cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.905qfttp6
title: NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations

description: We developed a method to detect copy number variation and loss of
 heterozygosity in genome-edited cell lines by only sequencing the edited
 site. We introduced different substitutions on both chromosomes of diploid
 H9 human embryonic stem cells using CRISPR/Cas9 and a mixture of
 homology-directed repair donor DNAs carrying different substitutions.
 Here, we deposit the associated sequencing data (BAM-files) generated by
 extracting genomic DNA from genome-edited H9 cells, PCR amplifying the
 region of interest and sequencing on a MiSeq platform. We sequenced the
 edited site of cell bulks to investigate the editing efficiencies of
 individual donors from the donor mixtures. For proof of concept, we
 isolated over 850 cellular clones from the edited cell bulks and sequenced
 the edited site and heterozygous positions flanking the edited site to
 determine the number of alleles at the edited site and detect copy-neutral
 loss of heterozygosity. Additionally, we sequenced the DNA donors to
 assess, the distribution of individual donors in the mixtures.
DOI: 10.5061/dryad.qrfj6q5k6
title: Something in the wind: The influence of wind speed and direction on African lion movement behaviour

description: Olfaction is a key sense, enabling animals to locate forage, select mates,
 navigate their environment, and avoid predation. Wind is an important
 abiotic factor that modulates the strength of olfactory information
 detected by animals. In theory, when airflow is unidirectional, an animal
 can maximise the size of their olfactory search area and increase odour
 detection probability by moving crosswind. Given energetic costs inherent
 to activity and locomotion, behavioural search strategies that optimize
 the benefit-cost ratio should be advantageous. We tested whether African
 lions (Panthera leo) modify their movement directionality and distance
 according to wind speed and direction during hours of darkness when they
 are most likely to hunt mobile and elusive prey. We tracked 29 lions in
 southern Zimbabwe using GPS collars and deployed a weather station to
 collect detailed abiotic data. We found that when wind speeds increased
 lions were more likely to move crosswind. We also found that female lions,
 which tend to hunt more often than males, travelled farther when wind
 speeds were stronger. The results of our analysis suggest that lions adapt
 their movement behaviour according to wind speed and direction. We
 inferred that this was a behavioural decision to maximise the amount of
 olfactory information gained per unit of energy spent. Our findings not
 only offer one of the first detailed insights on large carnivore
 anemotaxis (movement direction relative to wind) but also make an
 important contribution towards understanding the influence of wind on
 predator ecology in general which remains understudied to date. Keywords:
 Panthera Leo, anemotaxis, wind, movement behaviour, olfaction
DOI: 10.15468/dl.6zyc5f
title: Occurrence Download

description: A dataset containing 520 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tripolium pannonicum"
 ]
}

 The dataset includes 520 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003213-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.63xsj3v58
title: EPA particulate matter data – Analyses using Local Control Strategy

description: Analyses of large observational datasets tend to be complicated and prone
 to fault depending upon the variable selection, data cleaning and analytic
 methods employed. Here, we discuss the analysis of 2016 US environmental
 epidemiology data and outline a new “benchmark” Non-parametric and
 Unsupervised analysis of these data. Readers are invited to download our
 CSV file from the archive and apply whatever analytic approach they think
 appropriate. We hope to encourage the development of a widely-held
 “consensus view” on the effects of Secondary Organic Aerosols (Volatile
 Organic Compounds that have predominantly Biogenic or Anthropogenic
 origin) within PM2.5 particulate matter on Circulatory and/or Respiratory
 mortality. For example, the reanalyses described here focus on the
 question: “Can life in a region with an abundance of trees be relatively
 dangerous?”
description: The data set was constructed following the directions given in
 Pye et al. 2021. Pye, H.O.T., Ward-Caviness, C.K., Murphy,
 B.N., Appel, K.W. and Seltzer, K.M. (2021), “Secondary organic aerosol association with
 cardiorespiratory disease mortality in the United
 States”. Nature
 Communications 12, 7215. https://doi.org/10.1038/s41467-021-27484-1. Variable names were shortened and simplified.
description: The file is .csv. Excel can be used to open the files.
 A file named
 Supp_to_LCSonEPA.PDF
 contains R-code that
 recreates many of the analyses and graphics displayed here. This PDF file
 can be downloaded from http://localcontrolstatistics.org.
DOI: 10.18112/openneuro.ds007327.v1.0.1
title: Basketball Motor Observation and Motor Imagery EEG Dataset
DOI: 10.5061/dryad.0cfxpnw5s
title: Phenological and physiological advantages of invasive annuals are strengthened by nitrogen enrichment

description: Anthropogenic nitrogen (N) deposition exerts profound influence on the
 composition and function of native ecosystems, commonly resulting in
 reduced plant richness and increases in nonnative plant invasion.
 Identifying differences in plant N responses and functional traits could
 help to explain the ongoing invasion and biological impoverishment of
 ecosystems subject to N deposition. We compared the growth, emergence
 phenology, and functional traits of thirty native and invasive annual
 plant species under high and low N availability, with the goal of
 evaluating if invasives exhibit functionally dissimilar responses to N
 compared to the native species they displace. Invasives grew larger than
 natives, especially under increased N availability. Overall, invasives and
 natives did not differ in emergence phenology. However, these groups of
 species differed in relationships between growth and days to emergence,
 and N addition further strengthened these differences; invasives
 consistently grew larger than natives that emerged around the same time,
 while natives showed a strong negative effect of delayed emergence on
 plant growth. Relative N responses for measures of plant growth and
 allocation did not differ between native and invasive species, but
 invasives exhibited greater plasticity in physiological traits. This
 included significantly lower leaf N content, higher CN ratios, and greater
 water-use efficiency (WUE) in plants grown under high N. Invasives also
 showed functionally different patterns of growth and water use. Across
 species, invasives showed a positive relationship between shoot growth and
 WUE. Native species showed a tradeoff between root allocation and WUE,
 while invasives displayed high values for WUE even despite reduced
 root:shoot ratios under high N. Our results highlight the ability of
 invasives to rapidly accrue biomass, disproportionately benefit from early
 emergence and N addition, and use water efficiently despite rapid growth.
 Natives, on the other hand, pay a higher cost for delayed emergence and
 may experience tradeoffs between growth and water-use. The more pronounced
 functional differences between natives and invasives observed under high N
 likely play an important role in driving invasion and reduced species
 diversity under N enrichment. These differences could be used to inform
 successful management strategies for N-impacted and water-limited
 ecosystems.
DOI: 10.6086/d1xm45
title: Inflammatory gene expression during acute high‐altitude exposure

description: The molecular signaling pathways that regulate inflammation and the
 response to hypoxia share significant crosstalk and appear to play major
 roles in high-altitude acclimatization and adaptation. Several studies
 demonstrate increases in circulating candidate inflammatory markers during
 acute high-altitude exposure, however significant gaps remain in our
 understanding of how inflammation and immune function change at high
 altitude and if these responses contribute to high-altitude pathologies,
 such as Acute Mountain Sickness. To address this, we used an unbiased
 transcriptomic approach, including RNA sequencing and direct digital mRNA
 detection with NanoString, to identify changes in the inflammatory profile
 of peripheral blood throughout three days of high-altitude acclimatization
 in healthy sea-level residents (N = 15; 5 women). Several
 inflammation-related genes were upregulated on the first day of
 high-altitude exposure, including a large increase
 in HMGB1 (High Mobility Group Box 1), a danger
 associated molecular pattern (DAMP) molecule which amplifies immune
 responses during tissue injury. Differentially expressed genes on the
 first and third days of acclimatization was enriched for several
 inflammatory pathways including NF-kB and toll-like receptor (TLR)
 signaling. Indeed, both TLR4 and LY96, which
 encodes the lipopolysaccharide binding protein (MD-2), were upregulated at
 high altitude.
 Finally, FASLG and SMAD7 were
 associated with AMS scores and pulse oxygen saturation levels on the first
 day at high altitude, suggesting a potential role of immune regulation in
 response to high-altitude hypoxia. These results indicate that acute
 high-altitude exposure upregulates inflammatory signaling pathways and may
 sensitize the TLR4 signaling pathway to subsequent inflammatory stimuli.
DOI: 10.5061/dryad.prr4xgxpz
title: Population genomics of an emergent tri-species hybrid zone

description: Isolating barriers that drive speciation are commonly studied in the
 context of two-species hybrid zones. There is however evidence that more
 complex introgressive relationships are common in nature. Here, we use
 field observations and genomic analysis, including the sequencing and
 assembly of a novel reference genome, to study an emergent hybrid zone
 involving two colliding hybrid zones of three woodpecker species:
 red-breasted, red-naped, and yellow-bellied sapsuckers (Sphyrapicus ruber,
 S. nuchalis, and S. varius). Surveys of the area surrounding Prince
 George, British Columbia, Canada, show that all three species are
 sympatric, and Genotyping-by-Sequencing identifies hybrids from each
 species pair and birds with ancestry from all three species. Observations
 of phenotypes and genotypes of mated pairs provide evidence for
 assortative mating, though there is some heterospecific pairing.
 Hybridization is more extensive in this tri-species hybrid zone than in
 two di-species hybrid zones. However, there is no evidence of a hybrid
 swarm, and admixture is constrained to contact zones, so we classify this
 region as a tension zone and invoke selection against hybrids as a likely
 mechanism maintaining species boundaries. Analysis of sapsucker age
 classes does not show disadvantages in hybrid survival to adulthood, so we
 speculate the selection upholding the tension zone may involve hybrid
 fecundity. Gene flow among all sapsuckers in di-species hybrid zones
 suggests introgression likely occurred before the formation of this
 tri-species hybrid zone and might result from bridge hybridization,
 vagrancies, or other three-species interactions.
description: See README for details on use of data files and scripts.
 Multiplexed *.fastq.gz files are described in the data processing scripts,
 but for re-use please see individual demultiplexed files from NCBI SRA
 database number SUB11950717. The pg_variants* files are called within the
 R PCA scripts. Descriptions of all variables in .csv data files are
 included in csv_variables_descriptions.txt. 
description: Canu v 1.9, Purge Haplotigs, Repeat Masker v 4.1.1, BUSCO v
 5.1.2, Satsuma v 2.0, VCFtools v 0.1.16, GATK v 3.8, ADMIXTURE v 1.3.0,
 R,  Ternary v 1.2.2, R scripts from Irwin et al. 2016 and 2018.
DOI: 10.5281/zenodo.18401462
title: LINF_320013700

description: Cyclin; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18401463
title: LINF_320013700

description: Cyclin; Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.31167985
title: Characterisation of gas liquid two phase flow transition

description: The research focused on experimental investigation of behaviour of gas-liquid two-phase flow as it transitions from horizontal to vertical section of pipe.
DOI: 10.6084/m9.figshare.31167985.v4
title: Characterisation of gas liquid two phase flow transition

description: The research focused on experimental investigation of behaviour of gas-liquid two-phase flow as it transitions from horizontal to vertical section of pipe.
DOI: 10.5061/dryad.zcrjdfngj
title: Prey availability influences the effect of boldness on reproductive success in a mammalian predator

description: Boldness is an important trait in wild populations and among-individual
 differences can link to individual fitness. The strength and direction of
 relationships between behavioral and life-history traits may however vary
 according to environmental conditions, where fluctuating selection acting
 on behavioral traits contributes to the maintenance of personality
 differences. We explored sources of variation in Arctic fox (Vulpes
 lagopus) boldness and investigated how temporal variation in the abundance
 of a main prey (lemmings) influences the relationship between fox boldness
 and reproductive success. We measured the behavioral reaction of
 individuals when escaping after handling, as an indicator of their
 boldness. We obtained 70 measurements from 42 individuals during two years
 of low lemming abundance and two years of high lemming abundance and
 assessed fox litter size as an indicator of reproductive success. First,
 individual characteristics (age, sex, mass) did not affect Arctic fox
 boldness, while individual identity generated variation in boldness. Next,
 we found that during years of low lemming density, individuals behaving
 boldly had more pups than those behaving less boldly, suggesting boldness
 may provide an advantage when lemmings are scarce by increasing hunting
 success or allowing access to alternative resources. However, all
 individuals tended to show high levels of boldness when lemming density
 was high, and all produced large litters. Temporal variation in the
 abundance of a main prey might therefore influence the relation between
 boldness and reproductive success of a predator, and if individuals
 consistently differ in their level of boldness, fluctuating selection
 could contribute to the maintenance of personality.
description: The README file contains column descriptions. General information
 for the analyses is presented in the article.
DOI: 10.6084/m9.figshare.31167985.v3
title: Characterisation of gas liquid two phase flow transition in horizontal to upward vertical pipe systems

description: The research focused on experimental investigation of behaviour of gas-liquid two-phase flow as it transitions from horizontal to vertical section of pipe.
DOI: 10.5061/dryad.76hdr7t0q
title: Soil disturbance and invasion magnify CO2 effects on grassland productivity, reducing diversity

description: Climate change, disturbance, and plant invasion threaten grassland
 ecosystems, but their combined and interactive effects are poorly
 understood. Here, we examine how the combination of disturbance and plant
 invasion influences the sensitivity of mixedgrass prairie to elevated
 carbon dioxide (eCO2) and warming. We established subplots of intact
 prairie and disturbed/invaded prairie within a free-air CO2 enrichment (to
 600 ppmv) by infrared warming (+1.5 °C day, 3 °C night) experiment and
 followed plant and soil responses for five years. Elevated CO2 initially
 led to moderate increases in biomass and plant diversity in both intact
 and disturbed/invaded prairie, but these effects shifted due to strong
 eCO2 responses of the invasive forb Centaurea diffusa. In the
 final three years, biomass responses to eCO2 in disturbed/invaded
 prairie were 10 times as large as those in intact prairie (+186% vs.
 +18%), resulting in reduced rather than increased plant diversity (-17%
 vs. +10%). At the same time, warming interacted with disturbance/invasion
 and year, reducing the rate of topsoil carbon recovery following
 disturbance. The strength of these interactions demonstrates the need to
 incorporate disturbance into predictions of climate change effects. In
 contrast to expectations from studies in intact ecosystems,
 eCO2 may threaten plant diversity in ecosystems subject to soil
 disturbance and invasion.
description: <strong>USAGE NOTES:</strong>
 Climate treatments included: (1) <strong>ct</strong>:
 ambient CO<sub>2</sub> and temperature, (2)
 <strong>cT</strong>: infrared warming to increase canopy
 temperature 1.5 ˚C during the day and 3 ˚C at night, (3)
 <strong>Ct</strong>: free-air CO<sub>2</sub>
 enrichment to 600 ppmv, and (4)
 <strong>CT</strong>: CO<sub>2<sup>
 </sup></sub>enrichment plus warming.
 Climate treatments were applied to “rings” (i.e. whole plots).
 Within rings, vegetation treatments (i.e. subplots) included (1) intact
 prairie, and (2) disturbed/invaded prairie. Within disturbed/invaded
 prairie subplots, we tilled two 20-cm × 100-cm strips, separated by a
 15-cm x 100-cm strip of existing prairie vegetation in the center, and
 bordered by two 7.5-cm x 100-cm strips of prairie vegetation on the sides.
 For Centaurea diffusa biomass data in Table 2, strip types are coded as
 (1) tilled, and (2) vegetated. For both tables, the harvested area is
 indicated in the “area of harvested subplot” column.
 For more details, please refer to Figures 1 and S1 in the
 associated manuscript. <strong>DATA
 DESCRIPTION:</strong> This dataset includes two
 data tables and a readme file.
DOI: 10.5068/d1dt2t
title: Abiotic conditions shape spatial and temporal morphological variation in North American birds

description: Quantifying environment-morphology relationships is important not only for
 understanding the fundamental processes driving phenotypic diversity
 within and among species, but also for predicting how species will respond
 to ongoing global change. Despite a clear set of expectations motivated by
 ecological theory, broad evidence in support of generalizable effects of
 abiotic conditions on spatial and temporal intraspecific morphological
 variation has been limited. Using standardized data from over 250,000
 captures of 105 landbird species, we assessed intraspecific shifts in the
 morphology of adult male birds since 1989 while simultaneously measuring
 spatial morphological gradients across the North American continent. We
 found strong spatial and temporal trends in average body size, with warmer
 temperatures associated with smaller body sizes both at more equatorial
 latitudes and in more recent years. The magnitude of these thermal effects
 varied both across and within species, with results suggesting it is the
 warmest, rather than the coldest, temperatures driving both spatial and
 temporal trends. Stronger responses to spatial – rather than temporal –
 variation in temperature suggests morphological change may not be keeping
 up with the pace of climate change. Additionally, as elevation increases,
 we found that body size declines as relative wing length increases, likely
 due to the benefits that longer wings confer for flight in thin air
 environments. Our results provide support for both existing and new
 large-scale ecomorphological ‘rules’ and highlight how the response of
 functional tradeoffs to abiotic variation drives morphological change.
description: Bird morphology data were collected as part of the Monitoring
 Avian Productivity and Survivorship (MAPS) program, a collaborative
 long-term bird-banding project operating across North America. Data were
 obtained from 1124 banding stations (Fig. 1), each consisting of 6–20 mist
 nets, over the period 1989–2018 (though most stations operated during only
 a subset of this period). Banding stations were operated 6–12 times per
 year, from May 1 to August 28, encompassing the breeding season for most
 birds in North America. Records consist of only male birds classified as
 After Hatch Year (captured at least one breeding season after the hatch
 year of the bird). All records with body mass or wing length measurements
 that were more than five median absolute deviations [MAD] away from the
 median were excluded, as these likely represented measurement or data
 entry errors. If an individual was captured more than once in a season,
 only measurements taken during the initial capture were included. Only
 species for which data were available for at least 375 captures (post data
 filtering) were included.
description: Data from the Monitoring Avian Productivity and Survivorship
 (MAPS) program are curated and managed by The Institute for Bird
 Populations and were queried from the MAPS database on
 2019-10-16.
DOI: 10.15468/dl.mzfna9
title: Occurrence Download

description: A dataset containing 265 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dolichos sericeus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 265 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003216-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g79cnp5sm
title: Data from: Common protein-coding variants and the racing phenotype in galloping racehorse breeds

description: Centuries-long selection for system-wide morphological, physiological, and
 metabolic adaptations has led to extreme athletic phenotypes among
 geographically diverse horse breeds. Here, we identify genes contributing
 to exercise adaptation in racehorses by applying genomics approaches for
 racing performance, an end-point athletic phenotype. Using an integrative
 genomics strategy to first combine population genomics results with
 skeletal muscle exercise and training transcriptomic data, followed by
 whole-genome resequencing of Asian horses, we identify protein-coding
 variants in genes of interest in galloping racehorse breeds (Arabian,
 Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1,
 MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism,
 and neurobiology, are key drivers of the racing phenotype. Although racing
 potential is a multifactorial trait, the genomic architecture shaping the
 common athletic phenotype in horse populations bred for racing provides
 evidence for the influence of protein-coding variants in fundamental
 exercise-relevant genes. Variation in these genes may therefore be
 exploited for genetic improvement of horse populations towards specific
 types of racing.
description: The file has been generated for the
 figure 2 in the manuscript, “Common protein-coding variants and the racing
 phenotype in galloping racehorse breeds”. The fastStructure software was
 used to generate the file.  
description: Microsoft Excel can be used to open
 the file.