cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25934/pr00012545.0
title: Available datapackage for study 'Effective, Reagent-Free Detection of the Odor Signature of COVID-19 Infection Using a Nano-Enabled Sensor Array'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5061/dryad.z34tmpg80
title: A practical method for estimating coupling functions in complex dynamical systems

description: A foremost challenge in modern network science is the inverse problem of
 reconstruction (inference) of coupling equations and network topology from
 the measurements of the network’s dynamics. Of particular interest are the
 methods that can operate on real (empirical) data without interfering with
 the system. One of such earlier attempts (Tokuda et al. 2007 Phys. Rev.
 Lett. 99, 064101) was a method suited for general limit-cycle oscillators,
 yielding both oscillators’ natural frequencies and coupling functions
 between them (phase equations) from empirically measured time series. The
 present paper reviews the above method in a way comprehensive to
 domain-scientists other than physics. It also presents applications of the
 method to (i) detection of the network connectivity, (ii) inference of the
 phase sensitivity function, (iii) approximation of the interaction among
 phase-coherent chaotic oscillators, and (iv) experimental data from a
 forced Van der Pol electric circuit. This reaffirms the range of
 applicability of the method for reconstructing coupling functions and
 makes it accessible to a much wider scientific community.
description: External forcing was injected from a function generator (Keysight
 33500B) to Van der Pol circuit. To obtain the phase
 sensitivity function, impulses (stimulus duration: 380 µs, stimulus
 strength: 3 V) were randomly injected as the external force. The circuit
 output as well as the input impulses were simultaneously
 measured. The first file (PRC.csv) contains phase
 sensitivity function (also called ``infinitesimal phase response
 curve''). The amount of phase shift induced by external stimulus
 is described as a function of the timing at which the stimulus was
 injected. As the external force, impulses (stimulus duration: 380 µs,
 stimulus strength: 3 V) were randomly injected. Natural frequency of the
 oscillator circuit measured before the stimulus experiment was 110.5
 Hz. The second file (106hz100m100m1p5v12p5ksmpl.csv)
 contains Van der Pol circuit dynamics with a sinusoidal forcing (forcing
 frequency: 106 Hz). The forcing amplitude was varied from 0 V to 1.5 V.
 The circuit output as well as the forcing waveforms were simultaneously
 measured with a sampling frequency of 12.5 kHz.
DOI: 10.5061/dryad.cjsxksn1n
title: Convergent evolution in lemur environmental niches

description: Aim: To test the hypothesis that adaptive convergent evolution of climate
 niches occurred in multiple independent lemur lineages. 
 Location: Madagascar Taxon: Lemurs Methods: I collected climate and
 altitude data from WorldClim and summarized the niches of almost all
 living lemurs (83 species) into phylogenetically-controlled principal
 components. To test for convergent evolution, I searched for multiple,
 similar climate optima using multi-peak Ornstein-Uhlenbeck models
 (surface, l1-ou, bayou). I compared the observed level of climate
 convergence to that simulated under neutral and single-optimum models. To
 test if behavioral or morphological traits were related to climate niches,
 I used phylogenetic regressions with activity pattern, diet, and body
 size. Results: From an ancestral niche with high rainfall and low
 seasonality, four lemur lineages independently converged on climate niche
 optima characterized by high temperatures and low rainfall, supporting
 adaptive evolution in southwest deciduous and arid habitats. The observed
 level of convergence was more frequent than expected under Brownian motion
 and single-optimum simulations, which illustrates that the results are
 likely not a result of stochastic evolution over long time periods.
 Nocturnal and cathemeral activity patterns were common among lineages in
 the arid climate niche.  Conclusion: Lemur climate niche
 evolution demonstrated that convergence explains the distribution of four
 independent clades in hot, arid environments of southwest Madagascar. The
 timing of these convergent shifts coincided with the origination of modern
 arid-adapted plant genera, some of which are important lemur food sources.
 These communities have high endemicity and are especially threatened by
 habitat loss. Arid environments are arenas in which convergent evolution
 is predicted to occur frequently.
DOI: 10.15468/dl.w39gwh
title: Occurrence Download

description: A dataset containing 343 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-71.8945 45.40815,-71.89255 45.40586,-71.89437 45.40518,-71.89355 45.40403,-71.89087 45.40471,-71.89009 45.40362,-71.88882 45.4041,-71.88991 45.4071,-71.89267 45.4085,-71.8945 45.40815))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 343 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001929-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pzgmsbcfr
title: Data from: Pervasive introgression of MHC genes in newt hybrid zones

description: Variation in the vertebrate major histocompatibility complex (MHC) genes
 is crucial for fighting pathogen assault. Because new alleles confer a
 selective advantage, MHC should readily introgress between species, even
 under limited hybridization. Using replicated transects through two hybrid
 zones between strongly reproductively isolated European newts, Lissotriton
 montandoni and L. vulgaris, we demonstrated recent and ongoing MHC class I
 and II introgression in the Carpathian region. The extent of introgression
 correlated with the age of contact. In the older zone, MHC similarity
 between species within transects exceeded similarity between transects
 within species, implying pervasive introgression –  a massive
 exchange of MHC genes, not limited to specific variants. In simulations,
 the observed pattern emerged under the combined action of balancing
 selection and hybridization, but not when these processes acted
 separately. Thus, massive introgression at advanced stages of divergence
 can introduce novel and restore previously lost MHC variation, boosting
 the adaptive potential of hybridizing taxa. In consequence, MHC genes may
 be the last to stop introgressing between incipient species.
description: Dudek_et_al_ genotypes_haplotypes.xlsx: Genotypes of all
 individuals used in the study, composition of eight MHC class I and II
 haplotypes, expression status of MHC class I alleles
 Dudek_et_al_MHCI_alleles.fas: Sequences of all MHC class I
 alleles described in the current study as well as these reported earlier
 by Fijarczyk et al.
 (2018, http://dx.doi.org/10.1098/rspb.2018.0819).
 Dudek_et_al_MHCII_alleles.fas: Sequences of all MHC class II
 alleles described in the current study.
DOI: 10.15468/dl.d4utja
title: Occurrence Download

description: A dataset containing 343 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-71.8945 45.40815,-71.89255 45.40586,-71.89437 45.40518,-71.89355 45.40403,-71.89087 45.40471,-71.89009 45.40362,-71.88882 45.4041,-71.88991 45.4071,-71.89267 45.4085,-71.8945 45.40815))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 343 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001928-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.prr4xgxgn
title: Data from: Facile fabrication of fluoro-polymer self-assembled ZnO nanoparticles mediated, durable and robust omniphobic surfaces on polyester fabrics

description: Omniphobic surfaces have been widely used in many applications, especially
 due to their self-cleaning property. Omniphobicity of a surface is
 directly interpreted by measuring the contact angle that it makes with a
 liquid of interest. In this study, polyester fabric was made omniphobic
 with a measured water contact angle (WCA) of 152° by reducing the surface
 free energy of the fabric surface via the polymerization of
 3,3,4,4,5,5,6,6,7,7,8,8,8-tridecafluorooctyl methacrylate(TDM) on a ZnO
 seed layer. The fabrics with and without the seed layer were characterized
 using various analytical techniques. The WCA of the fabric with the seed
 layer was 153° compared to 142° of the fabric without the seed layer. The
 treated fabric made a contact angle of 132° with SAE 40 motor oil
 indicating its oleophobicity while non-treated fabric made no contact
 angle. In addition to that, the treated fabric is omniphobic against milk
 tea, coffee, coconut oil, and ethanol. The morphological analysis using
 scanning electron microscopy (SEM) of the treated and non-treated fabrics
 revealed that the particle size of the seed layer applied fabric was
 ranging from 100-300 nm and upon the TDM application it became less than
 100 nm. Elemental analysis by EDS showed the presence of fluorine and
 FT-IR analysis confirmed the polymerization of TDM. The polymerization of
 fluoropolymer was further confirmed by TGA and DSC analyses. The contact
 angle of the surface-modified fabric remained unchanged even after 1.5 h
 washing and 50 cycles of abrasion. The modified fabric is robust and no
 change was observed in the colour of the fabric during the process. More
 importantly the preparation method of the fabric is simple, low cost and
 quick.
DOI: 10.5061/dryad.hmgqnk9bs
title: Fire refugia facilitate forest and savanna co‐existence as alternative stable states

description: Aim: Does complex topography facilitate the establishment and persistence
 of fire‐ sensitive (forest) vegetation in a fire‐prone landscape? We test
 the prediction that fire‐sensitive vegetation will establish and persist
 in areas where the fire return interval is lower due to a topographic
 hindrance on fire spread. Location: Hluhluwe–iMfolozi Park, KwaZulu Natal,
 South Africa. Methods: Using aerial photographs from six time periods
 between 1937 and 2013, we mapped vegetation changes in Hluhluwe–iMfolozi
 Park (HiP). Using a general‐ ized additive model (GAM), we built a habitat
 suitability index (HSI) map for forest vegetation based on topographic
 variables related to fire behaviour and the vegeta‐ tion distribution maps
 from each time period. We investigated transitions between vegetation
 types between time periods based on the HSI map, as well as the effects of
 neighbourhood vegetation on transition probabilities. Results: Forest
 cover has increased overall from 1937 to 2013, however, this has not been
 a linear increase with a peak in extent in the early 1990s. The HSI, using
 topo‐ graphic predictors associated with fire behaviour, correlates with
 areas of expansion and contraction of forest vegetation. The patterns of
 expansion and contraction are, however, more nuanced, with the in situ
 vegetation neighbourhood playing a large role. Main Conclusions: Forest
 distributions in HiP have not remained static over time and have expanded
 into areas that were once savannas. This is a dynamic system where both
 forest and savanna boundaries can change considerably. Fire refugia are
 impor‐ tant for the long‐term persistence of forests in fire‐prone
 landscapes.
description: Vegetation maps and elevation rasters
DOI: 10.5061/dryad.qc5ft8n
title: Data from: Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome

description: Theoretical work suggests that sexual conflict should promote the
 maintenance of genetic diversity by the opposing directions of selection
 on males and females. If such conflict is pervasive, it could potentially
 lead to genomic heterogeneity in levels of genetic diversity an idea that
 so far has not been empirically tested on a genome-wide scale. We used
 large-scale population genomic and transcriptomic data from the collared
 flycatcher (Ficedula albicollis) to analyse how sexual conflict, for which
 we use sex-biased gene expression as a proxy, relates to genetic
 variability. Here, we demonstrate that the extent of sex-biased gene
 expression of both male-biased and female-biased genes is significantly
 correlated with levels of nucleotide diversity in gene sequences and that
 this correlation extends to diversity levels also in intergenic DNA and
 introns. We find signatures of balancing selection in sex-biased genes but
 also note that relaxed purifying selection could potentially explain part
 of the observed patterns. The finding of significant genetic
 differentiation between males and females for male-biased (and
 gonad-specific) genes indicates ongoing sexual conflict and sex-specific
 viability selection, potentially driven by sexual selection. Our results
 thus indicate that sexual antagonism could potentially be considered as
 one viable explanation to the long-standing question in evolutionary
 biology of how genomes can remain so genetically variable in face of
 strong natural and sexual selection.
description: ArchiveContains all the data for figure and table in the article, as well as a README.
DOI: 10.5061/dryad.69p8cz8x6
title: Data from: Two New Species of Aira (Poaceae) from the Iberian Peninsula and the Balearic Islands

description: Two new diploid species, Aira minoricensis and Aira hercynica are
 described and illustrated, along with chromosome counts, risk assessment,
 distribution and habitat, phenology, and comparisons with morphologically
 similar species. A comparative table and a key for the species of Aira for
 the Iberian Peninsula and the Balearic Islands are provided to assist in
 the identification of these overlooked species, and their relationships to
 other taxa are discussed.
description: Supplementary Appendix<br> I. Specimens examined for
 morphometric analyses<br> II. Other specimens examined for
 comparative morphology<br> III. Voucher of chromosome
 numbers
DOI: 10.5061/dryad.138fd23
title: Data from: Climate severity and land-cover transformation determine plant community attributes in Colombian dry forests

description: Tropical dry forests (TDF) are known to be resource-limited due to a
 marked seasonality in precipitation. However, TDF are also shaped by
 factors such as solar radiation, wind speed, soil fertility and land-cover
 transformation. Together, these factors may determine gradients of
 environmental harshness, that are likely to drive changes in plant
 community attributes. Here we evaluated the effects of environmental
 harshness on plant community diversity and structure of Colombian TDF
 based on floristic and environmental data from 15 1-ha permanent plots. We
 also analyzed effects on groups of legumes species only (including
 deciduous and non-deciduous species), deciduous species only (including
 legumes and non-legumes species), and the whole community excluding either
 legumes or deciduous separately. Drier conditions and higher land-cover
 transformation had the strongest negative effects on species diversity,
 basal area and canopy height. Soil fertility, on the contrary, did not
 have a significant effects on any of the evaluated variables.
 Interestingly, legumes maintained their diversity and basal area along the
 climatic gradient, while deciduous species were negatively affected by
 drier conditions and an increase in secondary vegetation at the landscape
 level. Our results suggest that although TDF are limited by water
 availability, land-cover transformation strongly increases environmental
 harshness. Yet, both legumes group and deciduous group were differentially
 impacted by climatic and land transformation variables. Thus, to better
 understand TDF plant community attributes, it is necessary to consider
 these gradients and to disentangle their effects on different plant
 functional groups.
description: dataRDS: Environmental
 drivers of Colombian dry forestsThis file contains the
 data serialisation of vegetation and environmental datasets of Colombian
 dry forests. File was assembled based on .RDS structure (R program version
 3.4.2). For opening use 'readRDS" function, and save it in an
 object of R. RDS contains two main trees: a) vegetation data sets
 ($vegetation.datasets) of diversity ($diversity) and forest structure
 ($forest.structure) for the Whole Plant Community (WPC), WPC excluding
 legumes, legumes only, WPC excluding deciduous and deciduous species
 groups. b) environmental data sets ($environmental.datasets) whit Climate,
 Soils and Land-cover. Additionally, one file with the first two PCA axes
 for Climate, Soils and Land-cover. For descriptions, abbreviations and
 units see: González-M. et al. Biotrópica.Colombian.dry.forests.rds
DOI: 10.5061/dryad.x95x69pcv
title: Mere presence of co-eater automatically shifts foraging tactics toward “fast and easy” food in humans

description: Competition for food resources is widespread in nature. The
 foraging behavior of social animals should thus be adapted to
 potential food competition. We hypothesized that in the presence of
 co-foragers, animals would shift their tactics to forage more frequently
 for smaller food. Because smaller foods are more abundant in nature and
 allow faster consumption, such tactics should allow animals to consume
 food more securely against scrounging. We tested whether humans would
 exhibit such a shift. To prevent subjects from having rivalry, they were
 instructed to engage in a “taste test” in a laboratory, alone or
 in pairs. Even though the other subject was merely present and there was
 no real competition for food, subjects in pairs immediately exhibited a
 systematic behavioral shift to reaching for smaller food amounts more
 frequently, which was clearly distinct from their reaching patterns both
 when eating alone and when simply weighing the same food without eating
 any. These patterns suggest that behavioral shifts in the presence of
 others may be built-in tactics in gregarious animals to adapt to potential
 food competition in social foraging.
description: Ogura_et_al_2019_RSOS.Rmd: a Rmd file that contains all R codes
 we used for analysis. source: Custom R functions for
 analysis. study1_human/rawdata: raw csv/excel
 files. study1_human/stancode: stan codes used for
 state-space modelling.
 study1_human/brms_reach,
 study1_human/brms_amount, study1_human/brms_supplementary, study1_human/brms_potato_weight_distribution,  study2_chick/brms_peck,  study2_chick/brms_amount: All fitting objects (results) of Bayesian multilevel modelling are contained in rds files. rds is a file format that can be used with R. study1_human/dataset: Cleansed datasets. study1_human/fit_statespace: All fitting objects (results) of state-space modelling.
DOI: 10.5061/dryad.v4h6741
title: Data from: Variation in activity rates may explain sex-specific dorsal color patterns in Habronattus jumping spiders

description: In many animals, color pattern and behavior interact to deceive predators.
 For mimics, such deception can range from precise (near-perfect mimicry)
 to only subtle resemblance (imperfect mimicry) and such strategies often
 differ by sex because of differing ecological selection pressures. In this
 field study, we examine variation in behavior and ecology that may be
 linked with sex differences in dorsal color pattern in three sympatric
 species of Habronattus jumping spiders (H. clypeatus, H. hallani, H.
 pyrrithrix). Males of these species have conspicuous dorsal patterning
 that is subtly reminiscent of the general color patterns of wasps and
 bees, while females are cryptic. We show that, compared with females,
 these conspicuous males exhibited increased leg-waving behavior outside of
 the context of courtship; such behavior is common in jumping spiders that
 mimic wasps and bees presumably because a mimic’s waving legs resemble
 antennae. Males of a fourth sympatric species (H. hirsutus) without
 conspicuous dorsal patterning did not exhibit increased leg-waving. These
 results are consistent with and offer preliminary support for the idea
 that male color and behavior may work together to deceive predators. We
 also examined whether higher movement rates of males (who must wander to
 find females) and/or different use of the microhabitat by the sexes could
 explain sexual dichromatism. We found that microhabitat use was similar
 for males and females, but males of all three conspicuously-colored
 species spent more time actively moving than females. To our knowledge,
 this is the first study to speculate that conspicuous male dorsal
 coloration in Habronattus may have a deceptive function, and to explore
 why dorsal coloration differs between the sexes.
description: Field study examining
 dorsal color patterns in HabronattusThis file includes
 behavioral data collected on Habronattus jumping spiders from focal
 observations in the field.DRYAD_back_pattern_field_study.xlsx
DOI: 10.5061/dryad.qs23971
title: Data from: Effects of multiple climate change stressors on gene expression in blue rockfish (Sebastes mystinus)

description: Global climate change is predicted to increase the co-occurrence of high
 pCO2 and hypoxia in upwelling zones worldwide. Yet, few studies have
 examined the effects of these stressors on economically and ecologically
 important fishes. Here, we investigated short-term responses of juvenile
 blue rockfish (Sebastes mystinus) to independent and combined high pCO2
 and hypoxia at the molecular level, using changes in gene expression and
 metabolic enzymatic activity to investigate potential shifts in energy
 metabolism. Fish were experimentally exposed to conditions associated with
 intensified upwelling under climate change: high pCO2 (1200 μatm, pH~7.6),
 hypoxia (4.0 mg O2/L), and a combined high pCO2/hypoxia treatment for 12
 h, 24 h or two weeks. Muscle transcriptome profiles varied significantly
 among the three treatments, with limited overlap among genes responsive to
 both the single and combined stressors. Under elevated pCO2, blue rockfish
 increased expression of genes encoding proteins involved in the electron
 transport chain and muscle contraction. Under hypoxia, blue rockfish up
 regulated genes involved in oxygen and ion transport and down regulated
 transcriptional machinery. Under combined high pCO2 and hypoxia, blue
 rockfish induced a unique set of ionoregulatory and hypoxia responsive
 genes not expressed under the single stressors. Thus, high pCO2 and
 hypoxia exposure appears to induce a non-additive transcriptomic response
 that cannot be predicted from single stressor exposures alone, further
 highlighting the need for multiple stressor studies at the molecular
 level. Overall, lack of a major shift in cellular energetics indicates
 that blue rockfish may be relatively resistant to intensified upwelling
 conditions in the short term.
description: CBP-A_EnzymeData_190916 Citrate synthase (CS) and lactate dehydrogenase (LDH) enzyme activities measured in blue rockfish white muscle, gill and liver tissues after exposure to independent and combined high pCO2 and hypoxia.