cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v70ck
title: Data from: Curcumin improves glycolipid metabolism through regulating peroxisome proliferator activated receptor γ signalling pathway in high-fat diet-induced obese mice and 3T3-L1 adipocytes

description: Curcumin, an active component derived from the Curcuma longa L. which is a
 traditional Chinese medicine that is widely used for treating metabolic
 diseases through regulating different molecular pathway. Here, in this
 study, we aimed to comprehensively investigate the effects of curcumin on
 glycolipid metabolism in vivo and in vitro and then determine the
 underlying mechanism. Male C57BL/6J obese mice and 3T3-L1 adipocytes were
 used in vivo and in vitro study, respectively. Our results demonstrated
 that treatment with curcumin for 8 weeks decreased body weight, fat mass
 and serum lipid profiles. Meanwhile, it lowered fasting blood glucose and
 increased the insulin sensitivity in high-fat diet induced obese mice. In
 addition, curcumin stimulated lipolysis and improve glycolipid through
 upregulating the expressions of ATGL, HSL, PPARγ, C/EBPα and PPARα in
 adipose tissue of the mice. In differentiated 3T3-L1 cells, curcumin
 reduced glycerol release and increased glucose uptake via upregulating
 PPARγ and C/EBPα. We concluded that curcumin has potential to improve
 glycolipid metabolism disorders caused by obesity through regulating PPARγ
 signaling pathway.
description: Data S1 The body weight
 of mice in ND, HFD and HFD+Cur group.Data
 S1.xlsxData S2 The fat mass of
 body weight in each group at week 4 and week 8Data
 S2.xlsxData S3 The fasting
 blood glucose of mice in ND, HFD and HFD+Cur groupData
 S3.xlsxData S4 The results of
 OGTT at week 4 and week 8Data
 S4.xlsxData S5 The serum lipid
 profiles and FFA level of mice in ND, HFD and HFD+Cur
 groupData
 S5.xlsxFig.1 Chemical structure
 of curcumin.Its molecular formula is
 C21H20O6. MW (molecular weight): 368.37Fig.1.tifFig.2 Curcumin decreased the body weight and fat mass in HFD induced obese mice.(a) Body weight and (b) body weight gain of the mice in ND, HFD and HFD+Cur group, 10 samples per group were taken for each assay. The fat mass of body weight in each group at week 4 (c) and week 8 (d). Data are presented as meanSEM in each group. Significant difference: #p&lt;0.05, ##p&lt;0.01 vs. ND group, *p&lt;0.05, **p&lt;0.01 vs. HFD group.Fig.2.tif
DOI: 10.5061/dryad.3f4s88q
title: Data from: The analysis and interpretation of critical temperatures

description: Critical temperatures are widely used to quantify the upper and lower
 thermal limits of organisms. But measured critical temperatures often vary
 with methodological details, leading to spirited discussions about the
 potential consequences of stress and acclimation during the experiments.
 We review a model based on the simple assumption that failure rate
 increases with increasing temperature, independent of previous temperature
 exposure, water loss or metabolism during the experiment. The model
 predicts that mean critical thermal maximal temperatures (CTmax) increases
 nonlinearly with starting temperature and ramping rate, a pattern
 frequently observed in empirical studies. We then develop a statistical
 model that estimates a failure rate function (the relationship between
 failure rate and current temperature) using maximum likelihood; the best
 model accounts for 58% of the variation in CTmax in an exemplary dataset
 for tsetse flies. We then extend the model to incorporate potential
 effects of stress and acclimation on the failure rate function; the
 results show how stress accumulation at low ramping rate may increase the
 failure rate and reduce observed values of CTmax. We also applied the
 model to an acclimation experiment with hornworm larvae that used a single
 starting temperature and ramping rate; the analyses show that increasing
 acclimation temperature significantly reduced the slope of the failure
 rate function, increasing the temperature at which failure occurred. The
 model directly applies to critical thermal minima, and can utilize data
 from both ramping and constant temperature assays. Our model provides a
 new approach to analyzing and interpreting critical temperatures.
description: Kingsolver&Umbanhowar.supplThese supplementary files contain the data and code to recreate all of the analyses and figures associated with the paper. See the Readme file.
DOI: 10.5061/dryad.r75t5
title: Data from: Quick divergence but slow convergence during ecotype formation in lake and stream stickleback pairs of variable age

description: When genetic constraints restrict phenotypic evolution, diversification
 can be predicted to evolve along so-called lines of least resistance. To
 address the importance of such constraints and their resolution, studies
 of parallel phenotypic divergence that differ in their age are valuable.
 Here, we investigate the parapatric evolution of six lake and stream
 threespine stickleback systems from Iceland and Switzerland, ranging in
 age from a few decades to several millennia. Using phenotypic data, we
 test for parallelism in ecotypic divergence between parapatric lake and
 stream populations and compare the observed patterns to an ancestral-like
 marine population. We find strong and consistent phenotypic divergence,
 both among lake and stream populations and between our freshwater
 populations and the marine population. Interestingly, ecotypic divergence
 in low-dimensional phenotype space (i.e. single traits) is rapid and seems
 to be often completed within 100 years. Yet, the dimensionality of
 ecotypic divergence was highest in our oldest systems and only there
 parallel evolution of unrelated ecotypes was strong enough to overwrite
 phylogenetic contingency. Moreover, the dimensionality of divergence in
 different systems varies between trait complexes, suggesting different
 constraints and evolutionary pathways to their resolution among freshwater
 systems.
description: Morphological &
 genetic data for threespine sticklebacks from Switzerland and
 IcelandLucek_et_al_JEB-2013-00738.R2_Dryad.xlsx
DOI: 10.5061/dryad.f82c85f
title: Data from: A strengths-based data capture model: mining data-driven and person-centered health assets

description: With health care policy directives advancing value-based care, risk
 assessments and management have permeated health care discourse. The
 conventional problem-based infrastructure defines what data are employed
 to build this discourse and how it unfolds. Such a health care model tends
 to bias data for risk assessment and risk management toward problems and
 does not capture data about health assets or strengths. The purpose of
 this article is to explore and illustrate the incorporation of a
 strengths-based data capture model into risk assessment and management by
 harnessing data-driven and person-centered health assets using the Omaha
 System. This strengths-based data capture model encourages and enables use
 of whole-person data including strengths at the individual level and, in
 aggregate, at the population level. When aggregated, such data may be used
 for the development of strengths-based population health metrics that will
 promote evaluation of data-driven and person-centered care, outcomes, and
 value.
description: JAMIO-2017-0039.R2This data file contains data of de-identified client_IDs, codes for Omaha System problem concepts, related strength-indicators, signs/symptoms, Knowledge, Behavior, and Status scores as well as a data dictionary for codes and terms.
DOI: 10.5061/dryad.1087
title: Data from: A stochastic model for annual reproductive success

description: Demographic stochasticity can have large effects on the dynamics of small
 populations as well as on the persistence of rare genotypes and lineages.
 Survival is sensibly modeled as a binomial process, but annual
 reproductive success (ARS) is more complex and general models for
 demographic stochasticity do not exist. Here we introduce a stochastic
 model framework for ARS and illustrate some of its properties. We model a
 sequence of stochastic events: nest completion, the number of eggs or
 neonates produced, nest predation, and the survival of individual
 offspring to independence. We also allow multiple nesting attempts within
 a breeding season. Most of these components can be described by Bernoulli
 or binomial processes; the exception is the distribution of offspring
 number. Using clutch and litter size distributions from 53 vertebrate
 species, we demonstrate that among‐individual variability in offspring
 number can usually be described by the generalized Poisson distribution.
 Our model framework allows the demographic variance to be calculated from
 underlying biological processes and can easily be linked to models of
 environmental stochasticity or selection because of its parametric
 structure. In addition, it reveals that the distributions of ARS are often
 multimodal and skewed, with implications for extinction risk and evolution
 in small populations.
description: MLE LL
 EstimatesMLE_LL_estimates.txt
DOI: 10.5061/dryad.9c698
title: Data from: Pardon the interruption: goal proximity, perceived spare time, and impatience

description: There is no worse time to be interrupted than right now. Being close to
 attaining a goal to complete a focal task increases the attractiveness of
 that task compared to an interrupting task (study 1), makes people less
 willing to take on some otherwise attractive interruption than if they
 were farther away from completion (studies 2, 3, and 4), and causes them
 to perceive that in that moment they have little spare time (studies 3 and
 4). Consumers immersed in goal pursuit are affected by local progress on
 an individual subgoal that supports an overarching goal even if this has
 no effect on the timing of attaining the overarching goal. Observers do
 not appreciate the motivating power of proximity to completing subgoals,
 and this leads them to mispredict the behavior of others (study 5).
description: Pardon the Interruption:
 Goal Proximity, Perception of Spare Time, and
 Impatience.7 SPSS files (5
 experiments) reported in the articleJhang and Lynch JCR
 2015.zip
DOI: 10.5061/dryad.3q0d3rb4
title: Data from: Spatial heterogeneity in genetic relatedness among house sparrows along an urban-rural gradient as revealed by individual-based analysis

description: Understanding factors that shape patterns of kinship in sedentary species
 is important for evolutionary ecologists as well as conservation
 biologists. Yet, how patterns of relatedness are hierarchically structured
 in space remains poorly known, even in common species. Here we use
 information from 16 polymorphic microsatellite DNA markers to study how
 small-scale kinship structure varies among house sparrows (Passer
 domesticus) along an urban-rural gradient. Average levels of relatedness
 were higher among urban individuals than among individuals from rural
 areas, suggesting lower rates of dispersal in more built up habitats.
 Comparison of observed levels of relatedness with simulated distributions
 of known kinship values showed that central urban individuals had the
 highest proportion of closely-related conspecifics in their immediate
 neighbourhood. Spatial auto-correlograms supported this small-scale
 genetic structure and further indicated stronger effects of genetic drift
 and/or limited dispersal in urban populations. Results of this study
 underscore the importance of individual-level analyses as a complementary
 approach to traditional population-level analyses when studying genetic
 population structure over small spatial scales.
description: Dryad Data Vangestel et
 al
DOI: 10.5061/dryad.1521
title: Data from: Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae)

description: Epigenetic information includes heritable signals that modulate gene
 expression but are not encoded in the primary nucleotide sequence. We have
 studied natural epigenetic variation in three allotetraploid sibling
 orchid species that differ radically in geography/ecology. The epigenetic
 variation released by genome doubling has been restructured in
 species-specific patterns that reflect their recent evolutionary history,
 and have an impact on their ecology and evolution, hundreds of generations
 after their formation. Epigenome scans pinpointed epiloci under divergent
 selection that correlate with eco-environmental variables, mainly related
 to water availability and temperature. The stable epigenetic divergence in
 this group is largely responsible for persistent ecological differences,
 which then set the stage for species-specific genetic patterns to
 accumulate in response to further selection and/or drift. Our results
 strongly suggest a need to expand our current evolutionary framework to
 encompass a complementary epigenetic dimension when seeking to understand
 population processes that drive phenotypic evolution and adaptation.
description: Methylation sensitive
 AFLP data of Dactylorhiza allopolyploidsThe data is provided in
 four tabs: the "Original" tab contains the initial information
 obtained from the two paired profiles per individual (i.e., MspI and
 HpaII); the "Unmethylated" tab includes fragments present in
 both profiles simultaneously; the "MeCpG" tab includes the
 information from MspI; the "hemiMeCpCpG" tab includes the
 information from HpaII. Redundant information between the last 3 tabs has
 been retained only once.data.xls
DOI: 10.5061/dryad.s01rg
title: Data from: From global to local genetic structuring in the red gorgonian Paramuricea clavata: the interplay between oceanographic conditions and limited larval dispersal

description: Defining the scale of connectivity among marine populations and
 identifying the barriers to gene flow are tasks of fundamental importance
 for understanding the genetic structure of populations and for the design
 of marine reserves. Here we investigated the population genetic structure
 at three spatial scales of the red gorgonian Paramuricea clavata
 (Cnidaria, Octocorallia) a key species dwelling in the coralligenous
 assemblages of the Mediterranean Sea. Colonies of P. clavata were
 collected from 39 locations across the Mediterranean Sea from Morocco to
 Turkey and analysed using microsatellite loci. Within three regions
 (Medes, Marseille and North Corsica) sampling was obtained from multiple
 locations and at different depths. Three different approaches (measures of
 genetic differentiation, Bayesian clustering and spatially explicit
 maximum-difference algorithm) were used to determine the pattern of
 genetic structure. We identified genetic breaks in the spatial
 distribution of genetic diversity which were concordant with oceanographic
 conditions in the Mediterranean Sea. We revealed a high level of genetic
 differentiation among populations and a pattern of isolation by distance
 across the studied area and within the three regions, underlining short
 effective larval dispersal in this species. We observed genetic
 differentiation among populations in the same locality dwelling at
 different depths which may be explained by local oceanographic conditions
 and which may allow a process of local adaptation of the populations to
 their environment. We discuss the implications of our results for the
 conservation of the species which is exposed to various threats.
description: Microsatellite
 Data_Paramuricea clavataMicrosatellite data at 6
 loci for the 39 Paramuricea clavata samples studied in Mediterranean
 Sea
DOI: 10.5061/dryad.q401b
title: Data from: Seed banks are biodiversity reservoirs: species-area relationships above versus below ground

description: Soil seed banks offer plants the possibility to disperse through time.
 This has implications for population and community dynamics, as recognised
 by ecological and evolutionary theory. In contrast, the conservation and
 restoration literature often find seed banks to be depauperate, weedy and
 without much conservation value or restoration potential. One explanation
 for these contrasting views might lie in a systematic bias in the sampling
 of seed banks versus established plant communities. We use the
 species–area relationship as a tool to assess and compare the per-area
 species richness and spatial structuring of the diversity of the
 established plant community versus soil seed banks. To allow this direct
 comparison we extensively survey the species–area relationship of the
 vegetation and underlying seed bank of a grassland community across twelve
 sites spanning regional bioclimatic gradients. We also compile a global
 dataset of established vegetation and seed banks from published sources.
 We find that seed banks have consistently higher intercepts and slopes of
 the relationship, and hence higher diversity at any given spatial scale,
 than the vegetation both in the field and literature study. This is
 consistent across habitat types, climate gradients, and biomes. Similarity
 indices are commonly used to compare vegetation and seed bank, and we find
 that sampling effort (% of the vegetation area sampled for seed bank) was
 the strongest predictor of vegetation–seed bank similarity for both the
 Sørensen (R2 = 0.70) and the Raup–Crick (R2 = 0.25) index. Our study
 suggests that the perception that seed banks are intrinsically less
 diverse than established plant communities has been based more on
 inadequate sampling than on biological reality. Across a range of
 ecosystems and climatic settings, we find high diversity in seed banks
 relative to the established community, suggesting potentially important
 roles of seed banks in population dynamics and diversity maintenance.
description: Vandvik_OIKOSThe vegetation data (Vandvik_Veg) was collected in grassland vegetation the SeedClim field sites in western Norway, in August 2008. The seed bank data (Vandvik_SB) was collected in a greenhouse experiment during 2009/2010.
DOI: 10.5061/dryad.nf91079h
title: Data from: Multilocus coalescence analyses support a mtDNA-based phylogeographic history for a widespread Palearctic passerine bird, Sitta europaea

description: Our understanding of species phylogeography in much of the Palearctic is
 incomplete. In addition, many existing studies based solely on
 mitochondrial DNA (mtDNA) can provide a biased view of phylogeographic
 history because of the effects of lineage sorting, natural selection or
 hybridization. We analyzed 13 introns to assess a mtDNA study of the
 Eurasian nuthatch (Sitta europaea) that suggested a seemingly
 contemporaneous origin of distinct taxa in the Caucasus, Europe, and Asia.
 Neutrality tests showed no evidence of selection on either the mtDNA or
 nuclear sequences. Most nuclear gene trees, except for Z-linked ones, did
 not recover the three lineages, which we attribute to recent splitting.
 Analyses of the 13 introns combined revealed the same three groups as did
 the mtDNA and suggested that nuthatches experienced a trichotomous (or two
 indistinguishable) split(s) 1-2 Ma ago and have remained isolated with
 trifling if not zero gene flow since then, and the Asian group increased
 in population size. This result demonstrates the usefulness of mtDNA in
 discovering phylogeographic patterns. The use of multiple nuclear loci
 facilitated detection of an introgressed individual and improved estimates
 of process parameters such as divergence time and population expansion. We
 recommend that phylogeographic studies should be based on both mtDNA and
 nuclear genes.
description: DATA for sitta to
 DRYADThis zip file contains
 the input files for several programs used in this
 papers.
DOI: 10.5061/dryad.6n385
title: Data from: Constraints on the adult-offspring size relationship in protists

description: The relationship between adult and offspring size is an important aspect
 of reproductive strategy. Although this filial relationship has been
 extensively examined in plants and animals, we currently lack comparable
 data for protists, whose strategies may differ due to the distinct
 ecological and physiological constraints on single-celled organisms. Here,
 we report measurements of adult and offspring sizes in 3,888 species and
 subspecies of foraminifera, a class of large marine protists. Foraminifera
 exhibit a wide range of reproductive strategies; species of similar adult
 size may have offspring whose sizes vary 100-fold. Yet, a robust pattern
 emerges. The minimum (5th percentile), median, and maximum (95th
 percentile) offspring sizes exhibit a consistent pattern of increase with
 adult size independent of environmental change and taxonomic variation
 over the past 400 million years. The consistency of this pattern may arise
 from evolutionary optimization of the offspring size-fecundity trade-off
 and/or from cell-biological constraints that limit the range of
 reproductive strategies available to single-celled organisms. When
 compared with plants and animals, foraminifera extend the evidence that
 offspring size covaries with adult size across an additional five orders
 of magnitude in organism size.
description: Caval-Holme_data1Data file describes the adult test volumes (in log10 mm^2) and diameters (in mm) of foraminiferan species and subspecies illustrated in the Ellis and Messina catalog of Foraminifera. Specimens were measured from paper copies of the catalog using digital calipers accurate to the nearest 0.01 mm. Higher taxonomy was assigned as per Loeblich and Tappan (1988). Geological age information was taken from the descriptions in the Ellis and Messina catalog.
DOI: 10.5061/dryad.4g349
title: Data from: Habitat discontinuities separate genetically divergent populations of a rocky shore marine fish

description: Habitat fragmentation has been suggested to be responsible for major
 genetic differentiations in a range of marine organisms. In this study, we
 combined genetic data and environmental information to unravel the
 relative role of geography and habitat heterogeneity on patterns of
 genetic population structure of corkwing wrasse (Symphodus melops), a
 rocky shore species at the northern limit of its distribution range in
 Scandinavia. Our results revealed a major genetic break separating
 populations inhabiting the western and southern coasts of Norway. This
 genetic break coincides with the longest stretch of sand in the whole
 study area, suggesting habitat fragmentation as a major driver of genetic
 differentiation of this obligate rocky shore benthic fish in Scandinavia.
 The complex fjords systems extending along the western coast of Norway
 appeared responsible for further regional genetic structuring. Our
 findings indicate that habitat discontinuities may lead to significant
 genetic fragmentation over short geographical distances, even for marine
 species with a pelagic larval phase, as for this rocky shore fish.
description: Microsatellite_data_corkwing_wrasseThis file contains the raw genotype data used in the manuscript "Habitat Discontinuities Separate Genetically Divergent Populations of a Rocky Shore Marine Fish" co-authored by Blanco Gonzalez E, Knutsen H, Jorde PEBlancoGonzalez_et_al..xls