cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c2fqz615c
title: Age-related change of axial length, spherical equivalent, prevalence of myopia and high myopia in school-age children in Shanghai: 2014 to 2018

description: Objective  To investigate the age-related
 changefor axial length (AL), Spherical equivalent
 (SE), prevalence of myopia and high myopiain children at 7 to 18
 year-olds in Shanghai in 2014 and 2018, respectively, to compare these
 parameters between 2014 and 2018, and to evaluated the potential factors
 associated with AL. Design An observational study.
 Setting Jinshan Hospital of Fudan University in Shanghai.
 Methods One primary school, one junior high school, and one
 senior high school were randomly selected in 2014 and 2018, respectively.
 AL, SE, prevalence of myopia and high myopia, height and weight were
 measured. A questionnaire regarding the lifestyles was completed.
 Results Mean AL were shorter in 2018 than in 2014 (P = 0.003),
 whereas mean SE was greater in 2018 than in 2014 (P &lt; 0.001). The
 prevalence of myopia and high myopia was lower in 2018 than in 2014 (P
 &lt; 0.001 and P = 0.013, respectively). Mean AL
 increased with age from 7 year-oldsto18 year-oldsin 2014and 2018
 (both P &lt; 0.001), respectively. Mean SE decreased with age in 2014
 and 2018 (both P &lt; 0.001), respectively. The prevalence of myopia
 and high myopia increased with age in 2014 and 2018 (all P &lt;
 0.001), respectively. Multivariate regression analysis revealed that
 longer AL was mainly associated male gender and body height.
 Conclusion This study shows normative growth values for AL and SE
 in Shanghai children at the age of 7 to 18 year-olds, as well as the
 age-specific prevalence of myopia and high myopia.
DOI: 10.5061/dryad.g1jwstqnn
title: Past and future decline of tropical pelagic biodiversity

description: A major research question concerning global pelagic biodiversity remains
 unanswered: when did the apparent tropical biodiversity depression (i.e.,
 bimodality of latitudinal diversity gradient [LDG]) begin? The bimodal LDG
 may be a consequence of recent ocean warming or of deep-time evolutionary
 speciation and extinction processes. Using rich time-slice datasets of
 planktonic foraminifers, we show here that a unimodal (or only weakly
 bimodal) diversity gradient, with a plateau in the tropics, occurred
 during the last ice age and has since then developed into a bimodal
 gradient through species distribution shifts driven by postglacial ocean
 warming. The bimodal LDG likely emerged before the Anthropocene (here
 defined as ∼1950) and perhaps ∼15,000 y ago, indicating a strong
 environmental control of tropical diversity even before the start of
 anthropogenic warming. However, our model projections suggest future
 anthropogenic warming further diminishes tropical pelagic diversity to a
 level not seen in millions of years.
description: Raw data for Figs 1–4.
DOI: 10.15468/dl.ydsjx8
title: Occurrence Download

description: A dataset containing 190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Archidendron vaillantii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 190 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002367-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0rxwdbrwt
title: Rapid adaptive evolution of the diapause program during range expansion of an invasive mosquito

description: In temperate climates, the recurring seasonal exigencies of winter
 represent a fundamental physiological challenge for a wide range of
 organisms. In response, many temperate insects enter diapause, an
 alternative developmental program, including developmental arrest, that
 allows organisms to synchronize their life cycle with seasonal
 environmental variation. Geographic variation in diapause phenology
 contributing to local climatic adaptation is well documented. However, few
 studies have examined how the rapid evolution of a suite of traits
 expressed across the diapause program may contribute to climatic
 adaptation on a contemporary timescale. Here, we investigate the evolution
 of the diapause program over the past 35 years by leveraging a “natural
 experiment” presented by the recent invasion of the Asian tiger mosquito,
 Aedes albopictus, across the eastern United States. We sampled populations
 from two distinct climatic regions separated by six degrees of latitude
 (~700 km). Using common-garden experiments, we identified regional genetic
 divergence in diapause-associated cold tolerance, diapause duration, and
 post-diapause starvation tolerance. We also found regional divergence in
 non-diapause thermal performance. In contrast, we observed minimal
 regional divergence in non-diapause larval growth traits and at neutral
 molecular marker loci. Our results demonstrate rapid evolution of the
 diapause program and imply strong selection caused by differences in
 winter conditions.
description: Files included in this repository: 
 Simulated_winter_cold_tolerance.csv -- Replicate-level hatch
 data for samples in simulated winter conditions (data for Figure
 2) Rapid_cold_shock_tolerance.csv -- Replicate-level
 data for rapid cold shock tolerance (data for Figure 3)
 Diapause_incidence_and_duration.csv -- Replicate-level
 measurements of diapause incidence from 14 - 175 dpov (data for Figure
 4A) Larval_starvation_tolerance.csv -- Individual
 larva-level data for post-diapause starvation tolerance experiment (data
 for Figure 4B) Adult_chill_coma_recovery.csv --
 Replicate-level adult chill coma recovery time measurements (data for
 Figure 5) Pairwise_Fst_by_distance.csv -- Population
 vs population Fst values and geographic distances (data for Figure
 6) Larval_growth_data.csv -- Individual-level data
 for age of pupation and mass at pupation
 mosquitoes_bam_output.tar.gz -- BAM output for all 365
 individual mosquito microhaplotype samples sequenced in this
 study.
 mosquito_gtseq1_2_q30mean10dp10maf001_noIndels.recode.vcf --
 Processed variant call file for microhaplotypes
 mosquito_targets_prelim192.fasta -- 192 sequences targeted for
 microhaplotype sequencing
 Haplotypes_by_individual.csv -- Haplotypes assigned by locus for
 each individual sample Haplotype_id_sequences.csv --
 Key for haplotype IDs in the Haplotypes_by_individual.csv file
DOI: 10.5061/dryad.g79cnp5mn
title: Data from: Vitis vinifera leaf images

description: This dataset captures the leaf shape of over 9,500 leaves from wine and
 table grape varieties (Vitis vinifera) in over 4,900 photographs sampled
 from the Wolfskill USDA National Clonal Germplasm Repository in
 Winters, California. This dataset is useful for morphometric, allometric,
 ampelographic, and genetic studies into the shape and size of
 grapevine leaves.
description: Photographs of leaves were collected from grapevines
 (<em>Vitis</em> spp.) maintained by the Wolfskill USDA
 National Clonal Germplasm Repository in Winters, California. More than
 9,500 leaves were collected from more than 1,200 different domesticated
 grape (<em>Vitis vinifera</em>) varieties from May 28 through
 June 1, 2011. Most varieties were represented by two clonal vines, from
 which four leaves were sampled from each (such that eight leaves were
 sampled from most varieties). If possible, consecutive leaves of similar
 developmental stage were sampled from the midpoints of two shoots on each
 vine. All leaves were fully expanded but not so old that they had begun to
 senesce. Each day, vines were randomly sampled from the overall
 population. Samples were collected before noon, placed into Ziploc bags,
 and placed into a cooler. Leaves remained in the cooler in a 4°C cold room
 for a maximum of 48 h before being photographed. Leaves were arranged
 under nonreflective glass over a light box (FB-WLT-1417; Fisher
 Scientific) so that veins were clearly visible. Olympus SP-500 UZ cameras
 were mounted on copy stands (Adorama; 36-inch Deluxe Copy Stand) and
 controlled remotely by computer using Cam2Com software (Sabsik).
description: Over 4,900 raw photographs, with the file name indicating the
 vineyard position that can be used to identify the genotype, are available
 (divided into five folders, I - V). The variety information for the leaves
 in each image can be found in the key ("key.csv") that is
 included. File names include block (L or K), row (the next two digits),
 vine (the next two digits), and a letter if multiple images were needed to
 accommodate the number of leaves from that particular vine. The file name
 information should be used to determine the variety, origin, and parentage
 information for each leaf found in the key.
DOI: 10.15468/dl.3zxaae
title: Occurrence Download

description: A dataset containing 1833 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Greece, Albania)",
 "Month is one of (April, May)",
 "OccurrenceStatus is Present",
 "TaxonKey is Lacertidae",
 "Year 2024-2025"
 ]
}

 The dataset includes 1833 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002368-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hhmgqnkdj
title: Data from: QTG-Finder2: a generalized machine-learning algorithm for prioritizing QTL causal genes in plants

description: Linkage mapping has been widely used to identify quantitative trait loci
 (QTL) in many plants and usually requires a time-consuming and
 labor-intensive fine mapping process to find the causal gene underlying
 the QTL. Previously, we described QTG-Finder, a machine-learning algorithm
 to rationally prioritize candidate causal genes in QTLs. While it showed
 good performance, QTG-Finder could only be used in Arabidopsis and rice
 because of the limited number of known causal genes in other species. Here
 we tested the feasibility of enabling QTG-Finder to work on species that
 have few or no known causal genes by using orthologs of known causal genes
 as training set. The model trained with orthologs could recall about 64%
 of Arabidopsis and 83% of rice causal genes when the top 20% ranked genes
 were considered, which is similar to the performance of models trained
 with known causal genes. The average precision was 0.027 for Arabidopsis
 and 0.029 for rice. We further extended the algorithm to include
 polymorphisms in conserved non-coding sequences and gene presence/absence
 variation as additional features. Using this algorithm, QTG-Finder2, we
 trained and cross-validated Sorghum bicolor and Setaria viridis models.
 The S. bicolor model was validated by causal genes curated from the
 literature and could recall 70% of causal genes when the top 20% ranked
 genes were considered. In addition, we applied the S. viridis model and
 public transcriptome data to prioritize a plant height QTL and identified
 13 candidate genes. QTL-Finder2 can accelerate the discovery of causal
 genes in any plant species and facilitate agricultural trait improvement.
DOI: 10.5061/dryad.vt4b8gtpd
title: Data from: Mechanism for analogous illusory motion perception in flies and humans.

description: Visual motion detection is one of the most important computations
 performed by visual circuits. Yet, we perceive vivid illusory motion in
 stationary, periodic luminance gradients that contain no true motion. This
 illusion is shared by diverse vertebrate species, but theories proposed to
 explain this illusion have remained difficult to test. Here, we
 demonstrate that in the fruit fly Drosophila, the illusory motion percept
 is generated by unbalanced contributions of direction-selective neurons’
 responses to stationary edges. First, we found that flies, like humans,
 perceive sustained motion in the stationary gradients. The percept was
 abolished when the elementary motion detector neurons, T4 and T5, were
 silenced. In vivo calcium imaging revealed that T4 and T5 neurons encode
 the location and polarity of stationary edges. Furthermore, our proposed
 mechanistic model allowed us to predictably manipulate both the magnitude
 and direction of the fly’s illusory percept by selectively silencing
 either T4 or T5 neurons. Interestingly, human brains possess the same
 mechanistic ingredients that drive our model in flies. When we adapted
 human observers to moving light edges or dark edges, we could manipulate
 the magnitude and direction of their percepts as well, suggesting that
 mechanisms similar to the fly’s may also underlie this illusion in humans.
 By taking a comparative approach that exploits Drosophila neurogenetics,
 our results provide a causal, mechanistic account for a long-known visual
 illusion. These results argue that this illusion arises from architectures
 for motion detection that are shared across phyla.
description: Data are provided as MATLAB version 7.3 MAT (.mat) files, created
 using MATLAB 9.7. The name of each data file matches the number of the
 figure in Agrochao, Tanaka, et al (2020) <em>Mechanism for analogous
 illusory motion perception in flies and humans</em>.
 The figures in Agrochao, Tanaka, et al (2020) <em>Mechanism
 for analogous illusory motion perception in flies and humans</em>
 can be reproduced using the dataset provided here and the code
 in https://github.com/ClarkLabCode/IllusionPaperCode.
DOI: 10.5061/dryad.dfn2z34xq
title: Supplementary material to: Segmental series and size: clade-wide investigation of molar proportions reveals a major evolutionary allometry in the dentition of placental mammals

description: Iterative segments such as teeth or limbs are a widespread characteristic
 of living organisms. While their proportions may be governed by similar
 developmental rules in vertebrates, there is no emerging pattern as
 regards their relation to size. Placental mammals span eight orders of
 magnitude in body size and show a wide spectrum of dietary habits
 associated with size and reflected in their dentitions, especially molars.
 Although variation in size constitutes an important determinant for
 variation in biological traits, few major allometric trends have been
 documented on placental molars so far. Molar proportions have been
 intensively explored in placentals in relation to developmental models,
 but often at a small phylogenetic scale. Here, we analyzed the diversity
 of upper molar proportions in relation to absolute size in a large sample
 of placental species (n = 286) encompassing most of the group’s dental
 diversity. Our phylogenetically informed analyses revealed a twofold
 pattern of evolutionary integration among upper molars: while molars
 covary in size with each other, their proportions covary with the absolute
 size of the entire molar field. With increasing absolute size, posterior
 molars increase in size relative to anterior ones, meaning that
 large-sized species have relatively large rear molars while the opposite
 is true for small-sized species. The directionality of proportional
 increase in the molar row exhibits a previously unsuspected allometric
 patterning among placentals, showing how large-scale variations in size
 may have influenced variation in dental morphology. This finding provides
 new evidence that processes regulating the size of individual molars are
 integrated with overall patterns of growth and calls for further testing
 of allometric variation in the dentition and in other segmental series of
 the vertebrate body.
DOI: 10.15468/dl.xdjt5s
title: Occurrence Download

description: A dataset containing 1998 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-100.99114 20.50417,-100.95234 20.50417,-100.95234 20.52096,-100.99114 20.52096,-100.99114 20.50417))",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 1998 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002369-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cz8w9gj0w
title: Data from: Measuring researchers’ potential scholarly impact with structural variations: four types of researchers in information science (1979–2018)

description: We propose a method to measure the potential scholarly impact of
 researchers based on network structural variations they introduced to the
 underlying author co-citation network of their field. We applied the
 method to the information science field based on 91,978 papers published
 between 1979 and 2018 from the Web of Science. We divided the entire
 period into eight consecutive intervals and measured structural variation
 change rates (DM) of individual authors in corresponding author
 co-citation networks. Four types of researchers are identified in terms of
 temporal dynamics of their potential scholarly impact—1) Increasing, 2)
 Decreasing, 3) Sustained, and 4) Transient. The study contributes to the
 understanding of how researchers’ scholarly impact might evolve in a broad
 context of the corresponding research community. Specifically, this study
 illustrated a crucial role played by structural variation metrics in
 measuring and explaining the potential scholarly impact of a researcher.
 This method based on the structural variation analysis offers a
 theoretical framework and a practical platform to analyze the potential
 scholarly impact of researchers and their specific contributions.
DOI: 10.5061/dryad.8gtht76kx
title: Effects of freshwater salinization and biotic stressors on amphibian morphology

description: Organisms are commonly exposed to numerous stressors that induce
 behavioral, physiological, or morphological changes in some combination.
 In northern temperate latitudes, de-icing agents are a major stressor to
 species in freshwater ecosystems (primarily sodium chloride; NaCl).
 Species-specific responses to road salt toxicity range from lethal to
 sublethal effects, but it remains unclear how these effects interact with
 biotic stressors. Morphology can be quite sensitive to environmental
 changes, yet we know little about how it is affected by road salt
 exposure. We exposed wood frog tadpoles (Rana sylvatica) to two road salt
 formulations (NaCl and a mixture of NaCl, MgCl2, and KCl), each at three
 concentrations (200, 600, and 1000 mg Cl-/L), crossed with three biotic
 stressor levels (predator cue, competition, and a no-stressor control). We
 then measured the impacts on relative morphology (snout-vent length, body
 width, forelimb length, forelimb width, hindlimb length, hindlimb width)
 of the emerging metamorphs. Salt concentration and biotic stressors both
 impacted relative morphology, but their effects did not interact. Exposure
 to road salts increased relative snout-vent length (SVL) and body width.
 In contrast, competition induced relatively shorter SVL and forelimb
 length while predator cues induced relatively longer hindlimbs and
 narrower forelimbs. This is the first discovery that road salts can induce
 changes in amphibian morphology and that these effects are independent of
 changes induced by biotic stressors. Future research should examine the
 effects on overwintering success and future fitness in amphibians as well
 as the impacts of salt on the morphology on other aquatic taxa that are
 being exposed to freshwater salinization.
DOI: 10.5061/dryad.qz612jmbn
title: Data from: Combining US and Canadian forest inventories to assess habitat suitability and migration potential of 25 tree species under climate change

description: Aim: To evaluate current and future dynamics of 25 tree species spanning
 USA and Canada. Location: USA and Canada Methods: We combine, for the
 first time, the species compositions from relative importance derived from
 the USA’s Forest Inventory Analysis (FIA) with gridded estimates based on
 Canada's National Forest Inventory (NFI-kNN) ) based photo plot data
 to evaluate future habitats and colonization potentials for 25 tree
 species. Using 21 climatic variables under RCP 4.5 and RCP 8.5, we model
 climatic habitat suitability (HQ) within a consensus based multi-model
 ensemble regression approach. A migration model is used to assess
 colonization likelihoods (CL) for ~100 years and combined with HQ to
 evaluate the various combinations of HQ+CL outcomes for the 25 species.
 Results: At a continental scale, many species in the conterminous USA lose
 suitable climatic habitat (especially under RCP 8.5) while Canada and
 USA’s Alaska gain climate habitat. For most species, even under optimistic
 migration rates, only a small portion of overall future suitable habitat
 is projected to be naturally colonized in ~ 100 years, although
 considerable variation exists among species. Main conclusions: For the
 species examined here, habitat losses were primarily experienced along
 southern range limits, while habitat gains were associated with northern
 range limits (especially under RCP 8.5). However, for many species,
 southern range limits are projected to remain relatively intact, albeit
 with reduced habitat quality. Our models predict that only a small portion
 of the climatic habitat generated by climate change will be colonized
 naturally by the end of the current century - even with optimistic tree
 migration rates. However, considerable variation among species points to
 the need for significant management efforts, including assisted migration,
 for economic or ecological reasons. Our work highlights the need to employ
 range-wide data, evaluate colonization potentials, and enhance
 cross-border collaborations.
description: This has been described in the parent manuscript.
description: This dataset provides the complete set of maps of habitat
 suitability and colonization potential described in the manuscript for the
 25 tree species that we have used. This is in the form of html files that
 have been organized to provide links to the images via the main file:
 index.html. The end user has to download the zip file,
 extract contents to a folder, and open index.html (in the "Data"
 folder) to view the maps. A brief description of the filenames is given in
 the file: _fileindex_DDI-2020-0041.html.