cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5qv9750
title: Data from: Longevity is determined by ETS transcription factors in multiple tissues and diverse species

description: Ageing populations pose one of the main public health crises of our time.
 Reprogramming gene expression by altering the activities of
 sequence-specific transcription factors (TF) can ameliorate deleterious
 effects of age. Here we explore how a circuit of TFs coordinates
 pro-longevity transcriptional outcomes, which reveals a multi-tissue and
 multi-species role for an entire protein family: the E-twenty-six (ETS)
 TFs. In Drosophila, reduced insulin/IGF signalling (IIS) extends lifespan
 by coordinating activation of Aop, an ETS transcriptional repressor, and
 Foxo, a Forkhead transcriptional activator. Aop and Foxo bind the same
 genomic loci, and we show that, individually, they effect similar
 transcriptional programmes in vivo. In combination, Aop can both moderate
 or synergise with Foxo, dependent on promoter context. Moreover, Foxo and
 Aop oppose the gene-regulatory activity of Pnt, an ETS transcriptional
 activator. Directly knocking down Pnt recapitulates aspects of the
 Aop/Foxo transcriptional programme and is sufficient to extend lifespan.
 The lifespan-limiting role of Pnt appears to be balanced by a requirement
 for metabolic regulation in young flies, in which the Aop-Pnt-Foxo circuit
 determines expression of metabolic genes, and where Pnt regulates
 lipolysis and responses to nutrient stress. Molecular functions are often
 conserved amongst ETS TFs, prompting us to examine whether other
 Drosophila ETS-coding genes may also affect ageing. We show that five out
 of eight Drosophila ETS TFs play a role in fly ageing, acting from a range
 of organs and cells including the intestine, adipose and neurons. We
 expand the repertoire of lifespan-limiting ETS TFs in C. elegans,
 confirming their conserved function in ageing and revealing that the roles
 of ETS TFs in physiology and lifespan are conserved throughout the family,
 both within and between species.
description: foxoXaopXebmXfre_luciferaseReporterFR = firefly luciferase / renilla, zeromedian = median of promoter without TFs, FC = fold-change relative to median i.e. (B-A) / A where A=median, B=value-i20190221_FxAxMotifs_allReps.csvaop X pntP1_luciferasecolumns as per other luciferase data.061217_aopXPnt_JS3promoter.csvPntP1Xstarvation_TAG&masstag_weight = tag µg / mg flypntDat_richard_starvation.csvPntP1_starvation_survivalDeaths of flies expressing PntP1 in gut+fatbody. PntP1 was induced in +RU condition for 1 week before starvation, RU was included in agarose food.pntXsugar_tagTAG of flies overexpressing PntP1 in gut and fat body, with/without high sugar. tag_weight = data from figure.sugarXpnt_survivalSurvival of flies expressing PntP1 in gut / fat body on 8x or 1x sugar. event: 1 = death, 0 = censored.pntXsugar_survival_dryad.csvlifespansall Drosophila ageing survival dataqPCR datageno: F=bears uas-foxo, A=bears uas-aop, FA=bears both. "expression" = ratio primer/tubulin, expressed as fold change relative to genotypic -RU median (B-A)/AplosGen_qPCR_dryad.csv
DOI: 10.5061/dryad.nn96ps3
title: Data from: A review and meta-analysis of intraspecific differences in phenotypic plasticity: implications to forecast plant responses to climate change

description: Aim: Many studies use differences among plant populations to infer future
 plant responses, but these predictions will only provide meaningful
 insights if plasticity patterns among populations are similar (i.e. in the
 absence of Population-by-Environment interaction, P × E). In this study,
 we test whether P × E is considered in climate change studies. We
 evaluated whether population differentiation varies across environments
 and is determined by aspects of the study system and experimental design.
 Location: Global. Methods: We conducted a literature search in the Web of
 Science database to identify studies assessing population differentiation
 in a climate change context. We quantified P × E and performed a
 meta-analysis to calculate the percentage of traits showing P × E in the
 study cases. Results: We identified 309 study cases (from 237 articles)
 assessing population differentiation in 172 plant species, of which 64 %
 included more than one test environment and tested P × E. In 77% of these,
 P × E was significant for at least one functional trait. The overall
 proportion of traits showing P × E was 33.4% (CI 27.7-39.3). These results
 were generally consistent across life forms, ecoregions and type of
 experiment. Furthermore, population differentiation varied across test
 environments in 76% of cases. The overall proportion of traits showing
 environment-dependent population differentiation was 53.7 % (CI
 37.9-69.3). Conclusions: Our findings revealed that differences in
 phenotypic plasticity among populations are common, but are usually
 neglected to forecast population responses to climate change. Future
 studies should assess population differentiation in multiple test
 environments that realistically reflect future environmental conditions,
 assessing climate change drivers that are rarely considered (e.g.
 multifactor experiments). Our review also revealed the predominant focus
 of population studies on trees from temperate climates, identifying
 underexplored life forms, phylogenetic groups and ecoregions that should
 receive more future attention.
description: Appendix
 1_FinalData file compiled for
 the revision and metanalyses. For each study, the literature reference,
 species, family, life form, ecoregion, number of populations, traits and
 test environments are shown. Number of traits that show significant PxE
 are also shown.
DOI: 10.5061/dryad.65v002b
title: Data from: The effects of genotype × phenotype interactions on transcriptional response to silver nanoparticle toxicity in organotypic cultures of murine tracheal epithelial cells

description: The airway epithelium is critical for maintaining innate and adaptive
 immune responses, and occupational exposures that disrupt its immune
 homeostasis may initiate and amplify airway inflammation. In our previous
 study, we demonstrated that silver nanoparticles (AgNP), which are
 engineered nanomaterials used in multiple applications but primarily in
 the manufacturing of many antimicrobial products, induce toxicity in
 organotypic cultures derived from murine tracheal epithelial cells (MTEC),
 and those differentiated toward a “Type 2 [T2]-Skewed” phenotype
 experienced an increased sensitivity to AgNP toxicity, suggesting that
 asthmatics could be a sensitive population to AgNP exposures in
 occupational settings. However, the mechanistic basis for this genotype ×
 phenotype interaction (G×P) has yet to be defined. In the present study,
 we conducted transcriptional profiling using RNA-sequencing (RNA-seq) to
 predict the enrichment of specific canonical pathways and upstream
 transcriptional regulators to assist in defining a mechanistic basis for
 G×P effects on AgNP toxicity. Organotypic cultures were derived from MTEC
 across two genetically inbred mouse strains (A/J and C57BL/6J mice), two
 phenotypes (“Normal” and “T2-Skewed”), and one AgNP exposure (an acute 24
 h exposure) to characterize G×P effects on transcriptional response to
 AgNP toxicity. The “T2-Skewed” phenotype was marked by increased
 pro-inflammatory T17 responses to AgNP toxicity, which are significant
 predictors of neutrophilic/difficult-to-control asthma and suggests that
 asthmatics could be a sensitive population to AgNP exposures in
 occupational settings. This study highlights the importance of considering
 G×P effects when identifying these sensitive populations, whose underlying
 genetics or diseases could directly modify their response to AgNP
 exposures.
description: RNA-seq (Gene
 Counts)average read counts of
 RNA-seq data
DOI: 10.5061/dryad.68db279
title: Data from: The role of deliberate practice in expert performance: revisiting Ericsson, Krampe, & Tesch-Römer

description: We sought to replicate Ericsson, Krampe, and Tesch-Römer's (1993)
 seminal study on deliberate practice. Ericsson et al. (1993) found that
 differences in retrospective estimates of accumulated amounts of
 deliberate practice corresponded to each skill level of student
 violinists. They concluded, "individual differences in ultimate
 performance can largely be accounted for by differential amounts of past
 and current levels of practice" (p. 392). We reproduced the
 methodology with notable exceptions, namely 1) employing a double-blind
 procedure, 2) conducting analyses better suited to the study design, and
 3) testing previously-unanswered questions about teacher-designed
 practice—that is, we examined the way Ericsson et al. (1993)
 operationalized deliberate practice (practice alone), and their
 theoretical but previously unmeasured definition of deliberate practice
 (teacher-designed practice), and compared them. We did not replicate the
 core finding, that accumulated amounts of deliberate practice corresponded
 to each skill level. Overall, the size of the effect was substantial, but
 considerably smaller than the original study’s effect size.
 Teacher-designed practice was perceived as less relevant to improving
 performance on the violin than practice alone. Further, amount of
 teacher-designed practice did not account for more variance in performance
 than amount of practice alone. Implications for the deliberate practice
 theory are discussed.
description: Macnamara & Maitra
 Replication - Open Data
DOI: 10.5281/zenodo.18311702
title: SS433: TDS spectra and measurements of the HeII 4686 line.

description: Observational data from the paper"The radial velocity curve for He II emission cannot be used for component mass determination in SS433"

1. Bcurve.txt is the light curve of SS433 in the B band, used in the paper.

2. The HeII4686.txt contains measurements of the HeII 4686A line.

3. The fits-files contain spectra of SS433 obtained with the TDS spectrograph.The header of the primary extention of the files contain details of observations and quasi-simultaneous photometry, if available:   the B, V, R, I magnitudes (keyword [BVRI]MAG);   the magnitudes corrected for contribution from spectral lines ([BVRI]MAG_C);   Heliocentric Julian Dates of phorometric observetion (HJD[BVRI]MAG).

The second extention (named 'merged') contains the fits-table for 1D spectrum of SS433:   wave -- heliocentric wavelength (air), A;   flux -- flux, erg/(s cm^2 A), may be inaccurate by some factor due to slit losses;   SNR -- estimate of signal to noise ratio (after 2021-04-27);   cont -- continuum-normalized spectrum;   absflux -- flux, erg/(s cm^2 A), corrected for the slit losses by using the simultaneous photometry, if available.
DOI: 10.5281/zenodo.18311703
title: SS433: TDS spectra and measurements of the HeII 4686 line.

description: Observational data from the paper"The radial velocity curve for He II emission cannot be used for component mass determination in SS433"

1. Bcurve.txt is the light curve of SS433 in the B band, used in the paper.

2. The HeII4686.txt contains measurements of the HeII 4686A line.

3. The fits-files contain spectra of SS433 obtained with the TDS spectrograph.The header of the primary extention of the files contain details of observations and quasi-simultaneous photometry, if available:   the B, V, R, I magnitudes (keyword [BVRI]MAG);   the magnitudes corrected for contribution from spectral lines ([BVRI]MAG_C);   Heliocentric Julian Dates of phorometric observetion (HJD[BVRI]MAG).

The second extention (named 'merged') contains the fits-table for 1D spectrum of SS433:   wave -- heliocentric wavelength (air), A;   flux -- flux, erg/(s cm^2 A), may be inaccurate by some factor due to slit losses;   SNR -- estimate of signal to noise ratio (after 2021-04-27);   cont -- continuum-normalized spectrum;   absflux -- flux, erg/(s cm^2 A), corrected for the slit losses by using the simultaneous photometry, if available.
DOI: 10.5258/soton/wp00879
title: Degree of Urbanisation classes using WorldPop Global2 R2025A population data with the GHSL GHS-DUG tool.

description: Degree of Urbanisation classes using WorldPop Global2 R2025A population data with the GHSL GHS-DUG tool. DEGURBA Project - Funded by European Commission. WorldPop - School of Geography and Environmental Science, University of Southampton 2026.
DOI: 10.5061/dryad.nt8705p
title: Data from: At the invasion front, male cane toads (Rhinella marina) have smaller testes

description: As a colonizing species expands its range, individuals at the invasion
 front experience different evolutionary pressures than do those at the
 range-core. For example, low densities at the edge of the range mean that
 males should rarely experience intense sperm competition from rivals; and
 investment into reproduction may trade-off with adaptations for more rapid
 dispersal. Both of these processes are predicted to favour a reduction in
 testis size at the invasion front. To explore effects of invasion stage in
 Australian cane toads (Rhinella marina), we collected and dissected 214
 adult males from three regions: one in the species’ range-core
 (northeastern Australia), and two from invasion fronts (one in
 northwestern Australia, and one in southeastern Australia). Despite the
 brief duration of separation between toads in these areas (approximately
 85 years), testis masses averaged &gt;30% higher (as a proportion of
 body mass) in range-core males than in conspecifics sampled from either
 vanguard of the invasion. Previous work has documented low reproductive
 frequencies in female cane toads at the invasion front also, consistent
 with the hypothesis that evolutionary and ecological pressures unleashed
 by an invasion can favour relatively low resource allocation to
 reproduction in both sexes.
description: Testis mass data Friesen
 and ShineExcel file with data on
 morphology of cane toads
DOI: 10.5061/dryad.ct2895s
title: Data from: Accurate inference of tree topologies from multiple sequence alignments using deep learning

description: Reconstructing the phylogenetic relationships between species is one of
 the most formidable tasks in evolutionary biology. Multiple methods exist
 to reconstruct phylogenetic trees, each with their own strengths and
 weaknesses. Both simulation and empirical studies have identified several
 “zones” of parameter space where accuracy of some methods can plummet,
 even for four-taxon trees. Further, some methods can have undesirable
 statistical properties such as statistical inconsistency and/or the
 tendency to be positively misleading (i.e. assert strong support for the
 incorrect tree topology). Recently, deep learning techniques have made
 inroads on a number of both new and longstanding problems in biological
 research. Here we designed a deep convolutional neural network (CNN) to
 infer quartet topologies from multiple sequence alignments. This CNN can
 readily be trained to make inferences using both gapped and ungapped data.
 We show that our approach is highly accurate on simulated data, often
 outperforming traditional methods, and is remarkably robust to
 bias-inducing regions of parameter space such as the Felsenstein zone and
 the Farris zone. We also demonstrate that the confidence scores produced
 by our CNN can more accurately assess support for the chosen topology than
 bootstrap and posterior probability scores from traditional methods. While
 numerous practical challenges remain, these findings suggest that deep
 learning approaches such as ours have the potential to produce more
 accurate phylogenetic inferences.
description: Supplementary_Text_v1Supplementary TextFigS1_Suppl_BL_spaceFigure S1S1_Suppl_BL_space.pdfFigS2_Suppl_3DSurfaceFigure S2S2_Suppl_3DSurface.pdfFigS3_Suppl_Bias_gapFigure S3S3_Suppl_Bias_gap.jpegFigS4_Suppl_Bias_nogapFigure S4S4_Suppl_Bias_nogap.jpegFigS5_Suppl_Precision_recallFigure S5S5_Suppl_Precision_recall.pdfTabS1_Suppl_500regionaccuracyTable S1S1_Suppl_tab_500regionaccuracy.docxTabS2_Suppl_consistencyTable S2S2_Suppl_tab_consistency.docxSuppl_fig_tab_legends_v1Supplementary Figure and Table legends
DOI: 10.5061/dryad.b3g0n1j
title: Data from: Re-analysis of data reveals no evidence for neonatal imitation in rhesus macaques

description: Over the past decade, a growing number of publications have claimed to
 provide evidence for the existence and function of neonatal imitation in
 rhesus macaques. Here I show that there is in fact no empirical basis for
 these claims. Studies of the phenomenon have consistently failed to
 implement the gold standard cross-target analytical approach, which
 controls for increases in matching responses that may not be a function of
 the specific modelled behaviour. Critically, a preregistered re-analysis
 of the entire set of existing data using this cross-target approach shows
 that macaque neonates have failed to produce matching tongue protrusion or
 lipsmacking responses at levels greater than chance. Furthermore, there is
 no evidence for intra-individual consistency in “imitative” responses
 across different actions, as imitation scores for the two actions are
 negatively correlated with each other. Macaque tongue protrusion and
 lipsmacking responses may vary as a function of general factors that
 fluctuate over testing sessions, rather than as a function of the specific
 model or of between-individual variations in imitative tendencies.
description: Cross-target responses
 to tongue protrusion and lipsmacking models in neonatal
 macaquesCSV file with
 cross-target responses to tongue protrusion and lipsmacking models
 (adapted from Paukner et al., 2017)Paukner2017_CSV_end_file.csv
DOI: 10.5061/dryad.390n07q
title: Data from: Parasitism and alternative reproductive tactics in Northern chamois

description: Alternative reproductive tactics (ARTs), discrete phenotypic variations
 evolved to maximize fitness, may entail different cost-benefit trade-offs.
 In large mammals, differences in costs associated with ARTs – including
 energy expenditure and parasite infection – are typically greatest during
 the breeding season. Nonetheless, physiological and behavioural
 differences between ARTs can manifest throughout the year, possibly
 involving costs that may contribute to maintain ARTs within populations.
 Using the number of nematode larvae per gram of faeces (LPG) as a proxy,
 we explored the temporal changes in lung parasite infection in territorial
 and nonterritorial male chamois Rupicapra rupicapra in the Gran Paradiso
 National Park (Italy), between 2011 and 2012. We aimed to identify which
 tactic-specific physiological and behavioural features (including age,
 hormonal levels, inter- and intrasexual interactions and space use) or
 climatic factors (temperature and precipitation) best explained yearly
 variation in parasite infection within and between ARTs. Generalized
 additive mixed models showed that the faecal larval counts of lung
 nematodes underwent strong temporal changes in both male types.
 Differences between ARTs (with higher LPG values in territorial than
 nonterritorial males) were greatest during the rut and – to a lesser
 extent – in spring, respectively at the peak and at the onset of
 territoriality. The difference in LPG between tactics was largely
 explained by the greater levels of hormone metabolites in territorial
 males during the rut. The other variables did not contribute significantly
 to explain the different shedding of larvae within and between ARTs. Our
 analysis suggests that different values of LPG between territorial and
 nonterritorial males are largely a result of tactic-specific differences
 in the secretion of hormone metabolites, but only during the rut. To
 clarify whether rut-related parasitism contributes to the maintenance of
 ARTs, tactic-specific life history trade-offs, e.g., between reproduction
 and parasite-related mortality, must be investigated.
description: Corlatti_et_al_Parasites
 & ARTs chamois_Supporting Information_2Parasite data and
 individual / environmental covariates.
DOI: 10.5061/dryad.sr6888t
title: Data from: Food web interaction strength distributions are conserved by greater variation between than within predator-prey pairs

description: Species interactions in food webs are usually recognized as dynamic,
 varying across species, space and time due to biotic and abiotic drivers.
 Yet food webs also show emergent properties that appear consistent, such
 as a skewed frequency distribution of interaction strengths (many weak,
 few strong). Reconciling these two properties requires an understanding of
 the variation in pairwise interaction strengths and its underlying
 mechanisms. We estimated stream sculpin feeding rates in three seasons at
 nine sites in Oregon to examine variation in trophic interaction strengths
 both across and within predator-prey pairs. Predator and prey densities,
 prey body mass, and abiotic factors were considered as putative drivers of
 within-pair variation over space and time. We hypothesized that
 consistently skewed interaction strength distributions could result if
 individual interaction strengths show relatively little variation, or
 alternatively, if interaction strengths vary but shift in ways that
 conserve their overall frequency distribution. Feeding rate distributions
 remained consistently and positively skewed across all sites and seasons.
 The mean coefficient of variation in feeding rates within each of 25 focal
 species pairs across surveys was less than half the mean coefficient of
 variation seen across species pairs within a survey. The rank order of
 feeding rates also remained conserved across streams, seasons and
 individual surveys. On average, feeding rates on each prey taxon
 nonetheless varied by a hundredfold, with some feeding rates showing more
 variation in space and others in time. In general, feeding rates increased
 with prey density and decreased with high stream flows and low water
 temperatures, although for nearly half of all species pairs, factors other
 than prey density explained the most variation. Our findings show that
 although individual interaction strengths exhibit considerable variation
 in space and time, they can nonetheless remain relatively consistent, and
 thus predictable, compared to the even larger variation that occurs across
 species pairs. These results highlight how the ecological scale of
 inference can strongly shape conclusions about interaction strength
 consistency and collectively help reconcile how the skewed nature of
 interaction strength distributions can persist in highly dynamic food
 webs.
description: Abiotic_Raw_DryadRaw data on abiotic variables from surveyed stream reaches.Abiotic_Summarized_DryadSummarized data on abiotic variables from surveyed stream reaches.FeedingRates_DryadSculpin feeding rates from nine reaches in three Oregon streams across three seasons.PreyItems_DryadSculpin stomach contents data.SculpinDensity_DryadSculpin density data from electroshock surveys.Surbers_Raw_DryadRaw benthic macroinvertebrate data from Surber samples.Surbers_Summarized_DryadSummarized benthic macroinvertebrate data from Surber samples.