cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1rd0m
title: Data from: The emergence of earliest angiosperms may be earlier than fossil evidence indicates

description: Gaps between molecular ages and fossils undermine the validity of
 time-calibrated molecular phylogenies. An example of the time gap
 surrounds the age of angiosperms' origin. We calculate molecular ages
 of the earliest flowering plant lineages using 22 fossil calibrations (101
 genera, 40 families). Our results reveal the origin of angiosperms at the
 late Permian, ∼275 million years ago. Different prior probability curves
 of molecular age calculations on dense calibration point distributions had
 little effect on overall age estimates compared to the effects of altered
 calibration points. The same is true for reasonable root age constraints.
 We conclude that our age estimates based on multiple datasets, priors, and
 calibration points are robust and the true ages are likely between our
 extremes. Our results, when integrated with the ecophysiological evolution
 of early angiosperms, imply that the ecology of the earliest angiosperms
 is critical to understand the pre-Cretaceous evolution of flowering
 plants.
description: BA Method Paper phyA
 newPhyA
 dataBA Method Paper gp
 18.06.2013chloroplast
 dataBA Method Paper combined
 2 with hotspots 17.06.2013combined data, indels
 includedBA Method Paper combined
 2 without hotspots 21.06.2013combined data indels
 excludedFigure
 S1Supplemental figure
 S1Fig
 S1.pdfTable
 S1List of all fossils used
 in the analysis and the justification for their placement on the tree as
 calibrations.Table
 S2Regions removed from the
 alignment of DNA sequences and rationale for the
 removal.Table
 S3Primers used for
 PCR.Table
 S4Details of settings used
 in BEAST.
DOI: 10.5061/dryad.686rq
title: Data from: Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees (Poecile gambeli)

description: Montane habitats are characterized by predictably rapid heterogeneity
 along elevational gradients and are useful for investigating the
 consequences of environmental heterogeneity for local adaptation and
 population genetic structure. Food-caching mountain chickadees inhabit a
 continuous elevation gradient in the Sierra Nevada, and birds living at
 harsher, high elevations have better spatial memory ability and exhibit
 differences in male song structure and female mate preference compared to
 birds inhabiting milder, low elevations. While high elevation birds breed,
 on average, two weeks later than low elevation birds, the extent of gene
 flow between elevations is unknown. Despite phenotypic variation and
 indirect evidence for local adaptation, population genetic analyses based
 on 18 073 single nucleotide polymorphisms across three transects of high
 and low elevation populations provided no evidence for genetic
 differentiation. Analyses based on individual genotypes revealed no
 patterns of clustering, pairwise estimates of genetic differentiation
 (FST, Nei's D) were very low, and AMOVA revealed no evidence for
 genetic variation structured by transect or by low and high elevation
 sites within transects. In addition, we found no consistent evidence for
 strong parallel allele frequency divergence between low and high elevation
 sites within the three transects. Large elevation-related phenotypic
 variation may be maintained by strong selection despite gene flow and
 future work should focus on the mechanisms underlying such variation.
description: MOCH movt from fall 2014
 to 2015Final_chick_gprobs_names
DOI: 10.5061/dryad.sk652
title: Data from: pLARmEB: integration of least angle regression with empirical Bayes for multilocus genome-wide association studies

description: Multilocus genome-wide association studies (GWAS) have become the
 state-of-the-art procedure to identify quantitative trait nucleotides
 (QTNs) associated with complex traits. However, implementation of
 multilocus model in GWAS is still difficult. In this study, we integrated
 least angle regression with empirical Bayes to perform multilocus GWAS
 under polygenic background control. We used an algorithm of model
 transformation that whitened the covariance matrix of the polygenic matrix
 K and environmental noise. Markers on one chromosome were included
 simultaneously in a multilocus model and least angle regression was used
 to select the most potentially associated single-nucleotide polymorphisms
 (SNPs), whereas the markers on the other chromosomes were used to
 calculate kinship matrix as polygenic background control. The selected
 SNPs in multilocus model were further detected for their association with
 the trait by empirical Bayes and likelihood ratio test. We herein refer to
 this method as the pLARmEB (polygenic-background-control-based least angle
 regression plus empirical Bayes). Results from simulation studies showed
 that pLARmEB was more powerful in QTN detection and more accurate in QTN
 effect estimation, had less false positive rate and required less
 computing time than Bayesian hierarchical generalized linear model,
 efficient mixed model association (EMMA) and least angle regression plus
 empirical Bayes. pLARmEB, multilocus random-SNP-effect mixed linear model
 and fast multilocus random-SNP-effect EMMA methods had almost equal power
 of QTN detection in simulation experiments. However, only pLARmEB
 identified 48 previously reported genes for 7 flowering time-related
 traits in Arabidopsis thaliana.
description: data
DOI: 10.5061/dryad.vd68s
title: Data from: Functional niche partitioning in Therizinosauria provides new insights into the evolution of theropod herbivory

description: Dietary specialization is generally considered to be a crucial factor in
 driving morphological evolution across extant and extinct vertebrates. The
 ability to adapt to a specific diet and to exploit ecological niches is
 thereby influenced by functional morphology and biomechanical properties.
 Differences in functional behaviour and efficiency can therefore allow
 dietary diversification and the coexistence of similarly adapted taxa.
 Therizinosauria, a group of secondarily herbivorous theropod dinosaurs, is
 characterized by a suite of morphological traits thought to be indicative
 of adaptations to an herbivorous diet. Digital reconstruction, theoretical
 modelling and computer simulations of the mandibles of therizinosaur
 dinosaurs provides evidence for functional niche partitioning in
 adaptation to herbivory. Different mandibular morphologies present in
 therizinosaurians were found to correspond to different dietary strategies
 permitting coexistence of taxa. Morphological traits indicative of an
 herbivorous diet, such as a downturned tip of the lower jaw and an
 expanded postdentary region, were identified as having stress mitigating
 effects. The more widely distributed occurrence of these purported
 herbivorous traits across different dinosaur clades suggests that these
 features also could have played an important role in the evolution and
 acquisition of herbivory in other groups.
description: 3D_model_of_Falcarius_utahensis3D_model_of_Jianchangosaurus_yixianensis3D_model_of_Beipiaosaurus_inexpectus3D_model_of_Alxasaurus_elesitaiensis3D_model_of_Erlikosaurus_andrewsi3D_model_of_Segnosaurus_galbinensisSupplementary information
DOI: 10.5061/dryad.18pm5
title: Data from: Variable effects of climate on forest growth in relation to climate extremes, disturbance, and forest dynamics

description: Changes in the frequency, duration, and severity of climate extremes are
 forecast to occur under global climate change. The impacts of climate
 extremes on forest productivity and health remain difficult to predict due
 to potential interactions with disturbance events and forest
 dynamics—changes in forest stand composition, density, size and age
 structure over time. Such interactions may lead to non-linear forest
 growth responses to climate involving thresholds and lag effects.
 Understanding how forest dynamics influence growth responses to climate is
 particularly important given stand structure and composition can be
 modified through management to increase forest resistance and resilience
 to climate change. To inform such adaptive management, we develop a
 hierarchical Bayesian state space model in which climate effects on tree
 growth are allowed to vary over time and in relation to past climate
 extremes, disturbance events, and forest dynamics. The model is an
 important step toward integrating disturbance and forest dynamics into
 predictions of forest growth responses to climate extremes. We apply the
 model to a dendrochronology data set from forest stands of varying
 composition, structure, and development stage in northeastern Minnesota
 that have experienced extreme climate years and forest tent caterpillar
 defoliation events. Mean forest growth was most sensitive to water balance
 variables representing climatic water deficit. Forest growth responses to
 water deficit were partitioned into responses driven by climatic threshold
 exceedances and interactions with insect defoliation. Forest growth was
 both resistant and resilient to climate extremes with the majority of
 forest growth responses occurring after multiple climatic threshold
 exceedances across seasons and years. Interactions between climate and
 disturbance were observed in a subset of years with insect defoliation
 increasing forest growth sensitivity to water availability. Forest growth
 was particularly sensitive to climate extremes during periods of high stem
 density following major regeneration events when average inter-tree
 competition was high. Results suggest the resistance and resilience of
 forest growth to climate extremes can be increased through management
 steps such as thinning to reduce competition during early stages of stand
 development and small-group selection harvests to maintain forest
 structures characteristic of older, mature stands.
description: Northeastern Minnesota
 Tree Growth DataAnnual radial growth
 increment data for 2,291 trees located in 35 stands in and around Superior
 National Forest in northeastern Minnesota. Data includes stand-level
 measurements including water balance variables and years since cohort
 initiation.Itter_et_al_EAP16-0589.R1.tar
DOI: 10.5061/dryad.03n60
title: Data from: Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics

description: Traditional means for scoring the effects of anti-cancer drugs on the
 growth and survival of cell lines is based on relative cell number in
 drug-treated and control samples and is seriously confounded by unequal
 division rates arising from natural biological variation and differences
 in culture conditions. This problem can be overcome by computing drug
 sensitivity on a per-division basis. The normalized growth rate inhibition
 (GR) approach yields per-division metrics for drug potency (GR50) and
 efficacy (GRmax) that are analogous to the more familiar IC50 and Emax
 values. In this work, we report GR-based, proliferation-corrected, drug
 sensitivity metrics for ~4,700 pairs of breast cancer cell lines and
 perturbagens. Such data are broadly useful in understanding the molecular
 basis of therapeutic response and resistance. Here, we use them to
 investigate the relationship between different measures of drug
 sensitivity and conclude that drug potency and efficacy exhibit high
 variation that is only weakly correlated. To facilitate further use of
 these data, computed GR curves and metrics can be browsed interactively at
 http://www.GRbrowser.org/.
description: DS0: Reference files for
 annotating and processing the CTG values for the complete dose-response
 datasetDS0 consists of a
 downloadable zip file containing multiple reference files necessary for
 annotating the raw data file with reagent identifiers and perturbagen
 concentration details; reference file metadata in the form of data column
 lookup tables (LUTs); experimental metadata including a detailed protocol;
 and a ReadMe file.DS0.zipDS0_ReadMe.txtDS1: Relative cell counts and normalized growth rate inhibition values across technical replicatesDS1 consists of a downloadable zip file containing a data file; data file metadata in the form of a data column LUT; experimental metadata including a detailed protocol and reagent metadata tables; and a ReadMe file.DS1.zipDS1_ReadMe.txtDS2: Calculated dose response metricsDS2 consists of a downloadable zip file containing a data file; data file metadata in the form of a data column LUT; experimental metadata including a detailed protocol and reagent metadata tables; and a ReadMe file.DS2.zipDS2_ReadMe.txtDS3: Median, upper quartile, and lower quartile GR metrics per perturbagenDS3 consists of a downloadable zip file containing a data file; data file metadata in the form of a data column LUT; experimental metadata including a detailed protocol and reagent metadata tables; and a ReadMe file.DS3.zipDS3_ReadMe.txtDS4: Median, upper quartile, and lower quartile GR metrics per perturbagen classDS4 consists of a downloadable zip file containing a data file; data file metadata in the form of a data column LUT; experimental metadata including a detailed protocol; and a ReadMe file.DS4.zipDS4_ReadMe.txt
DOI: 10.5281/zenodo.18387955
title: Teaching First-Grade Students Addition Using Web-Based Interactive Digital Simulations

description: The dataset used in this study consists of quantitative and qualitative data collected during the implementation of web-based interactive digital simulations for teaching addition to first-grade students. The quantitative data include students’ pre-test and post-test scores, which were used to measure learning outcomes before and after the instructional intervention. The qualitative data comprise teachers’ and students’ responses collected through questionnaires administered after the use of the web-based interactive digital simulations. All data were collected for research purposes and anonymized to protect participants’ identities.
DOI: 10.5281/zenodo.18387954
title: Teaching First-Grade Students Addition Using Web-Based Interactive Digital Simulations

description: The dataset used in this study consists of quantitative and qualitative data collected during the implementation of web-based interactive digital simulations for teaching addition to first-grade students. The quantitative data include students’ pre-test and post-test scores, which were used to measure learning outcomes before and after the instructional intervention. The qualitative data comprise teachers’ and students’ responses collected through questionnaires administered after the use of the web-based interactive digital simulations. All data were collected for research purposes and anonymized to protect participants’ identities.
DOI: 10.5061/dryad.qq828
title: Data from: Cave Stedocys spitting spiders illuminate the history of the Himalayas and Southeast Asia

description: Stedocys spitting spiders (Araneae: Scytodidae) inhabit subterranean
 environments and have poor dispersal abilities. The Cenozoic
 Indian–Eurasian collision affected the regional biota of this genus, which
 occurs in parts of Indochina. Phylogeographical pattern of Stedocys based
 on multigene DNA sequence datasets reveals how tectonic history drove four
 biological splits. The first split dates to the late Paleocene–Eocene and
 involves the Truong Son Mountain Range and Mekong River. The other splits
 associate with the Eocene–Oligocene transition, including the Tonkin
 (Beibu) Gulf, the Ma River, and the Red River. These events indicate four
 early uplifts of the Himalayas and Tibetan Plateau. Our results cannot
 reject the hypothesis that uplifting of the Himalayas and Tibetan Plateau
 region due to crustal thickening and the lateral extrusion of Indochina
 occurred synchronously during the Paleocene–Oligocene transition in
 reaction to the Indian–Eurasian collision. Species of Stedocys cluster
 into groups I and II. Their evolution involves one dispersal and four
 vicariance events, which formed the following five Indochinese clades:
 Hainan clade (I-1); western Yunnan and central Laos clade (I-2); central
 Vietnam clade (I-3); northern Vietnam and southwestern China clade (I-4);
 and Thailand clade (II-1). The lateral extrusion of Indochina is the
 driver of these events. The drifting of Hainan Island to its present
 location owes to its southeastern movement from continental Vietnam and
 Guangxi, China around the Eocene–Oligocene boundary. This biogeographical
 pattern highlights the significant role geography plays in shaping
 evolutionary history in southeastern Asia. It also illuminates the how the
 timing of geological events drives the distributions of species.
description: The data matrix for
 Bayesian analysisThe data matrix for
 Bayesian analysisThe data matrix for
 maximum likelihood analysisThe data matrix for
 maximum likelihood analysisThe data matrix for
 Bayesian relaxed molecular clock analysisThe data matrix for
 Bayesian relaxed molecular clock analysisCOI sequences for
 network analysisCOI sequences for
 network analysis28S sequences for
 network analysis28S sequences for
 network analysis
DOI: 10.5061/dryad.t0r3p
title: Data from: Nature of the optical band shapes in polymethine dyes and H-aggregates: dozy chaos and excitons. Comparison with dimers, H*- and J-aggregates

description: Results on the theoretical explanation of the shape of optical bands in
 polymethine dyes, their dimers and aggregates are summarized. The
 theoretical dependence of the shape of optical bands for the dye monomers
 in the vinylogous series in line with a change in the solvent polarity is
 considered. A simple physical (analytical) model of the shape of optical
 absorption bands in H-aggregates of polymethine dyes is developed based on
 taking the dozy-chaos dynamics of the transient state and the Frenkel
 exciton effect in the theory of molecular quantum transitions into
 account. As an example, the details of the experimental shape of one of
 the known H-bands are well reproduced by this analytical model under the
 assumption that the main optical chromophore of H-aggregates is a tetramer
 resulting from the two most probable processes of inelastic binary
 collisions in sequence: first, monomers between themselves, and then,
 between the resulting dimers. The obtained results indicate that in
 contrast with the compact structure of J-aggregates (brickwork structure),
 the structure of H-aggregates is not the compact pack-of-cards structure,
 as stated in the literature, but a loose alternate structure. Based on
 this theoretical model, a simple general (analytical) method for treating
 the more complex shapes of optical bands in polymethine dyes in comparison
 with the H-band under consideration is proposed. This method mirrors the
 physical process of molecular aggregates forming in liquid solutions:
 aggregates are generated in the most probable processes of inelastic
 multiple binary collisions between polymethine species generally differing
 in complexity. The results obtained are given against a background of the
 theoretical results on the shape of optical bands in polymethine dyes and
 their aggregates (dimers, H*- and J-aggregates) previously obtained by
 V.V.E.
description: RSOS_Dryad_Egorov_Figure
 1, right panelMathcad program file
 validating the results in figure 1RSOS_Dryad_Egorov_Figure
 5, right panelMathcad program file
 validating the results in figure 5RSOS_Dryad_Egorov_Figure
 6, left panelMathcad program file
 validating the results in figure 6, left panelRSOS_Dryad_Egorov_Figure
 6, right panelMathcad program file
 validating the results in figure 6, right panelRSOS_Dryad_Egorov_Figure
 9, right panelMathcad program file
 validating the results in figure 9RSOS_Dryad_Egorov_Figure
 10Mathcad program file
 validating the results in figure 10RSOS_Dryad_Egorov_Figure
 11Mathcad program file
 validating the results in figure 11RSOS_Dryad_Egorov_Figure
 12, right panelMathcad program file
 validating the results in figure 12
DOI: 10.5061/dryad.80c1f
title: Data from: Failure to reproduce period-dependent song cycles in Drosophila is due to poor automated pulse-detection and low-intensity courtship

description: Stern has criticized a body of work from several groups that have
 independently studied the so-called “Kyriacou and Hall” courtship song
 rhythms of male Drosophila melanogaster, claiming that these ultradian
 ∼60-s cycles in the interpulse interval (IPI) are statistical artifacts
 that are not modulated by mutations at the period (per) locus [Stern DL
 (2014) BMC Biol 12:38]. We have scrutinized Stern’s raw data and observe
 that his automated song pulse-detection method identifies only ∼50% of the
 IPIs found by manual (visual and acoustic) monitoring. This critical error
 is further compounded by Stern’s use of recordings with very little song,
 the large majority of which do not meet the minimal song intensity
 criteria which Kyriacou and Hall used in their studies. Consequently most
 of Stern’s recordings only contribute noise to the analyses. Of the data
 presented by Stern, only perL and a small fraction of wild-type males sing
 vigorously, so we limited our reanalyses to these genotypes. We manually
 reexamined Stern’s raw song recordings and analyzed IPI rhythms using
 several independent time-series analyses. We observe that perL songs show
 significantly longer song periods than wild-type songs, with values for
 both genotypes close to those found in previous studies. These
 per-dependent differences disappear when the song data are randomized. We
 conclude that Stern’s negative findings are artifacts of his inadequate
 pulse-detection methodology coupled to his use of low-intensity courtship
 song records.
description: Read
 me2Description of all the
 datafilesCSmanualmanual analysis CS songsperLmanualmanual analysis of perL songsfirst25CSsongsManual analysis of first 24 CS songs plus cong CS71CS&perLplus5sBinned analysis of CS and perL songs 5s out of phaseTullyCSManual analysis of CSTully songs from Arthur et al 2013interobserverresults on inter-observer analyses of 3 songs