cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p65dp
title: Data from: Tissue-specific changes in apoplastic proteins and cell wall structure during cold acclimation of winter wheat crowns

description: The wheat (Triticum aestivum L.) crown is the critical organ of low
 temperature stress survival over winter. In cold-acclimated crowns, ice
 formation in the apoplast causes severe tissue disruption as it grows at
 the expense of intracellular water. While previous crown studies have
 shown the vascular transition zone (VTZ) to have a higher freezing
 sensitivity than the shoot apical meristem (SAM), the mechanism behind the
 differential freezing response is not fully understood. Cooling
 cold-acclimated crowns to –10 °C resulted in an absence of VTZ tetrazolium
 chloride staining, whereas the temperatures at which 50% of the SAM
 stained positive and 50% of plants recovered (LT50) were similar after
 cold acclimation for 21 (–16 °C) and 42 d (–20 °C) at 4 °C. Proteomic
 analysis of the apoplastic fluids identified dehydrins,
 vernalization-responsive proteins, and cold shock proteins preferentially
 accumulated in the SAM. In contrast, modifications to the VTZ centered on
 increases in pathogenesis-related proteins, anti-freeze proteins, and
 sugar hydrolyzing enzymes. Fourier transform infrared spectroscopy focal
 plane array analysis identified the biochemical modification of the cell
 wall to enhance methyl-esterified cross-linking of glucuronoarabinoxylans
 in the VTZ. These findings indicate that the SAM and VTZ express two
 distinct tissue-specific apoplastic responses during cold acclimation.
description: Supplementary Table
 S1List of identified and
 quantified apoplast proteins collected from the apical meristem and
 vascular transition zone of winter wheat cv. Norstar crowns. Plants were
 treated for 0, 21, or 42 d at four degrees Celsius to induce a cold
 acclimation response.Supplementary Table
 S2Apoplastic fluid malate
 dehydrogenase (MDH) specific activity in ‘Norstar’ shoot apical meristem
 (SAM) and vascular transition zone (VTZ) following 0, 21, or 42 d of cold
 acclimation. Means followed by the same letter within each column are not
 significantly different based on Fisher’s Least Significant Difference
 test (P &lt; 0.05).Supplementary Figures S1
 and S2For Supplementary Figure
 S1: Venn diagrams of 42/0 and 21/0 d apoplast cold responsive proteins in
 the shoot apical meristem (SAM) and vascular transition zone (VTZ). For
 Supplementary Figure S2: Second derivative of absorbance spectra collected
 from the SAM and VTZ.Supplementary Figs S1 and
 S2.pdf
DOI: 10.5061/dryad.f71vq
title: Data from: Managing seagrass resilience under cumulative dredging affecting light: predicting risk using dynamic Bayesian networks

description: Coastal development is contributing to ongoing declines of ecosystems
 globally. Consequently, understanding the risks posed to these systems,
 and how they respond to successive disturbances, is paramount for their
 improved management. We study the cumulative impacts of maintenance
 dredging on seagrass ecosystems as a canonical example. Maintenance
 dredging causes disturbances lasting weeks to months, often repeated at
 yearly intervals. We present a risk-based modelling framework for time
 varying complex systems centred around a dynamic Bayesian network (DBN).
 Our approach estimates the impact of a hazard on a system's response
 in terms of resistance, recovery and persistence, commonly used to
 characterise the resilience of a system. We consider whole-of-system
 interactions including light reduction due to dredging (the hazard), the
 duration, frequency and start time of dredging, and ecosystem
 characteristics such as the life-history traits expressed by genera and
 local environmental conditions. The impact on resilience of dredging
 disturbances is evaluated using a validated seagrass ecosystem DBN for
 meadows of the genera Amphibolis (Jurien Bay, WA, Australia), Halophila
 (Hay Point, Qld, Australia) and Zostera (Gladstone, Qld, Australia).
 Although impacts varied by combinations of dredging parameters and the
 seagrass meadows being studied, in general, 3 months of duration or more,
 or repeat dredging every 3 or more years, were key thresholds beyond which
 resilience can be compromised. Additionally, managing light reduction to
 less than 50% can significantly decrease one or more of loss, recovery
 time and risk of local extinction, especially in the presence of
 cumulative stressors. Synthesis and applications. Our risk-based approach
 enables managers to develop thresholds by predicting the impact of
 different configurations of anthropogenic disturbances being managed. Many
 real-world maintenance dredging requirements fall within these parameters,
 and our results show that such dredging can be successfully managed to
 maintain healthy seagrass meadows in the absence of other disturbances. We
 evaluated opportunities for risk mitigation using time windows; periods
 during which the impact of dredging stress did not impair resilience.
description: Validation
 dataValidation data used to
 validate the DBN model for Amphibolis in Jurien Bay, Halophila at Hay
 Point, and Zostera at Gladstone (supporting information S4 through S6,
 respectively).data_supp.xlsxLateral Growth from Existing IndividualsDBN CPT (visualised in supporting information S7)Physiological Status of PlantsDBN CPT (visualised in supporting information S7)Rate of Recovery in Shoot DensityDBN CPT (visualised in supporting information S7)Recruitment Rate from SeedsDBN CPT (visualised in supporting information S7)Seed DensityDBN CPT (visualised in supporting information S7)
DOI: 10.5061/dryad.8fh54
title: Data from: Combining noninvasive genetics and a new mammalian sex-linked marker provides new tools to investigate population size, structure and individual behaviour: an application to bats

description: Monitoring wild populations is crucial for their effective management.
 Noninvasive genetic methods provide robust data from individual
 free-ranging animals, which can be used in capture-mark-recapture (CMR)
 models to estimate demographic parameters without capturing or disturbing
 them. However, sex- and status-specific behaviour, which may lead to
 differences in detection probabilities, is rarely considered in
 monitoring. Here, we investigated population size, sex ratio, sex- and
 status-related behaviour in 19 Rhinolophus hipposideros maternity colonies
 (Northern France) with a noninvasive genetic CMR approach (using faeces)
 combined with parentage assignments. The use of the DDX3X/Y-Mam sexual
 marker designed in this study, which shows inter- and intra-chromosomal
 length polymorphism across placental mammals, together with 8 polymorphic
 microsatellite markers, produced high quality genetic data with limited
 genotyping errors and allowed us to reliably distinguish different
 categories of individuals (males, reproductive and non-reproductive
 females) and to estimate population sizes. We showed that visual counts
 represent well adult female numbers and that population composition in
 maternity colonies changes dynamically during the summer. Before
 parturition, colonies mainly harbour pregnant and non-pregnant females
 with a few visiting males whereas after parturition, colonies are mainly
 composed of mothers and their offspring with a few visiting non-mothers
 and males. Our approach gives deeper insight into sex- and status-specific
 behaviour, a prerequisite for understanding population dynamics and
 developing effective monitoring and management strategies. Provided
 sufficient samples can be obtained, this approach can be readily applied
 to a wide range of species.
description: Rscript_Import_from_GM_ZL2017R script to import data from GeneMapperImport_from_GM_ZL2017 .RRscrit_Consensus_ADOFA_QI_ZL2017R script to generate consensus genotypes and calculate genotyping error rates (ADO; FA) and Quality IndexConsensus_ADOFA_QI_ZL2017.RRhinolophus_hipposideros_binsetInformation about GeneMapper Binset for our Rhinolophus hipposideros samplesRHINO_BS-Rhinolophe-2_bins.txtinfocolInformation about the surveyed R. hipposideros maternity coloniesGenotypes Table (Stringent approach)Genotypes obtained using our "Stringent" approachRHINO15-1A-2C-S Genotypes Table.csvGenotypes Table (Non Stringent approach)Genotypes obtained using our "Non Stringent" approachRHINO15-1A-2C-NS Genotypes Table.csvGenotypes Table (AFLP approach)Genotypes obtained using our "AFLP" approachRHINO15-1A-2C-AFLP Genotypes Table.csv
DOI: 10.5061/dryad.m00q4
title: Data from: Genetic mapping and phylogenetic analysis reveal intraspecific variation in sex chromosomes of the Virginian strawberry

description: With their extraordinary diversity in sexual systems, flowering plants
 offer unparalleled opportunities to understand sex determination and to
 reveal generalities in the evolution of sex chromosomes. Comparative
 genetic mapping of related taxa with good phylogenetic resolution can
 delineate the extent of sex chromosome diversity within plant groups, and
 lead the way to understanding the evolutionary drivers of such diversity.
 The North American octoploid wild strawberries provide such an
 opportunity. We performed linkage mapping using targeted sequence capture
 for the subdioecious western Fragaria virginiana ssp. platypetala and
 compared the location of its sex-determining region (SDR) to those of two
 other (sub)dioecious species, the eastern subspecies, F. virginiana ssp.
 virginiana (whose SDR is at 0–5.5 Mb on chromosome VI of the B2
 subgenome), and the sister species F. chiloensis (whose SDR is at 37 Mb on
 chromosome VI of the Av subgenome). Male sterility was dominant in F.
 virginiana ssp. platypetala and mapped to a chromosome also in homeologous
 group VI. Likewise, one major QTL for female fertility overlapped the male
 sterility region. However, the SDR mapped to a yet another subgenome (B1),
 and to a different location (13 Mb), but similar to the location inferred
 in one population of the naturally occurring hybrid between F. chiloensis
 and F. virginiana (F. x ananassa ssp. cuneifolia). Phylogenetic analysis
 of chromosomes across the octoploid taxa showed consistent subgenomic
 composition reflecting shared evolutionary history but also reinforced
 within-species variation in the SDR-carrying chromosome, suggesting either
 repeated evolution, or recent turnovers in SDR.
description: Fragaria_Baits_v2Morphological data of F1 progenyTargeted capture genotypes of F1 progeny
DOI: 10.17632/9gvjnv378n.2
title: Research Data
DOI: 10.5061/dryad.4s1gg
title: Data from: Inferring the geographic origin of a range expansion: latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program X-ORIGIN

description: Climatic or environmental change is not only driving distributional shifts
 in species today, but it has also caused distributions to expand and
 contract in the past. Inferences about the geographic locations of past
 populations, especially regions that served as refugia (i.e., source
 populations) and migratory routes are a challenging endeavor. Refugial
 areas may be evidenced from fossil records or regions of temporal
 stability inferred from ecological niche models. Genomic data offer an
 alternative and broadly applicable source of information about the
 locality of refugial areas, especially relative to fossil data, which are
 either unavailable or incomplete for most species. Here we present a
 pipeline we developed (called x-origin) for statistically inferring the
 geographic origin of range expansion using a spatially explicit coalescent
 model and an Approximate Bayesian Computation testing framework. In
 addition to assessing the probability of specific latitudinal and
 longitudinal coordinates of refugial or source populations, such
 inferences can also be made accounting for the effects of temporal and
 spatial environmental heterogeneity, which may impact migration routes. We
 demonstrate x-origin with an analysis of genomic data collected in the
 Collared pika that underwent post-glacial expansion across Alaska, as well
 as present an assessment of its accuracy under a known model of expansion
 to validate the approach.
description: Pika samples SNP
 fileThe complete SNP file
 for all the Pika samples we used.hlOch_jawboneIncluded.snapppika sampling locationsampling location of all the sampleshlOch_jawboneIncluded_loc.txtpika vcfvcf file of all the pika samplesochotona_allind.vcf
DOI: 10.5061/dryad.jv5rj
title: Data from: Dispersing hydrophobic natural colorant β-carotene in shellac particles for enhanced stability and tunable color

description: Color is one of the most important visual attributes of food and is
 directly related to the perception of food quality. The interest in
 natural colorants, especially β-carotene that not only imparts color but
 also has well-documented health benefits, has triggered the research and
 development of different protocols designed to entrap these hydrophobic
 natural molecules to improve their stability against oxidation. Here, we
 report a versatile microfluidic approach that utilizes single emulsion
 droplets as templates to prepare microparticles loaded with natual
 colorants. The solution of β-carotene and shellac in the solvent is
 emulsified by microfluidics into droplets. Upon solvent diffusion,
 β-carotene and shellac co-precipitates, forming solid microparticles of
 β-carotene dispersed in the shellac polymer matrix. We substantially
 improve the stability of β-carotene that is protected from oxidation by
 the polymer matrix and achieve different color appearances by loading
 particles with different β-carotene concentrations. These particles
 demonstrate great promise for practical use in natural food coloring.
description: Dispersing Hydrophobic
 Natural Colorant β-carotene in Shellac Particles for Enhanced Stability
 and Tunable ColorDispersing Hydrophobic
 Natural Colorant β-carotene in Shellac Particles for Enhanced Stability
 and Tunable ColorSupporting
 Information.doc
DOI: 10.18150/f5cuab
title: Data accompanying the chapter 'The Semiotics of Scientific Scrutiny: Unveiling Peer Review through Digital Symptomatology'

description: This dataset accompanies the chapter 'The Semiotics of Scientific Scrutiny: Unveiling Peer Review through Digital Symptomatology' (under review). It was generated using our Genre Modeler package (https://github.com/cognitive-metascience/genre-modeler) based on open corpora. The dataset contains also a visualization script for Figure 5 and the data exported from Sketch Engine for the MDPI 2 Peer Review corpus collocations of the verb "lack". The corpus is also available on RePOD: https://repod.icm.edu.pl/dataset.xhtml?persistentId=doi:10.18150/SHKP7B
DOI: 10.5061/dryad.36q03
title: Data from: Evolution of density-dependent movement during experimental range expansions

description: Range expansions and biological invasions are prime examples of transient
 processes that are likely impacted by rapid evolutionary changes. As a
 spatial process, range expansions are driven by dispersal and movement
 behaviour. While it is widely accepted that dispersal and movement may be
 context-dependent, for instance density-dependent, and best represented by
 reaction norms, the evolution of density-dependent movement during range
 expansions has received little experimental attention. We therefore tested
 current theory predicting the evolution of increased movement at low
 densities at range margins using highly replicated and controlled range
 expansion experiments across multiple genotypes of the protist model
 system Tetrahymena thermophila. Although rare, we found evolutionary
 changes during range expansions even in the absence of initial standing
 genetic variation. Range expansions led to the evolution of negatively
 density-dependent movement at range margins. In addition, we report the
 evolution of increased intra-strain competitive ability and concurrently
 decreased population growth rates in range cores. Our findings highlight
 the importance of understanding movement and dispersal as evolving
 reaction norms and plastic life-history traits of central relevance for
 range expansions, biological invasions and the dynamics of spatially
 structured systems in general.
description: data
DOI: 10.5061/dryad.dn160
title: Data from: Cryptic species diversity and reproductive isolation among sympatric lineages of Strongylocentrotus sea urchins in the northwest Atlantic

description: Distinguishing between intra- and inter-specific variation in genetic
 studies is critical to understanding evolution because the mechanisms
 driving change among populations are expected to be different than those
 that shape reproductive isolation among lineages. Genetic studies of north
 Atlantic green sea urchins Strongylocentrotus droebachiensis (Müller,
 1776) have detected significant population substructure and asymmetric
 gene flow from Europe to Atlantic Canada and interspecific hybridization
 between S. droebachiensis and Strongylocentrotus pallidus (Sars, 1871).
 However, combined with patterns of divergence at mtDNA sequences,
 morphological divergence at gamete traits suggests that the European and
 North American lineages of S. droebachiensis may be cryptic species. Here,
 we use a combination of cytochrome c oxidase subunit I (COI) sequences and
 single nucleotide polymorphisms (SNPs) to test for cryptic species within
 Strongylocentrotus sea urchins and hybrids between S. droebachiensis and
 S. pallidus populations. We detect striking patterns of habitat and
 reproductive isolation between two S. droebachiensis lineages, with
 offshore deep-water collections consisting of S. pallidus in addition to a
 cryptic lineage sharing genetic similarity with previously published
 sequences from eastern Atlantic S. droebachiensis. We detected only
 limited hybridization among all three lineages of sea urchins, suggesting
 that shared genetic differences previously reported may be a result of
 historical introgression or incomplete lineage sorting.
description: 110 ASU_supplement
 dataset_FACETS_09262017Excel spreadsheet with
 SNP locus info (reference/alternate alleles) and frequency in the GBS
 sequence data. The second Tab is the STRUCTURE data file of all 3049 SNPs
 in the 110 individuals included in the study (ID = Depth_IndID_illumina
 lane)
DOI: 10.5061/dryad.tg5qb
title: Data from: Characterizing and comparing the seasonality of influenza-like illnesses and invasive pneumococcal diseases using seasonal waveforms

description: The seasonalities of influenza-like illnesses (ILIs) and invasive
 pneumococcal diseases (IPDs) remain incompletely understood. Experimental
 evidence indicates that influenza-virus infection predisposes to
 pneumococcal disease, so that a correspondence in the seasonal patterns of
 ILIs and IPDs might exist at the population level. We developed a method
 to characterize seasonality by means of easily interpretable summary
 statistics of seasonal shape—or seasonal waveforms. Non-linear
 mixed-effects models were used to estimate those waveforms based on weekly
 case reports of ILIs and IPDs in five regions spanning continental France
 from July 2000 to June 2014. We found high variability of ILI seasonality,
 with marked fluctuations of peak amplitudes and peak times, but a more
 conserved epidemic duration. In contrast, IPD seasonality was best modeled
 by a markedly regular seasonal baseline, punctuated by two winter peaks in
 late December–early January and January–February. Comparing ILI and IPD
 seasonal waveforms, we found indication of a small, positive correlation.
 Direct models regressing IPDs on ILIs provided comparable results, even
 though they estimated moderately larger associations. The method proposed
 is broadly applicable to diseases with unambiguous seasonality and is
 well-suited to analyze spatially or temporally grouped data, which are
 common in epidemiology.
description: Data and R codes
 associated with "Characterizing and Comparing the Seasonality of
 Influenza-Like Illnesses and Invasive Pneumococcal Diseases Using Seasonal
 Waveforms"The zipped folder
 contains the data and the R scripts needed to perform the estimation of
 the influenza-like illness (ILI) seasonal waveforms, based on region-level
 weekly incidence data in France during 2000/01–2013/14.supplement_code_AJE.zip
DOI: 10.5061/dryad.hj016
title: Data from: Genotype by sequencing identifies natural selection as a driver of intraspecific divergence in Atlantic populations of the high dispersal marine invertebrate, Macoma petalum

description: Mitochondrial DNA analyses indicate that the Bay of Fundy population of
 the intertidal tellinid bivalve Macoma petalum is genetically divergent
 from coastal populations in the Gulf of Maine and Nova Scotia. To further
 examine the evolutionary forces driving this genetic break, we performed
 double digest genotype by sequencing (GBS) to survey the nuclear genome
 for evidence of both neutral and selective processes shaping this pattern.
 The resulting reads were mapped to a partial transcriptome of its sister
 species, M. balthica, to identify single nucleotide polymorphisms (SNPs)
 in protein-coding genes. Population assignment tests, principle components
 analyses, analysis of molecular variance, and outlier tests all support
 differentiation between the Bay of Fundy genotype and the genotypes of the
 Gulf of Maine, Gulf of St. Lawrence, and Nova Scotia. Although both
 neutral and non-neutral patterns of genetic subdivision were significant,
 genetic structure among the regions was nearly 20 times higher for loci
 putatively under selection, suggesting a strong role for natural selection
 as a driver of genetic diversity in this species. Genetic differences were
 the greatest between the Bay of Fundy and all other population samples,
 and some outlier proteins were involved in immunity-related processes. Our
 results suggest that in combination with limited gene flow across the
 mouth of the Bay of Fundy, local adaptation is an important driver of
 intraspecific genetic variation in this marine species with high dispersal
 potential.
description: supplement
 dataset_macomaThe excel file has two
 tabs - the first tab is the SNP information including the ID, SNP position
 in contig, reference and alternate alleles, scoring frequency of the
 alleles in the GBS data, and the contig sequence from our reference
 assembly. The second tab on the worksheet includes the scoring for each
 SNP in each individual *STRUCTURE input file format).
DOI: 10.6084/m9.figshare.31157772
title: Appendix 1 from Emotions and Prior Outcomes Shape Risk Propensity and the Dynamics of Decision Making in the Balloon Analogue Risk Task

description: List of all stimuli used in the experiment.
DOI: 10.6084/m9.figshare.31157772.v1
title: Appendix 1 from Emotions and Prior Outcomes Shape Risk Propensity and the Dynamics of Decision Making in the Balloon Analogue Risk Task

description: List of all stimuli used in the experiment.