cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d2441
title: Data from: Visual environment, attention allocation, and learning in young children: when too much of a good thing may be bad

description: A large body of evidence supports the importance of focused attention for
 encoding and task performance. Yet young children with immature regulation
 of focused attention are often placed in elementary-school classrooms
 containing many displays that are not relevant to ongoing instruction. We
 investigated whether such displays can affect children’s ability to
 maintain focused attention during instruction and to learn the lesson
 content. We placed kindergarten children in a laboratory classroom for six
 introductory science lessons, and we experimentally manipulated the visual
 environment in the classroom. Children were more distracted by the visual
 environment, spent more time off task, and demonstrated smaller learning
 gains when the walls were highly decorated than when the decorations were
 removed.
description: VisualEnv-Attn-Learning-DataThe data file includes the pre-test scores, post-test scores, total time-off-task, and time-off-task by distracter type in the Decorated and Sparse experimental condition. Additional tabs include a detailed summary about these outcome variables for each science lesson in each experimental condition.
DOI: 10.5061/dryad.j66q1
title: Data from: Group size effect on cooperation in one-shot social dilemmas II: curvilinear effect

description: In a world in which many pressing global issues require large scale
 cooperation, understanding the group size effect on cooperative behavior
 is a topic of central importance. Yet, the nature of this effect remains
 largely unknown, with lab experiments insisting that it is either positive
 or negative or null, and field experiments suggesting that it is instead
 curvilinear. Here we shed light on this apparent contradiction by
 considering a novel class of public goods games inspired to the realistic
 scenario in which the natural output limits of the public good imply that
 the benefit of cooperation increases fast for early contributions and then
 decelerates. We report on a large lab experiment providing evidence that,
 in this case, group size has a curvilinear effect on cooperation,
 according to which intermediate-size groups cooperate more than smaller
 groups and more than larger groups. In doing so, our findings help fill
 the gap between lab experiments and field experiments and suggest concrete
 ways to promote large scale cooperation among people.
description: curvilinear effect
 dataThis file contains the
 data of our experiment.
DOI: 10.5061/dryad.8v38v
title: Data from: Generation of infectious recombinant Adeno-associated virus in Saccharomyces cerevisiae.

description: The yeast Saccharomyces cerevisiae has been successfully employed to
 establish model systems for a number of viruses. Such model systems are
 powerful tools to study the virus biology and in particular for the
 identification and characterization of host factors playing a role in the
 viral infection cycle. Adeno-associated viruses (AAV) are heavily studied
 due to their use as gene delivery vectors. AAV relies on other helper
 viruses for successful replication and on host factors for several aspects
 of the viral life cycle. However the role of host and helper viral factors
 is only partially known. Production of recombinant AAV (rAAV) vectors for
 gene delivery applications depends on knowledge of AAV biology and the
 limited understanding of host and helper viral factors may be precluding
 efficient production, particularly in heterologous systems. Model systems
 in simpler eukaryotes like the yeast S. cerevisiae would be useful tools
 to identify and study the role of host factors in AAV biology. Here we
 show that expression of AAV2 viral proteins VP1, VP2, VP3, AAP, Rep78,
 Rep52 and an ITR-flanked DNA in yeast leads to capsid formation, DNA
 replication and encapsidation, resulting in formation of infectious
 particles. Many of the AAV characteristics observed in yeast resemble
 those in other systems, making it a suitable model system. Future findings
 in the yeast system could be translatable to other AAV host systems and
 aid in more efficient production of rAAV vectors.
description: Data for Figures 3D and
 4AQuantification of
 AAV-GFP DNA and vector plasmid by droplet-digital PCR (Fig 3D).
 Quantification of AAV capsids and GFP DNA in rAAV purified from yeast (Fig
 4A).Barajas
 et al. PLOS ONE.xlsxCodon optimized
 sequencesAAP and Rep coding
 sequences from AAV2, codon optimized for expression in Saccharomyces
 cerevisiae.
DOI: 10.5061/dryad.dg4mc
title: Data from: Leaf litter species identity alters the structure of pond communities

description: The input of leaf litter resources is a major driver of ecosystem
 processes in terrestrial and freshwater habitats. Although variation
 exists in the quantity and composition of litter inputs due to natural and
 anthropogenic causes, few studies have examined how such variation
 influences the structure and composition of aquatic food webs. Using
 outdoor mesocosms, we examined the bottom–up effects of 10 chemically
 distinct tree litter species on microbial, algal, invertebrate and
 vertebrate fauna found in temperate ponds. We hypothesized that individual
 litter species, which differ in their traits, would differentially and
 predictably affect abiotic and biotic elements of pond communities. We
 further hypothesized that the presence of leaf litter, regardless of
 species, would elevate resource supply and increase the biomass of
 community members. Finally, we hypothesized that a mixture of litter
 species would have non-additive effects on community responses. We
 followed the system for &gt; 4 months and measured &gt; 30 abiotic
 and biotic responses related to primary and secondary production. The
 different species of leaf litter had major effects on abiotic and biotic
 responses, including phytoplankton, periphyton, zooplankton, snails,
 amphipods and tadpoles. Most biological responses were negatively
 associated with soluble carbon content of litter, or litter decay rate.
 Other litter traits, including phenolic concentrations and litter C:N were
 of secondary importance but did exhibit both positive and negative
 associations with several responses. The absence of litter had pervasive
 effects on abiotic attributes, but did not promote substantial changes in
 organism biomass. Most responses to the litter mixture were additive. Our
 results suggest that changes in temperate forest composition can strongly
 affect pond communities.
description: LitterDataStoler2015Data.xlsx
DOI: 10.5061/dryad.0r86b
title: Data from: Males migrate farther than females in a differential migrant: an examination of the fasting endurance hypothesis

description: Patterns of migration including connectivity between breeding and
 non-breeding populations and intraspecific variation in the distance
 travelled are important to study because they can affect individual
 fitness and population dynamics. Using data from 182 band recoveries
 across North America and 17 light-level geolocators, we examined the
 migration patterns of the northern flicker (Colaptes auratus), a migratory
 woodpecker. This species is unusual among birds because males invest more
 in parental care than females. Breeding latitude was positively correlated
 to migration distance because populations in the north appeared to travel
 farther distances than southern populations to find wintering locations
 with little snow cover. Connectivity was strong for populations west and
 east of the Continental Divide. Contrary to the three main hypotheses for
 intraspecific variation in migration distance, females wintered, on
 average, farther north than males, although there was overlap throughout
 their non-breeding range. This pattern contradicts those of other species
 found to date and is most consistent with the fasting endurance hypothesis
 if investment in parental care depletes the energy reserves of male
 flickers more than females. We thus propose a new factor, parental effort,
 which may influence optimal wintering areas and migration strategies
 within birds, and encourage future experimental studies to test the
 relationship between parental care roles and migration strategies of the
 sexes.
description: Northern Flicker
 wintering locations from GeolocatorsThe wintering locations
 and distances travelled of northern flickers carrying geolocators.
 Geolocators were attached on flickers at Riske Creek, BC, Canada 52.03ºN,
 122.515ºW.NOFL migration
 data.xlsx
DOI: 10.5061/dryad.tg782
title: Data from: Screening test for neutralizing antibodies against yellow fever virus, based on a flavivirus pseudotype

description: Given the possibility of yellow fever virus reintroduction in
 epidemiologically receptive geographic areas, the risk of vaccine supply
 disruption is a serious issue. New strategies to reduce the doses of
 injected vaccines should be evaluated very carefully in terms of
 immunogenicity. The plaque reduction test for the determination of
 neutralizing antibodies (PRNT) is particularly time-consuming and requires
 the use of a confinement laboratory. We have developed a new test based on
 the use of a non-infectious pseudovirus (WN/YF17D). The presence of a
 reporter gene allows sensitive determination of neutralizing antibodies by
 flow cytometry. This WN/YF17D test was as sensitive as PRNT for the
 follow-up of yellow fever vaccinees. Both tests lacked specificity with
 sera from patients hospitalized for acute Dengue virus infection.
 Conversely, both assays were strictly negative in adults never exposed to
 flavivirus infection or vaccination, and in patients sampled some time
 after acute Dengue infection. This WN/YF17D test will be particularly
 useful for large epidemiological studies and for screening for
 neutralizing antibodies against yellow fever virus.
description: Data from NOVAA-test
 sensitivity and specificity versus PRNTNOVAA-test is a new
 screening test for neutralizing antibodies against yellow fever.
 Percentage of Yellow fever pseudotype allowing VLP culture and titer of
 neutralization obtained on reference PRNT assay are
 compared.DATA PLOS
 ONE.xlsx
DOI: 10.5061/dryad.c69g0d5
title: Data from: Seed moisture content as a primary trait regulating the lethal temperature thresholds of seeds.

description: 1) Fire has shaped biological responses of plants and plant communities in
 fire-prone systems and is linked to myriad ecological processes but also
 frequently puts people and infrastructure at risk. Fuel or
 hazard-reduction burning is a common practice aimed at reducing the risk
 of high-severity fires, which ideally also incorporates consideration of
 biodiversity values. Within fire-prone systems, seed banks are often
 critical for plant species’ regeneration, and seeds are typically adapted
 to survive the passage of fire and to regenerate in response to cues
 associated with natural fire regimes. However, species-specific tolerances
 to the heat from fire exist; likely influenced by a range of physical,
 physiological, and morphological seed traits. Identification of these
 tolerances and associated seed traits may inform fire and
 species-management. 2) We determined the lethal temperatures for seeds in
 relation to their moisture content, and other key traits that we
 hypothesised may be associated with survival. Seeds from 14 native
 species, and 4 species invasive to fire-prone Mediterranean climate
 Banksia woodlands of southwestern Australia, were exposed to temperatures
 between 50 °C and 180 °C for 3 mins, at three different moisture contents.
 The temperature at which half the seeds were killed (T50) was estimated
 using non-linear log-logistic modelling. Seed mass, seed shape, embryo
 type, plant resprouting ability, seed storage syndrome, and
 native/invasive status, were measured and modelled for their correlation
 with T50. 3) Increased moisture content was a significant predictor of
 elevated seed mortality. Seeds with low moisture content (those
 pre-conditioned at 15 or 50% RH), were able to survive far hotter
 temperatures (median increase of 38 °C and 31°C respectively), than those
 with high moisture content (those pre-conditioned at 95% RH). Of other
 traits considered, seeds with basal embryos showed significantly lower T50
 than other embryo types. 4) Synthesis: Seeds with higher moisture contents
 have lower lethal temperature thresholds, leading to higher seed mortality
 during fire events when seeds (and soils) are moist. Thermal tolerance
 varied among co-existing species within this fire-prone system. These data
 suggest potential concern for the impacts of aseasonal burning practices
 (i.e. cool/wet season burning), and highlight the importance of taking
 seed moisture content into account when planning and implementing
 prescribed burning.
description: Seed
 viabilitySeed viability.zip
 contains all species viability data used in generating species species t50
 curves, all seed and plant traits used in the analysis as well as moisture
 content of seeds following hydration each RH level for two
 weeks.
DOI: 10.5061/dryad.p570g
title: Data from: Does the cost of development scale allometrically with offspring size?

description: 1.Within many species, larger offspring have higher fitness. While the
 presence of an offspring size-fitness relationship is canonical in
 life-history theory, the mechanisms that determine why this relationship
 exists are unclear. 2.Linking metabolic theory to life-history theory
 could provide a general explanation for why larger offspring often perform
 better than smaller offspring. In many species, energy reserves at the
 completion of development drive differences in offspring fitness.
 Development is costly so any factor that decreases energy expenditure
 during development should result in higher energy reserves and thus
 subsequently offspring fitness. 3.Metabolic theory predicts that larger
 offspring should have relatively lower metabolic rates and thus emerge
 with a higher level of energy reserves (assuming developmental times are
 constant). The increased efficiency of development in larger offspring may
 therefore be an underlying driver of the relationship between offspring
 size and offspring fitness, but this has not been tested within species.
 4.To determine how the costs of development scale with offspring size, we
 measured energy expenditure throughout development in the model organism
 Danio rerio across a range of natural offspring sizes. We also measured
 how offspring size affects the length of the developmental period. We then
 examined how hatchling size and condition scale with offspring size. 5.We
 find that larger offspring have lower mass-specific metabolic rates during
 development, but develop at the same rate as smaller offspring. Larger
 offspring also hatch relatively heavier and in better condition than
 smaller offspring. That the relative costs of development decrease with
 offspring size may provide a widely applicable explanation for why larger
 offspring often perform better than smaller offspring.
description: Zebrafish mass-metabolic
 rate dataMeasures of zebrafish
 embryo volume(um3), log volume, mass (ug), log mass and log10 metabolic
 rate; LOGMR (where MR is mJ h-1). Each experiment consists of a cohort of
 zebrafish embryos (where eggs were fertilised from 2 parent pairs) reared
 over 3 days (3 stages) with metabolic rate measured every 24 hours
 throughout development.Pettersen_et_al-Zebrafish_MassMR.csvZebrafish mass-volume relationshipMeasures of zebrafish embryo diameter, area, volume and mass from which we used to determine the relationship between zebrafish embryo diameter (um) and mass (ug) across two parental pairs.Pettersen_et_al-Zebrafish_mass_volume relationship.csv
DOI: 10.5061/dryad.rc638
title: Data from: Regulatory gene networks that shape the development of adaptive phenotypic plasticity in a cichlid fish

description: Phenotypic plasticity is the ability of organisms with a given genotype to
 develop different phenotypes according to environmental stimuli, resulting
 in individuals that are better adapted to local conditions. In spite of
 their ecological importance, the developmental regulatory networks
 underlying plastic phenotypes often remain uncharacterized. We examined
 the regulatory basis of diet-induced plasticity in the lower pharyngeal
 jaw (LPJ) of the cichlid fish Astatoreochromis alluaudi, a model species
 in the study of adaptive plasticity. Through raising juvenile A. alluaudi
 on either a hard or soft diet (hard shelled or pulverized snails) for
 between one and eight months, we gained insight into the temporal
 regulation of 19 previously identified candidate genes during the early
 stages of plasticity development. Plasticity in LPJ morphology was first
 detected between three and five months of diet treatment. The candidate
 genes, belonging to various functional categories, displayed dynamic
 expression patterns that consistently preceded the onset of morphological
 divergence and putatively contribute to the initiation of the plastic
 phenotypes. Within functional categories we observed striking
 co-expression, and transcription factor binding site analysis was used to
 examine the prospective basis of their co-regulation. We propose a
 regulatory network of LPJ plasticity in cichlids, presenting evidence for
 regulatory cross-talk between bone and muscle tissues, which putatively
 facilitates the development of this highly integrated trait. Through
 incorporating a developmental time-course into a phenotypic plasticity
 study, we have identified an interconnected, environmentally responsive
 regulatory network that shapes the development of plasticity in a key
 innovation of East African cichlids
description: Distance Matrices of
 hierarchical cluster analysesDistance matrices used
 for the hierarchical cluster analyses for the analysis using only the
 selected 15 genes (for genes and specimens) and for teh analysis including
 all 19 candidate genes (also for genes and specimens).distance_matrices.txtLinear morphometric measurementsLinear morphometric measurements of the 10 recorded variables for each of the 33 individuals, plus information on the timepoint, diet group and standard length of each.linear morphometric measurementsNormalized gene expression valuesStandardized and normalized gene expression values of the 19 candidate genes and the houskeeping genes for each individual, including timepoint and diet information.normalized gene expression plus houskeepers
DOI: 10.5061/dryad.ff853
title: Data from: Sympathetic nervous system activity and anti-lipolytic response to IV-glucose load in subcutaneous adipose tissue of obese and obese type 2 diabetic subjects

description: The study aim was to investigate the effect of endogenous insulin release
 on lipolysis in subcutaneous adipose tissue after adrenergic stimulation
 in obese subjects diagnosed with type 2 diabetes (T2D). In 14 obese female
 T2D subjects, or 14 obese non-T2D controls, glycerol concentration was
 measured in response to the α1,2,ß-agonist norepinephrine, the α1-agonist
 norfenefrine and the ß2-agonist terbutaline (each 10-4 M), using the
 microdialysis technique. After 60 minutes of stimulation, an intravenous
 glucose load (0.5 g/kg lean body mass) was given. Local blood flow was
 monitored by means of the ethanol technique. Norepinephrine and
 norfenefrine induced a four and three fold rise in glycerol dialysate
 concentration (p&lt;0.001, each), with a similar pattern in adipose
 tissue. Following agonist stimulation and glucose infusion, endogenous
 insulin release inhibited lipolysis in the presence of norepinephrine,
 which was more rapid and pronounced in healthy obese controls than in T2D
 subjects (p=0.024 obese vs T2D subjects). Insulin-induced inhibition of
 lipolysis in the presence of norfenefrine was similar in all study
 participants. In the presence of terbutaline the lipolysis rate increased
 two fold until the effect of endogenous insulin (p&lt;0.001). A
 similar insulin-induced decrease in lipolysis was observed for each of the
 norfenefrine groups and the terbutaline groups, respectively. Adipose
 tissue blood flow remained unchanged after the iv-glucose load. Both
 norepinephrine and norfenefrine diminished blood flow slightly, but
 insulin reversed this response (p&lt;0.001 over the entire time).
 Terbutaline alone and terbutaline plus increased endogenous insulin
 augmented local blood flow (p&lt;0.001 over the entire time). In
 conclusion, a difference in insulin-induced inhibition of lipolysis was
 observed in obese T2D subjects compared to obese healthy controls
 following modulation of sympathetic nervous system activity and is assumed
 to be due to ß1-adrenoceptor mediated stimulation by norepinephrine.
description: SchumannDataDataset-file from Sympathetic nervous system activity and anti-lipolytic response to IV-glucose load in subcutaneous adipose tissue of obese and obese type 2 diabetic subjects
DOI: 10.5061/dryad.n0b44
title: Data from: The south-western Carpathians as a centre of ancient diversity of freshwater gammarid amphipods: insights from the Gammarus fossarum species complex

description: Gammarus fossarum is a diverse species complex of epigean freshwater
 amphipods throughout Europe. Due to their poor dispersal capabilities and
 ubiquity, these crustaceans may serve as a model for investigating the
 influence of historical factors on the contemporary distribution and
 diversity patterns of freshwater macrozoobenthos. Here, we investigate the
 fine-scale phylogeographic structure of this complex across its range in
 the southwestern Carpathian Mountains, which comprises two areas that are
 geographically isolated from its main European distribution area as well
 as from each other. Given the Tertiary age of many freshwater Gammarus
 species, we hypothesize that the southwestern Carpathian populations
 reflect a relict distribution pattern. We used two mitochondrial and three
 nuclear markers from 32 localities to reconstruct phylogenetic
 relationships and estimate the timings of divergence among southwestern
 Carpathian and non-Carpathian lineages. Cryptic diversity was evaluated
 from mitochondrial markers by employing phylogenetic and distance-based
 methods. We distinguished at least 16 cryptic microendemic taxa, some of
 them coexisting, distributed in the southwestern Carpathians in a
 mosaic-like pattern. These lineages form a monophyletic group together
 with several lineages from southeastern Europe. Estimated divergence times
 indicate a Middle Miocene origin of this clade, with many deep splits
 dating back to more than 10 Ma. This time frame corresponds with a period
 of intense geological subsidence in the region that gave birth to the
 Pannonian Basin. We conclude that subsidence could have been an important
 driver of diversification in freshwater Gammarus and that the southwestern
 Carpathians represent an ancient centre of diversity for these
 crustaceans.
description: Copilas-Ciocianu&Petrusek_Gammarus_fossarum_SW_Carpathians_alignments&treesThe archive contains alignments (fasta format) and maximum likelihood trees (newick format) for each of the markers used in this study as well as a concatenated supermatrix.