cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nzs7h44qq
title: Interaction between surface waves on wire lines

description: This paper investigates coupling between EM surface waves on parallel
 wires. Finite Element Method (FEM) based and analytical models
 are developed for single and double wire Sommerfeld and Goubau lines.
 Models are validated via measurements for Goubau lines and a comparison
 between the analytic and the FEM-based computations for coupled Sommerfeld
 and Goubau type lines. The measurement and calculations show remarkable
 agreement. The FEM-based and the analytical models match remarkably well
 too. The results exhibit new favourable effects for surface waves
 propagation over multiple conductors. The short range behaviour of the
 coupled wires and, consequently, the existence of an optimum separation of
 coupled wires, is one of the most significant findings of this paper. We
 comment on the relevance of our results particularly in relation to
 applications of high bandwidth demands and cross-coupling
 effects. 
description: Matlab source code used to obtain the results of the presented
 model in the paper is deposited. These files are Galpha.m, Gprop.m and
 Sline to obtain the single wire propagation charateristics described in
 the paper.  For the coupled wires we have SommerfeldApproach.m and
 GoubauTwoWire_1.m for the Sommerfeld and Goubau type coupling described in
 the article.  Raw data are 9mm_exp_data and
 25mm_exp_data that were collected as described in the text. Additionally,
 the matlab file CoupledGoubauMeasvsSim_pub.m is used to plot these results
 and compare them to simulation.
DOI: 10.5061/dryad.gmsbcc2m7
title: Data from: Nocturnal foraging lifts time-constraints in winter for migratory geese but hardly speeds up fueling

description: Climate warming advances the optimal timing of breeding for many animals.
 For migrants to start breeding earlier, a concurrent advancement of
 migration is required, including pre-migratory fueling of energy reserves.
 We investigate whether barnacle geese are time-constrained during
 pre-migratory fueling and whether there is potential to advance or shorten
 the fueling period to allow an earlier migratory departure. We equipped
 barnacle geese with GPS-trackers and accelerometers to remotely record
 birds’ behavior, from which we calculated time budgets. We examined how
 time spent foraging was affected by the available time (during daylight
 and moonlit nights) and thermoregulation costs. We used an energetic model
 to assess onset and rates of fueling, and whether geese can further
 advance fueling by extending foraging time. We show that during winter,
 when facing higher thermoregulation costs, geese consistently foraged at
 night, especially during moonlit nights, in order to balance their energy
 budgets. In spring, birds made use of the increasing day length and gained
 body stores by foraging longer during the day, but birds stopped foraging
 extensively during the night. Our model indicates that by continuing
 night-time foraging throughout spring, geese may have some leeway to
 advance and increase fueling rate, potentially reaching departure body
 mass 4 days earlier. In light of rapid climatic changes on the breeding
 grounds, whether this advancement can be realized and whether it will be
 sufficient to prevent phenological mismatches remains to be determined.
description: GPS and tri-axial acceleration data was collected from wild
 Barnacle Geese using UvA-BiTS GPS loggers. GPS data was
 resampled to 30 minute intervals. From tri-axial
 accelerometer data we classified behaviors using a random forest
 classifier, see methods in the paper.
DOI: 10.15468/dl.4ztsqh
title: Occurrence Download

description: A dataset containing 1670 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Ehretia acuminata"
 ]
}

 The dataset includes 1670 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002720-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cjsxksn54
title: Data from: The rise to dominance of lanternfishes (Teleostei, Myctophidae) in the oceanic ecosystems: a paleontological perspective

description: Lanternfishes currently represent one of the dominant groups of
 mesopelagic fishes in terms of abundance, biomass and diversity. Their
 otolith record dominates pelagic sediments below 200 m in dredges,
 especially during the entire Neogene. Here we provide an analysis of their
 diversity and rise to dominance primarily based on their otolith record.
 The earliest unambiguous fossil myctophids are known based on otoliths
 from the late Paleocene and early Eocene. During their early evolutionary
 history myctophids were likely not adapted to a high oceanic lifestyle,
 but occurred over shelf and upper slope regions where they were locally
 abundant during the middle Eocene. A distinct up-scaling in otolith size
 is observed in the early Oligocozoicne, which also marks their earliest
 occurrence in bathyal sediments. We interpret this transition to be
 related to the change from a halothermal deep ocean circulation (HTC) to a
 thermohaline regime (THC), and the associated cooling of the deep ocean
 and rearrangement of nutrient and silica supply. The early Oligocene
 myctophid size acme shows a remarkable congruence with diatom abundance,
 the main food resource for the zooplankton and thus for myctophids and
 whales. The warmer late Oligocene to early middle Miocene period was
 characterized by an increase in disparity of myctophids but with a
 reduction in their otolith sizes. A second and persisting secular pulse in
 myctophid diversity (particularly within the genus Diaphus) and
 increase in size begins with the Biogenic Bloom in late Miocene,
 paralleled with diatom abundance and mysticete gigantism
DOI: 10.5061/dryad.rjdfn2z94
title: Strain diversity and spatial distribution are linked to epidemic dynamics in host populations

description: The inherently variable nature of epidemics renders predictions of when
 and where infection is expected to occur challenging. Differences in
 pathogen strain composition, diversity, fitness, and spatial distribution
 are generally ignored in epidemiological modeling and are rarely studied
 in natural populations, yet they may be important drivers of epidemic
 trajectories. To examine how these factors are linked to epidemics in
 natural host populations, we collected epidemiological and genetic data
 from fifteen populations of the powdery mildew fungus, Podosphaera
 plantaginis, on Plantago lanceolata in the Åland Islands, Finland. In each
 population, we tracked spatiotemporal disease progression throughout one
 epidemic season and coupled our survey of infection with intensive field
 sampling of the pathogen. We found that strain composition varied greatly
 among populations in the landscape. Within populations, strain composition
 was driven by the sequence of strain activity: early-active strains
 reached higher abundances, leading to consistent strain compositions over
 time. Co-occurring strains also varied in their contribution to the growth
 of the local epidemic, and these fitness inequalities were linked to
 epidemic dynamics: a higher proportion of hosts became infected in
 populations containing strains that were more similar in fitness. Epidemic
 trajectories in the populations were also linked to strain diversity and
 to spatial dynamics: higher infection rates occurred in populations
 containing higher strain diversity, while spatially-clustered epidemics
 experienced lower infection rates. Together, our results suggest that
 spatial and/or temporal variation in strain composition, diversity, and
 fitness of pathogen populations are important factors generating variation
 in epidemiological trajectories among infected host populations.
description: We collected epidemiological and genetic data from fifteen
 populations of the powdery mildew fungus,
 <i>Podosphaera plantaginis</i>, on
 <i>Plantago lanceolata</i> in the Åland Islands, Finland. In
 each population, we tracked spatiotemporal disease progression throughout
 one epidemic season and coupled our survey of infection with intensive
 field sampling of the pathogen. Pathogen samples were assigned multi-locus
 genotypes ("strains") using a SNP panel.
description: Please see the README file associated with this dataset for
 descriptions of the variables and values.
DOI: 10.17608/k6.auckland.26010052
title: Brain Contour Data

description: Brain contour scan data
DOI: 10.17608/k6.auckland.26010052.v2
title: Brain Contour Data

description: Brain contour scan data
DOI: 10.17608/k6.auckland.26010052.v1
title: Brain Contour Data

description: Brain contour scan data
DOI: 10.6071/m3t09x
title: Data from: Measuring attitude towards chemistry, biology, and math at a Hispanic-serving institution

description: This work describes the evaluation of the Attitude toward the Subject of
 Chemistry Inventory (ASCI), as well as two modifications (one for attitude
 toward math and one for attitude toward biology), for college students at
 a Hispanic Serving Institution. Confirmatory factor analysis supported a
 two-factor structure, similar to an existing model of a revised version of
 the ASCI, for all three instruments. These instruments show little change
 in student attitude with respect to biology, chemistry, or math during a
 typical semester. However, major perturbations, such as switching to
 remote instruction mid-semester, can lead to small but significant
 increases and decreases in attitude.
description: Survey data was collected anonymously through qualtrics.
DOI: 10.5061/dryad.3bk3j9kj0
title: Supporting data for 'Stabilizing selection on Atlantic cod supergenes through a millennium of extensive exploitation'

description: Life on earth has been characterized by recurring cycles of ecological
 stasis and disruption, relating biological eras to geological and climatic
 transitions through the history of our planet. Due to the increasing
 degree of ecological abruption caused by human influences many advocate
 that we now have entered the geological era of the Anthropocene, or ‘the
 age of man’. Considering the ongoing mass extinction and ecosystem
 reshuffling observed worldwide, a better understanding of the drivers of
 ecological stasis will be a requisite for identifying routes of
 intervention and mitigation. Ecosystem stability may rely on one or a few
 keystone species, and the loss of such species could potentially have
 detrimental effects. The Atlantic cod (Gadus morhua) have historically
 been highly abundant and is considered a keystone species in ecosystems of
 the northern Atlantic Ocean. Collapses of cod stocks have been observed on
 both sides of the Atlantic and reported to have detrimental effects that
 include vast ecosystem reshuffling. By whole-genome re-sequencing we
 demonstrate that stabilizing selection maintains three extensive
 ‘supergenes’ in Atlantic cod, linking these genes to species persistence
 and ecological stasis. Genomic inference of historic effective population
 sizes shows continued declines for cod in the North Sea – Skagerrak –
 Kattegat system through the past millennia, consistent with an early onset
 of the marine Anthropocene through industrialization and commercialization
 of fisheries throughout the medieval period.
DOI: 10.5061/dryad.zgmsbcc9c
title: Murine locomotion and diversification

description: The relationship between organismal function and form is a cornerstone of
 biology because functional diversity is key to generating and maintaining
 ecological diversity. Morphological changes often occur in unison with
 behavioral or ecological transitions, and this process may foster
 diversification, but alternately could trap a species on an adaptive peak.
 We estimated the most comprehensive phylogenetic hypothesis of Murinae, a
 young (~15 My) and diverse (~700 species) clade of mammals. We then tested
 for correlated evolution among four morphological traits with potential
 links to locomotor modes (Arboreal, General, Terrestrial, and Amphibious),
 then investigated the effects of locomotion on morphological and lineage
 diversification. We found unique combinations of trait values for each
 locomotor mode, including strong covariance between the tail and hind foot
 lengths of specialized Arboreal and ecologically flexible General species.
 Low diversification rates and long branch lengths suggest that specialized
 lineages represent stable evolutionary “cul-de-sacs”. General species,
 characterized by the classic “rat-like” body plan and broad locomotor
 abilities, have narrow optimal trait values and slow phenotypic evolution,
 but high lineage diversification rates. Our findings suggest that
 versatile, generalist forms act as seeds of species diversity and
 morphological specialization, which together build ecologically diverse
 radiations.Muri
description: All data were collcted by authors and all analyses performed in R
 or RevBayes.
description: All data and scripts for all analyses are included in this Dryad
 repository. Please see
 https://github.com/jonnations/murine_locomotion_and_diversification for
 useage instructions.
DOI: 10.5061/dryad.k0p2ngf77
title: Transcriptomic data and analyses of shMeg3 muscle in vitro and in vivo

description: Formation of skeletal muscle is among the most striking examples of
 cellular plasticity in animal tissue development, and while muscle
 progenitor cells are reprogrammed by epithelial-mesenchymal transition
 (EMT) to migrate during embryonic development, regulation of EMT in
 postnatal myogenesis remains poorly understood. Here, we demonstrate that
 the long noncoding RNA (lncRNA) Meg3 regulates EMT in
 myoblast differentiation and skeletal muscle regeneration. Chronic
 inhibition of Meg3 in C2C12 myoblasts induced EMT, and
 supressed cell state transitions required for differentiation.
 Furtheremore, adenoviral Meg3 knockdown compromised
 muscle regeneration, which was accompanied by abnormal mesenchymal gene
 expression and interstitial cell proliferation. Transcriptomic and pathway
 analyses of Meg3-depleted C2C12 myoblasts and injured skeletal
 muscle revealed a significant dysregulation of EMT-related genes, and
 identified TGFβ as a key upstream regulator. Importantly, inhibition
 of TGFβR1 and its downstream effectors, and the
 EMT-related transcriptional repressor Snai2, restored many
 aspects of myogenic differentiation in Meg3-depleted
 myoblasts in vitro. We further demonstrate that reduction
 of Meg3-dependent Ezh2 activity results in epigenetic alterations
 associated with TGFβ activation.
 Thus, Meg3 regulates myoblast identity to facilitate
 progression into muscle differentiation.
description: C2C12 myotubes were collected on day 3 differentiation using
 Trizol and active lysis. TA muscle tissue was harvested 7 days
 post-injury, and injured muscle tissue was snap-frozen, and treated with
 Trizol with Polytron dissociation. RNA was purified by phenol-chlorophorm
 extraction and isopropanol precipitation. A minimum of 100 ng RNA per
 sample was provided to the Boston University Microarray and Sequencing
 Resource Core. Briefly, samples were evaluated for quality by Bioanalyzer
 to confirm RIN scores were above 7. Subsequently, second-strand synthesis
 was prepared using TruSeq mRNA stranded library preparation kit, and
 samples were subsequently sequenced by high-output 75 bp paired-end read
 Illumina NextSeq500 sequencing. Raw counts were then preprocessed using
 the Illumina BaseSpace RNA Express application, to assess for quality via
 FastQC and RSeQC, and aligned to mouse genome build mm10 via STAR.
 Quantification of pairs uniquely aligned to each Ensembl gene (via HTSeq)
 produced counts, which were converted to regularized algorithm (rlog)
 transformed expression values (via DESeq2) for statistical and expression
 analyses. IPA summary files in this dataset were conducted by Tiffany Dill
 by restricting the gene set list to significantly dysregulated transcripts
 (p &lt; 0.05). All other files in this dataset were produced by Adam
 Gower at the Boston University Microarray and Sequencing Resource
 Core.
DOI: 10.5061/dryad.15dv41nwb
title: Field-based body temperatures reveal behavioral thermoregulation strategies of the Atlantic marsh fiddler crab Minuca pugnax

description: Behavioral thermoregulation is an important defense against the negative
 impacts of climate change for ectotherms. In this study we examined the
 use of burrows by a common intertidal crab, Minuca pugnax, to control body
 temperature. To understand how body temperatures respond to changes in the
 surface temperature and explore how efficiently crabs exploit the cooling
 potential of burrows to thermoregulate, we measured body, surface, and
 burrow temperature data during low tide on Sapelo Island, GA in March,
 May, August, and September of 2019 . We found that an increase in
 1 °C in the surface temperature led to a 0.70-0.71 °C increase in
 body temperature for females and an increase in 0.75-0.77 °C in body
 temperature for males. Body temperatures of small females were 0.3 °C
 warmer than large females for the same surface temperature. Female crabs
 used burrows more efficiently for thermoregulation compared to the males.
 Specifically, an increase of 1°C in the cooling capacity (the difference
 between the burrow temperature and the surface temperature) led to an
 increase of 0.42-0.50°C for females and 0.34-0.35°C for males in the
 thermoregulation capacity (the difference between body temperature and
 surface temperature). The body temperature that crabs began to use burrows
 to thermoregulate was estimated to be around 24°C, which is far below the
 critical body temperatures that could lead to death. Many crabs experience
 body temperatures of 24°C early in the reproductive season, several months
 before the hottest days of the year. Because the use of burrows involves
 fitness trade-offs, these results suggest that warming temperatures could
 begin to impact crabs far earlier in the year than expected.
description: The data were collected in the field on Sapelo Island, Georgia,
 USA between March and October 2019. The dataset includes field based body
 temperatures for male and female adult <em>Minuca pugnax</em>,
 along with the corresponding surface and burrow temperatures.
DOI: 10.5061/dryad.vt4b8gtr4
title: Ontogenetic development underlies population response to mortality

description: Understanding demographic responses to mortality is crucial to predictive
 ecology. While classic ecological theory posits reductions in population
 biomass in response to extrinsic mortality, models containing realistic
 developmental change predict the potential for counterintuitive increase
 in stage-specific biomass, i.e., biomass overcompensation. Patterns of
 biomass overcompensation should be predictable based on differences in the
 relative energetic efficiencies of juvenile maturation and adult
 reproduction. Specifically, in populations where reproduction is the
 limiting process, adult-specific mortality should enhance total
 reproduction and thus juvenile biomass. We tested this prediction by
 inducing an array of stage-specific harvesting treatments across replicate
 populations of Daphnia pulex. In accordance with reproductive regulation,
 the greatest biomass response occurred in the juvenile Daphnia stage and
 this response occurred most strongly in response to adult mortality.
 Nevertheless, we failed to detect significant biomass overcompensation and
 instead report largely compensatory effects. In total, our work
 demonstrates that knowledge of population structure is necessary to
 accurately predict population dynamics, but cautions that further research
 is needed to illuminate the factors generating overcompensatory versus
 compensatory responses across natural populations.
DOI: 10.5061/dryad.1jwstqjtd
title: The plot thickens: Haploid and triploid-like thalli, hybridization, and biased mating type ratios in Letharia

description: The study of the reproductive biology of lichen fungal symbionts has been
 traditionally challenging due to their complex and symbiotic lifestyles.
 Against the common belief of haploidy, a recent genomic study found a
 triploid-like signal in Letharia. Here, we used genomic data from a pure
 culture and from thalli, together with a PCR survey of the MAT locus, to
 infer the genome organization and reproduction in Letharia. We found that
 the read count variation in the four Letharia specimens, including the
 pure culture derived from a single sexual spore of L. lupina, is
 consistent with haploidy. By contrast, the L. lupina read counts from a
 thallus' metagenome are triploid-like. Characterization of the
 mating-type locus revealed a conserved heterothallic configuration across
 the genus, along with auxiliary genes that we identified. We found that
 the mating-type distributions are balanced in North America for L. vulpina
 and L. lupina, suggesting widespread sexual reproduction, but highly
 skewed in Europe for L. vulpina, consistent with predominant asexuality.
 Taken together, we propose that Letharia fungi are heterothallic and
 typically haploid, and provide evidence that triploid-like individuals are
 rare hybrids between L. lupina and an unknown Letharia lineage,
 reconciling classic systematic and genetic studies with recent genomic
 observations.
description: This data submission contains the files necessary to re-create
 several figures of the paper, in particular those that use sequence data
 extracted from SPAdes assemblies, or produced by PCR and aligned for
 phylogenetic analyses (including partition files). It also includes the
 genome assembly of the pure culture from a <em>L. lupina
 </em>spore, which is used as a reference for a Snakemake pipeline,
 and the gene annotation of the mating type locus. No columns were removed
 from the alignments before analyses.
description: See included README file.