cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c866t1g49
title: Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis

description: Knowledge of how animal species use food resources available in the
 environment increases our understanding of ecological processes. However,
 obtaining this information using traditional methods is a hard task for
 species feeding on a large variety of food items in highly diverse
 environments. We amplified the DNA of plants for 306 scat and 40 soil
 samples, and applied an eDNA metabarcoding approach to investigate food
 preferences, degree of diet specialization and diet overlap of seven
 herbivore rodent species of the Ctenomys genus distributed in southern and
 midwestern Brazil. The metabarcoding approach revealed that species
 consume more than 60% of the plant families recovered in soil samples,
 indicating generalist feeding habits of ctenomyids. The Poaceae family was
 the most common food resource retrieved in scats of all species as well in
 soil samples. Niche overlap analysis indicated high overlap in the plant
 families and Molecular Operational Taxonomic Units consumed, mainly among
 the southern species. Interspecific difference in diet composition was
 influenced, among other factors, by the availability of resources in the
 environment. In addition, our results provide support for the hypothesis
 that the allopatric distributions of ctenomyids allow them to exploit the
 same range of resources when available, possibly because of the absence of
 interspecific competition.
description: The GMW_consensus_sequences_fastq.zip files contain unfiltered
 sequencing data (i.e. consensus sequences not assigned to the original
 samples), from fecal, soil, and positive and negative control
 samples. Each .fastq file correspond to a different sequencing
 library. Ngsfilter.txt files contain information to
 distinguish between sequences from different PCR products pooled in the
 same sequencing library.
DOI: 10.5066/p13cgu4f
title: Public-Supply Water Use in Kansas, 2016

description: This U.S. Geological Survey (USGS) Data Release provides derivative statistics of water used by Kansas public-supply systems in 2016. Gallons per capita per day (gpcd) was calculated using self-reported information in the “Part B: Monthly Water Use Summary” and “Part C: Population, Service Connections, and Water Rates” sections of the Kansas Department of Agriculture, Division of Water Resources' (DWR) annual municipal water-use report (see appendixes at http://dx.doi.org/10.3133/ds964 for an example of a municipal water-use report form). Percent unaccounted for water was calculated using self-reported information in “Part B: Monthly Water Use Summary” of the DWR’s municipal water-use report. The published statistics from the previous 4 years (2012–2015) are also shown with the 2016 statistics and are used to calculate a 5-year average. Derivative statistics of 2012, 2013, 2014, 2015, 2016, and 5-year averages for gpcd are also provided by the Kansas Water Authority's 14 regional planning areas, and the DWR regions used for analysis of per capita water use in Kansas. An overall Kansas average (yearly and 5-year average) was also calculated. Kansas statewide average per capita municipal water use in 2016 was 102 gpcd.
DOI: 10.5061/dryad.stqjq2c1d
title: Data from: Phosphorus limitation does not drive loss of bony lateral plates in freshwater stickleback (Gasterosteus aculeatus)

description: Connecting the selective forces that drive the evolution of phenotypes to
 their underlying genotypes is key to understanding adaptation, but such
 connections are rarely tested experimentally. Threespine stickleback
 (Gasterosteus aculeatus) are a powerful model for such tests because
 genotypes that underlie putatively adaptive traits have been identified.
 For example, a regulatory mutation in the Ectodysplasin (Eda) gene causes
 a reduction in the number of bony armor plates, which occurs rapidly and
 repeatedly when marine sticklebacks invade freshwater. However, the source
 of selection on plate loss in freshwater is unknown. Here, we tested
 whether dietary reduction of phosphorus can account for selection on plate
 loss due to a growth advantage of low-plated fish in freshwater. We
 crossed marine fish heterozygous for the 16 kilobase freshwater Eda
 haplotype and compared the growth of offspring with different genotypes
 under contrasting levels of dietary phosphorus in both saltwater and
 freshwater. Eda genotype was not associated with growth differences in any
 treatment, or with mechanisms that could mitigate the impacts of
 phosphorus limitation, like differential phosphorus deposition, phosphorus
 excretion, or intestine length. This study highlights the importance of
 experimentally testing the putative selective forces acting on phenotypes
 and their underlying genotypes in the wild.
description: These datasets were used to assess whether a reduction in dietary
 phosphorus causes a growth trade-off with bony lateral plate development
 (via the <em>Ectodysplasin</em> locus) in marine threespine
 stickleback reared in freshwater conditions.  Wild
 marine stickleback fish carrying freshwater alleles at
 <em>Ectodysplasin</em> (<em>Eda</em>) were used to
 make F2 stickleback families which were each split equally among four
 experimental conditions: high-phosphorus diet + saltwater, high-phosphorus
 diet + freshwater, low-phosphorus diet + saltwater, low-phosphorus diet +
 freshwater. F2 fish were grown to a pre-bony plate
 developmental stage (Timepoint 1), and two different during-bony plate
 developmental stages (Timepoints 2 & 3).  F2
 fish were genotyped at <em>Eda, </em>sex was determined using
 molecular markers, and growth was assessed using standard length and
 weight. For fish collected at Timepoint 3, additional measurements were
 taken: count of bony lateral plates, % phosphorus content of bone,
 intestine length/weight, and phosphorus excretion rate. 
 Please see accompanying manuscript and README.txt file for
 further information on data collection and sample information. 
description: See README.txt file for explanations of variables and data
 processing.
DOI: 10.5061/dryad.f7m0cfxsm
title: Data and code for "Biomechanical properties of a buzz-pollinated flower"

description: Approximately half of all bee species use vibrations to remove pollen from
 plants with diverse floral morphologies. In many buzz-pollinated flowers,
 these mechanical vibrations generated by bees are transmitted through
 floral tissues, principally pollen-containing anthers, causing pollen to
 be ejected from small openings (pores or slits) at the tip of the stamen.
 Despite the importance of substrate-borne vibrations for both bees and
 plants, few studies to date have characterised the transmission properties
 of floral vibrations. In this study, we use contactless laser vibrometry
 to evaluate the transmission of vibrations in the corolla and anthers of
 buzz- pollinated flowers of Solanum rostratum, and measured vibrations in
 three spatial axes. We found that floral vibrations conserve their
 dominant frequency (300Hz) as they are transmitted throughout the flower.
 We also found that vibrations are generally amplified (up to &gt;400%)
 as they travel from the receptacle at the base of the flower to other
 floral structures, and that anthers vibrate with a higher amplitude
 velocity than petals. Together, these results suggest that vibrations
 travel differently through floral structures and across different spatial
 axes. As pollen release is a function of vibration amplitude, we
 conjecture that bees might benefit from applying vibrations in the axes
 associated with higher vibration amplification.
description: This dataset contains a series of text (.txt) files corresponding
 to the vibration data recorded with laser Doppler vibrometry from flowers
 vibrated by a shaker. The text files contains two columns, one referring
 to the time in seconds, other referring to the displacement of the floral
 structure measured. Additionally the R code used to analyse the data is
 provided as a pdf file and a table with the legends for the variable names
 used during the analysis is provided as a .csv file. All the files are in
 a single folder and a .zip file reader software might me be needed to open
 the folder and extract the files.
DOI: 10.5061/dryad.mpg4f4qwj
title: Data from: Pantropical geography of lightning-caused disturbance and its implications for tropical forests

description: Lightning is a major agent of disturbance, but its ecological effects in
 the tropics are unquantified.  Here, we used ground and satellite
 sensors to quantify the geography of lightning strikes in terrestrial
 tropical ecosystems, and to evaluate whether spatial variation in
 lightning frequency is associated with variation in tropical forest
 structure and dynamics.  Between 2013 and 2018, tropical
 terrestrial ecosystems received an average of 100.4 million lightning
 strikes per year, and the frequency of strikes was spatially
 autocorrelated at local-to-continental scales.  Lightning strikes
 were more frequent in forests, savannas, and urban areas than in
 grasslands, shrublands, and croplands.  Higher lightning
 frequency was positively associated with woody biomass turnover and
 negatively associated with aboveground biomass and the density of large
 trees (trees ha-1) in forests across Africa, Asia, and the
 Americas.  Extrapolating from the only tropical forest study that
 comprehensively assessed tree damage and mortality from lightning strikes,
 we estimate that lightning directly damages ca. 832 million trees in
 tropical forests annually, of which ca. 194 million die.  The
 similarly high lightning frequency in tropical savannas suggests that
 lightning also influences savanna tree mortality rates and ecosystem
 processes.  These patterns indicate that lightning-caused
 disturbance plays a major and largely unappreciated role in pantropical
 ecosystem dynamics and global carbon cycling.
DOI: 10.5061/dryad.q2bvq83gn
title: Endothelial and leukocyte-derived microvesicles and cardiovascular risk after stroke: PROSCIS-B

description: Objective: To determine the role of circulating endothelial microvesicles
 (EMV) and microvesicles (MV) of other origins on long-term cardiovascular
 outcomes after stroke, we measured them in a cohort of first-ever stroke
 patients and observed them for three years. Methods: In the PROSpective
 Cohort with Incident Stroke Berlin (PROSCIS-B), patients with first-ever
 ischemic stroke were followed for three years. The primary combined
 endpoint consisted of recurrent stroke, myocardial infarction, and
 all-cause mortality. Levels of EMV, leukocyte-derived MV (LMV), monocytic
 MV (MMV), and platelet-derived MV (PMV) were measured in citrate blood
 using flow cytometry. Kaplan-Meier curves and Cox proportional hazards
 models were used to estimate the effect of MV levels on the combined
 endpoint after adjustment confounding. Results: 571 patients were
 recruited (median age 69y; 39% female; median NIHSS 2, interquartile range
 1-4). During the follow-up, 95 endpoints occurred. Patients with levels of
 EMV [adjusted hazard ratio (HR)=2.5, 95% confidence interval (CI) 1.2-4.9]
 or LMV (HR=3.1, 95%CI 1.4-6.8) in the highest quartile were more likely to
 experience an event than participants with lower levels using the lowest
 quartile as reference category. The association was less pronounced for
 PMV (HR=1.7, 95%CI 0.9-3.2) and absent for MMV (HR=1.1, 95%CI 0.6-1.8).
 Conclusion: High levels of EMV and LMV after ischemic stroke were
 associated with worse cardiovascular outcome within three years. These
 results reinforce that endothelial dysfunction and vascular inflammation
 affect the long-term prognosis after stroke. EMV and LMV might play a
 potential role in risk prediction for stroke patients.
description: Study Registration
 https://clinicaltrials.gov/ct2/show/NCT01363856 UID: NCT01363856
DOI: 10.5061/dryad.x69p8czfs
title: Neurology paper "Sequence of Alzheimer disease biomarker changes in cognitively normal adults: A cross-sectional study" Table e-1

description: Our Neurology 2020 paper titled "Sequence of Alzheimer disease
 biomarker changes in cognitively normal adults: A cross-sectional
 study" explores the cascades
 of  changes of several well-known Alzheimer
 disease (AD) markers including cerebrow spinal fluid
 (CSF), imaging (PET-PIB and MRI) and cognitive markers in cognitively
 normal participants. The baseline marker data of participants
 is modeled as a piecewise linear function of baseline age
 allowing one change point, without and with adjustment for
 covariates.  The change point of a marker
 incicates the acceleration time of point after
 which a greater percentage of the participants present
 preclinical AD compared to before the change point. Cosnistent with
 previous research, the study confirmed that Abeta42 showed the earliest
 change-point around 50 years old and cognition had a late change
 point around 62. The study further found Tau, pTau and MRI
 hippalcampal volume had their change point closer to
 cognition. We identified change points in all participants, as
 well as by stratification of APOE4 status. The data here
 displays the Supplemental table Table e-1 accompanying the paper
 where the change point results by stratification of APOE4 status
 are presented.    
description: The baseline marker data of participants is modeled as a
 piecewise linear function of baseline age allowing one change point. We
 identified the change points in the AD markers among all the participants,
 and then by stratification of APOE4 status. The change points in all
 participants are consistent with those identified in the APOE4 negative
 subset.
description: The data here presents the Supplemental table Table e-1
 accompanying the paper where we identified change points by stratification
 of APOE4 status.
DOI: 10.5061/dryad.ngf1vhhrd
title: Pinyon jay (Gymnorhinus cyanocephalus) nest site selection in central New Mexico: Habitat Data to be used with AICc

description: Pinyon Jays (Gymnorhinus cyanocephalus) are experiencing range wide
 population declines primarily in response to habitat degradation. Studies
 examining Pinyon Jay nest site selection in pinyon-juniper woodlands would
 be helpful in determining potential habitat management prescriptions.
 Therefore, we conducted a nest site selection study in Pinyon Jay breeding
 habitat in central New Mexico. We compared size and foliage
 characteristics of pinyon and juniper trees in 42 17.5-m radius plots
 around Pinyon Jay nests to 41 same-sized vegetation plots in random
 locations using binomial generalized linear models. The strongest model
 indicated that Pinyon Jays preferred nesting in areas with fewer dead
 juniper trees within pinyon-juniper habitats. Furthermore, Pinyon Jays
 built nests in pinyon and juniper trees with greater height (p &lt;
 0.001) and nests were built below the average tree height in the plot (p =
 0.001). Results suggest selective cutting of dead juniper and retention of
 tall, live pinyon or juniper trees may be used in pinyon-juniper woodlands
 to improve Pinyon Jay nesting habitat in the western United States.
description: This data was collected by measuring the length, width, and
 height of all vegetation over 1m tall in a 17.5m radius around pinyon jay
 nests as well as a similar number of randomized locations within
 pinyon-juniper habitat. Anyone looking to process these data should
 standardize it, then processes it using AICc in R.
description: Anyone looking to process these data should standardize it, then
 processes it using AICc in R.
DOI: 10.5061/dryad.np5hqbzqh
title: Data from: Ancient drainage networks mediated a large-scale genetic introgression in the East Asian freshwater snails

description: Biogeography and genetic variation of freshwater organisms are influenced
 not only by current freshwater connections but also by past drainage
 networks. The Seto Inland Sea is a shallow enclosed sea in Japan, but
 geological evidence showed that a large freshwater drainage had
 intermittently appeared in this area between the late Pliocene and
 Pleistocene. Here we demonstrated that this paleodrainage greatly affected
 the genetic variation of the East Asian freshwater snails, Semisulcospira
 spp. We found that the mtDNA haplotypes originated in the Lake Biwa
 endemic Semisulcospira species at the upstream side of the paleodrainage
 were frequently observed in the riverine Semisulcospira species at its
 downstream side. The genome-wide DNA and morphological analyses
 consistently showed that there was no clear evidence of nuclear
 introgression between the Lake Biwa endemics and riverine species. These
 results suggest that the large paleodrainage had facilitated mitochondrial
 introgression and had broadly spread the introgressed mtDNA haplotypes to
 its downstream region around the Seto Inland Sea. Our study highlights the
 role of paleodrainages in shaping the genetic variation of freshwater
 organisms.
description: There are two phylogenies: One is based on the mtDNA sequences,
 and the other is based on the genome DNA sequences. The mtDNA phylogeny
 was constructed by Maximum likelihood algorithms (with HKY + G + I model)
 using MEGA 7.0.18. The genome phylogeny was constructed by Maximum
 likelihood algorithms (with GTR + G model) using RAxML 8.0.20.
description: The phylogenetic tree and sequence alignment were integrated into
 a single nexus file using Mesquite 3.61 for each analysis (mtDNA and
 genome DNA). It may be necessary to use Mesquite to open the file
 correctly. Please check Appendix 1 and 2 in the paper for the sample IDs
 and their geographical origins.
DOI: 10.5061/dryad.g4f4qrfn4
title: Data from: Estimating polymorphic growth curve sets with non-chronological data

description: 1. When we collect the growth curves of many individuals, orderly
 variation in the curves is often observed rather than a completely random
 mixture of various curves. Small individuals may exhibit similar growth
 curves, but the curves differ from those of large individuals, whereby the
 curves gradually vary from small to large individuals. It has been
 recognized that after standardization with the asymptotes, if all the
 growth curves are the same (anamorphic growth curve set), the growth curve
 sets can be estimated using non-chronological data; otherwise, i.e., if
 the growth curves are not identical after standardization with the
 asymptotes (polymorphic growth curve set), this estimation is not
 feasible. However, because a given set of growth curves determines the
 variation in the observed data, it may be possible to estimate polymorphic
 growth curve sets using non-chronological data. 2. In this study, we
 developed an estimation method by deriving the likelihood function for
 polymorphic growth curve sets. The method involves simple maximum
 likelihood estimation. The weighted nonlinear regression and least squares
 method after the log-transform of the anamorphic growth curve sets were
 included as special cases. 3. The growth curve sets of the height of
 cypress (Chamaecyparis obtusa) and larch (Larix kaempferi) trees were
 estimated. With the model selection process using the AIC and likelihood
 ratio test, the growth curve set for cypress was found to be polymorphic,
 whereas that for larch was found to be anamorphic. Improved fitting using
 the polymorphic model for cypress is due to resolving underdispersion
 (less dispersion in real data than model prediction). 4. The likelihood
 function for model estimation depends not only on the distribution type of
 asymptotes, but the definition of the growth curve set as well.
 Consideration of these factors may be necessary, even if environmental
 explanatory variables and random effects are introduced.
description: The program is constructed using the "inheritance" of
 Java language. Please read "readme.txt" in the file
 set.
description: Java code set for demonstrating the estimation of polymorphic
 growth curve sets. This code set is executable on
 Apache NetBeans (https://netbeans.apache.org/) with JDK version 8 or later
 (available at https://adoptopenjdk.net/). This codeset uses jar files
 distributed by Apache Commons Math Library
 (https://commons.apache.org/proper/commons-math/). The jar file will be
 retrieved at the first execution by Maven automatically.
DOI: 10.5061/dryad.547d7wm5r
title: Verifiability of genus-level classification under quantification and parsimony theories: a case study of follicucullid radiolarians

description: The classical taxonomy of fossil invertebrates is based on subjective
 judgments of morphology, which can cause confusion since there are no
 codified standards for the classification of genera. Here, we explore the
 validity of the genus taxonomy of 75 species and morphospecies of the
 Follicucullidae, a Late Paleozoic family of radiolarians, using a new
 method, Hayashi’s quantification theory II (HQT-II), a general
 multivariate statistical method for categorical datasets relevant to
 discriminant analysis. We identify a scheme of ten genera rather than the
 currently accepted three genera (Follicucullus, Ishigaconus and
 Parafollicucullus). As HQT-II cannot incorporate stratigraphic data, a
 phylogenetic tree of Follicucullidae was reconstructed for 38 species
 using maximum parsimony. Six lineages emerged, roughly in concordance with
 the results of HQT-II. Combined with parsimony ancestral state
 reconstruction, the ancestral group of this family is Haplodiacanthus.
 Five other groups were discriminated, the Parafollicucullus,
 Curvalbaillella, Pseudoalbaillella, Longtanella, and Follicucullus–Cariver
 lineages. The morphological evolution of these lineages comprises a
 minimum essential list of eight states of four traits. HQT-II is a novel
 discriminant analytical multivariate method that may be of value in other
 taxonomic problems of paleobiology.