dental formula and the supraoccipital morphology. The
 diagnostic skullcap of a species formerly synonymized under “H. schinzii”
 is re-validated as the holotype of K. bronni (Krauss, 1858). On the basis
 of paleoecological implications, a hypothesis is established to explain
 the overlapping stratigraphic and biogeographic occurrences (i.e.,
 sympatry of both taxa). A diagnosis and up-to-date synonymy complement the
 taxonomical information. The revision of “H. schinzii” provides new data
 on the past sirenian diversity and forms the basis for a taxonomic and
 systematic re-evaluation of species originally grouped in the genus
 “Halitherium.”
description: SuppIementary data set
 1-4The Supplementary data
 set 1-4 includes material referred to the newly introduced species
 Kaupitherium gruelli n. gen. and n. sp. and Kaupitherium bronni (Krauss,
 1858) as well as cranial, mandibular, dental, and postcranial measurements
 of the respective species.SuppInfo.docx
DOI: 10.5061/dryad.55636
title: Data from: Performance improvement of miniaturized ZnO nanowire accelerometer fabricated by refresh hydrothermal synthesis

description: Miniaturized accelerometers are necessary for evaluating the performance
 of small devices such as haptics, robotics and simulators. In this study,
 we fabricated miniaturized accelerometers using well aligned ZnO
 nanowires. The layer of ZnO nanowires is used for active piezoelectric
 layer of the accelerometer and copper was chosen as a head mass. Seedless
 and refresh hydrothermal synthesis methods were conducted to grow ZnO
 nanowires on the copper substrate and effect of ZnO nanowire length on the
 accelerometer performance was investigated. The refresh hydrothermal
 synthesis exhibits longer ZnO nanowires, 12 μm, than the seedless
 hydrothermal synthesis, 6 μm. Performance of the fabricated accelerometers
 was verified by comparing with a commercial accelerometer. The sensitivity
 of the fabricated accelerometer by the refresh hydrothermal synthesis is
 shown to be 37.7 pA/g, which is about 30 times larger than the previous
 result.
description: Supplementary
 information_figure dataData for Fig
 6,7,8,9,10.
DOI: 10.5061/dryad.h4r6h5n
title: Data from: Effects of carbon-based nanomaterials on seed germination, biomass accumulation and salt stress response of bioenergy crops

description: Bioenergy crops are an attractive option for use in energy production. A
 good plant candidate for bioenergy applications should produce a high
 amount of biomass and resist harsh environmental conditions. Carbon-based
 nanomaterials (CBNs) have been described as promising seed germination and
 plant growth regulators. In this paper, we tested the impact of two CBNs:
 graphene and multi-walled carbon nanotubes (CNTs) on germination and
 biomass production of two major bioenergy crops (sorghum and switchgrass).
 The application of graphene and CNTs increased the germination rate of
 switchgrass seeds and led to an early germination of sorghum seeds. The
 exposure of switchgrass to graphene (200 mg/l) resulted in a 28% increase
 of total biomass produced compared to untreated plants. We tested the
 impact of CBNs on bioenergy crops under salt stress conditions and
 discovered that CBNs can significantly reduce symptoms of salt stress
 imposed by the addition of NaCl into the growth medium. Using an ion
 selective electrode, we demonstrated that the concentration of Na+ ions in
 NaCl solution can be significantly decreased by the addition of CNTs to
 the salt solution. Our data confirmed the potential of CBNs as plant
 growth regulators for non-food crops and demonstrated the role of CBNs in
 the protection of plants against salt stress by desalination of saline
 growth medium.
description: Figure
 2Raw
 data for Figure 2Figure
 3Raw
 data for Figure 3Figure
 4Raw
 data fir Figure 4Figure
 5Raw
 data for Figure 5Figure
 6Raw
 data for Figure 6Figure
 7Raw
 data for Figure 7Figure
 8Calibration curve for
 Figure 8
DOI: 10.5061/dryad.8j413
title: Data from: Hindlimb muscle function in turtles: is novel skeletal design correlated with novel muscle function?

description: Variations in musculoskeletal lever systems have formed an important
 foundation for predictions about the diversity of muscle function and
 organismal performance. Changes in the structure of lever systems may be
 coupled with changes in muscle use and give rise to novel muscle
 functions. The two extant turtle lineages, cryptodires and pleurodires,
 exhibit differences in hindlimb structure. Cryptodires possess the
 ancestral musculoskeletal morphology, with most hip muscles originating on
 the pelvic girdle, which is not fused to the shell. In contrast,
 pleurodires exhibit a derived morphology, in which fusion of the pelvic
 girdle to the shell has resulted in shifts in the origin of most hip
 muscles onto the interior of the shell. To test how variation in muscle
 arrangement might influence muscle function during different locomotor
 behaviors, we combined measurements of muscle leverage in five major
 hindlimb muscles with data on muscle use and hindlimb kinematics during
 swimming and walking in representative semiaquatic cryptodires and
 pleurodires. We found substantial differences in muscle leverage between
 the two species. Additionally, we found that there were extensive
 differences in muscle use in both species, especially while walking, with
 some pleurodire muscles exhibiting novel functions associated with their
 derived musculoskeletal lever system. However, the two species shared
 similar overall kinematic profiles within each environment. Our results
 suggest that changes in limb lever systems may relate to changes in limb
 muscle motor patterns and kinematics, but that other factors must also
 contribute to differences in muscle activity and limb kinematics between
 these taxa.
description: MayerlEtal2017 -
 hindlimb muscle use in turtlesData used for statistics
 on muscle use, kinematics, and muscle anatomy.
DOI: 10.15468/dl.te6ydy
title: Occurrence Download

description: A dataset containing 182 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriolarynx australis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 182 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000903-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g93c2f47
title: Data from: Self-sustaining populations, population sinks or aggregates of strays: chum (Oncorhynchus keta) and Chinook salmon (O. tshawytscha) in the Wood River system, Alaska

description: Small populations can provide insights into ecological and evolutionary
 aspects of species distributions over space and time. In the Wood River
 system in Alaska, USA, small aggregates of Chinook (Oncorhynchus
 tshawytscha) and chum salmon (O. keta) spawn in an area dominated by
 sockeye salmon (O. nerka). Our objective was to determine whether these
 Chinook and chum salmon are reproductively isolated, self-sustaining
 populations, population sinks that produce returning adults but receive
 immigration, or strays from other systems that do not produce returning
 adults. DNA samples collected from adult chum salmon from 16 streams and
 Chinook salmon from four streams in the Wood River system over 3 years
 were compared to samples from large populations in the nearby Nushagak
 River system, a likely source of strays. For both species, microsatellite
 markers indicated no significant genetic differentiation between the two
 systems. Simulations of microsatellite data in a large source and a
 smaller sink population suggested that considerable immigration would be
 required to counteract the diverging effects of genetic drift and produce
 genetic distances as small as those observed, considering the small census
 sizes of the two species in the Wood River system. Thus, the Wood River
 system likely receives substantial immigration from neighbouring
 watersheds, such as the Nushagak River system, which supports highly
 productive runs. Although no data on population productivity in the Wood
 River system exist, our results suggest source–sink dynamics for the two
 species, a finding relevant to other systems where salmonid population
 sizes are limited by habitat factors.
description: Chum salmon
 microsatellite dataSamples were collected
 in the field, and the data are in GenePop format. Sample abbreviations
 match those in Table 1 of the manuscript.ChumAll10L.txtChinook salmon microsatellite dataSamples were collected in the field, and data are in GenePop format. Sample abbreviations match those in Table 2 of the manuscript.ChinookAll11L.txt
DOI: 10.5061/dryad.65t4k
title: Data from: Body condition explains migratory performance of a long-distance migrant

description: Body condition (i.e. relative mass after correcting for structural size)
 affects the behaviour of migrating birds, but how body condition affects
 migratory performance, timing and fitness is still largely unknown. Here,
 we studied the effects of relative body condition on individual departure
 decisions, wind selectivity, flight speed and timing of migration for a
 long-distance migratory shorebird, the red knot Calidris canutus rufa. By
 using automated VHF telemetry on a continental scale, we studied
 knots' migratory movements with unprecedented temporal resolution
 over a 3-year period. Knots with a higher relative body condition left the
 staging site later than birds in lower condition, yet still arrived
 earlier to their Arctic breeding grounds compared to knots in lower
 relative body condition. They accomplished this by selecting more
 favourable winds at departure, thereby flying faster and making shorter
 stops en route. Individuals with a higher relative body condition in
 spring migrated south up to a month later than individuals in lower
 condition, suggesting that individuals in better condition were more
 likely to have bred successfully. Moreover, individuals with a lower
 relative body condition in spring had a lower probability of being
 detected in autumn, suggestive of increased mortality. The pressure to
 arrive early to the breeding grounds is considered to be an important
 constraint of migratory behaviour and this study highlights the important
 influence of body condition on migratory decisions, performance and
 potentially fitness of migrant birds.
description: Red Knot VHF tracking
 dataPlease read the README
 file for details.