cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3j9kd51j5
title: Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila

description: 3D eukaryotic genome organization provides the structural basis for gene
 regulation. In Drosophila melanogaster, genome folding is characterized by
 somatic homolog pairing, where homologous chromosomes are intimately
 paired from end to end; however, how homologs identify one another and
 pair has remained mysterious. Recently, this process has been proposed to
 be driven by specifically interacting 'buttons' encoded along
 chromosomes. Here, we turned this hypothesis into a quantitative
 biophysical model to demonstrate that a button-based mechanism can lead to
 chromosome-wide pairing. We tested our model using live-imaging
 measurements of chromosomal loci tagged with the MS2 and PP7 nascent RNA
 labeling systems. We show solid agreement between model predictions and
 experiments in the pairing dynamics of individual homologous loci. Our
 results strongly support a button-based mechanism of somatic homolog
 pairing in Drosophila and provide a theoretical framework for revealing
 the molecular identity and regulation of buttons.
DOI: 10.5061/dryad.n8pk0p2vs
title: Data for: Traumatic mating causes strict monandry in a wolf spider

description: In nature, most animal species are polygamous, and strict female monandry
 is rare. Though traumatic mating has been reported to postpone female
 re-mating, it rarely leads to strict female monandry. We demonstrate that
 traumatic mating causes strict female monandry in a wandering wolf spider
 Pardosa pseudoannulata. We showed direct evidence that male damaged the
 inner walls of the female genital tracts with the sharp embolus on its
 pedipalps during insemination. To confirm that the trauma reduced female’s
 willingness to re-mate, we mimicked male pedipalp insertions by
 micro-injecting seminal fluids and/or causing trauma to female genital
 tracts and let them mate after the manipulations. Result of mating trials
 showed that seminal fluids have little impact to restrain female’s mating
 willingness. However, once female genital tracts were wounded, its mating
 willingness would be greatly suppressed. In addition, impermeable
 amorphous mating plugs appeared in female genital tracts after mating. The
 mating plugs blocked female’s genital tracts and completely prevented
 female from re-mating. We found that the components of mating plugs shared
 highly similar organic compounds and concentration percentage of free
 amino acids with female haemolymph, indicating that wounds caused by male
 traumatic mating lead to haemorrhages, which gradually turn into mating
 plugs. We thus provide evidence for strict female monandry being caused by
 male traumatic mating through two means together: genital trauma
 suppressed female’s re-mating willingness and haemorrhage from the wounds
 formed impermeable mating plugs that completely prevented female from
 re-mating.
DOI: 10.5061/dryad.fttdz08t3
title: Fitness cost from fluctuating ultraviolet radiation in Daphnia magna

description: Solar ultraviolet radiation (UVR) is an important environmental threat for
 organisms in aquatic systems, but its temporally variable nature makes the
 understanding of its effects ambiguous. The aim of our study was to assess
 potential fitness costs associated with fluctuating UVR in the aquatic
 zooplankter Daphnia magna. We investigated individual survival,
 reproduction and behaviour when exposed to different UVR treatments.
 Individuals exposed to fluctuating UVR, resembling natural variations in
 cloud cover, had the lowest fitness (measured as the number of offspring
 produced during their lifespan). In contrast, individuals exposed to the
 same, but constant UVR dose, had similar fitness as control
 individuals (not exposed to UVR), but they showed a significant reduction
 in daily movement. The re-occurring threat response to the fluctuating UVR
 treatment thus had strong fitness costs for D.
 magna, and we found no evidence for plastic behavioural
 responses when continually being exposed to UVR, despite the regular,
 predictable exposure schedule. In a broader context, our results imply
 that depending on how variable a stressor is in nature, populations may
 respond with alternative strategies, a framework that could promote rapid
 population differentiation and local adaptation.
description: Data of the study and a ReadMe file is provided, besides scripts
 to perform the graphs and data analysis.
DOI: 10.5061/dryad.mgqnk9906
title: Data for: Larval environmental conditions influence plasticity in resource use by adults in the burying beetle, Nicrophorus vespilloides

description: Recent studies have shown that intraspecific patterns of phenotypic
 plasticity can mirror patterns of evolutionary diversification among
 species. This appears to be the case
 in Nicrophorus beetles. Within species, body size is
 positively correlated with the size of carrion used to provision larvae
 and parental performance. Likewise, among species, variation in body size
 influences whether species exploit smaller or larger carrion and the
 extent to which larvae depend on parental care. However, it is
 unclear whether developmental plasticity in response to carcass size,
 parental care, or both underlie transitions to new carcass
 niches. We examined this by testing whether variation in the
 conditions experienced by N. vespilloides larvae
 influenced their ability to breed efficiently upon differently sized
 carcasses as adults. We found that the conditions experienced by larvae
 during development played a critical role in determining their ability to
 use large carcasses effectively as adults. Specifically, individuals that
 developed with parental care and on large carcasses were best able to
 convert the resources on a large carcass into offspring when breeding
 themselves. Our results suggest that parentally-induced plasticity can be
 important in the initial stages of niche expansion.
DOI: 10.5061/dryad.v41ns1rwj
title: CPCP-1: Anisotropy of magnetic susceptibility (AMS) data

description: The Colorado Plateau Coring Project Phase 1 (CPCP-1) acquired three
 continuous drill cores from Petrified Forest National Park (PFNP),
 Arizona, U.S.A. Two cores, CPCP-PFNP13-1A and CPCP-PFNP13-2B, hereafter
 CPCP-1A and CPCP-2B; respectively, intersected the Upper Triassic
 Chinle Formation, Lower(?)-Middle Triassic Moenkopi Formation (MF) and
 Permian Coconino Sandstone. We examined CPCP-1A and CPCP-2B cores to
 construct a high-resolution magnetostratigraphy of Moenkopi Formation
 strata. These data files contain anisotropy of magnetic susceptibility
 (AMS) data collected from the specimens from
 core CPCP-2B.
description: Anisotropy of magnetic susceptibility (AMS) data was obtained on
 all specimens of appropriate size/shape from the core CPCP-2B using an
 AGICO MFKI-A system equipped with an automatic 3D rotator.
description: AMS data can be opened in AGICO free AMS data viewing and
 processing software "Anisoft5". To view the data in geographic
 coordinate use an azimuth/hade of 113°/90° (CPCP-2B) and the following
 orientation parameters in Remasoft 3.0 (P1= 12; P2= 0; P3= 12; P4= 0 or
 90).
DOI: 10.5061/dryad.kkwh70s53
title: Community science butterfly data Northwest Arkansas

description: This data set contains the butterfly behavior observations of community
 members who visited the Botanical Gardens of the Ozarks, as well as
 students in the Principles of Zoology and Animal Behavior courses at the
 University of Arkansas from spring 2017 to fall 2020. This data was used
 to assess the relationship between butterfly color and butterfly flower
 color choice, as well as the relationship between butterfly color,
 behavior, abundance, and cloud cover in Northwest Arkansas. It corresponds
 to "Engaging the community in pollinator research: the effect of wing
 pattern and weather on butterfly behavior" in Integrative and
 Comparative Biology. This data set includes the original data reported by
 community observers as well as the cleaned values used in the manuscript.
description: This data was collected by community members and students, as
 described in "Engaging the community in pollinator research: the
 effect of wing pattern and weather on butterfly behavior".
DOI: 10.6076/d10w2n
title: U-net for automated thoracic CT semantic segmentation

description: Cardiac computed tomography has a clear clinical role in the
 evaluation of coronary artery disease and assessment of coronary
 artery calcium (CAC) but the use of ionizing radiation limits the
 clinical use.
 Beam-shaping “bow-tie” filters determine the
 radiation dose and the effective scan field-of-view diameter
 (SFOV) by delivering higher X-ray fluence to a region
 centered at the isocenter. A method for positioning the heart
 near the isocenter could enable reduced SFOV imaging and reduce
 dose in cardiac scans. We developed a predictive approach to center the
 heart and reduce the SFOV. As part of this effort, we used a UNet to
 segment noncontrast thoracic CT scans to estimate the associated dose
 reductions. Here we publish the UNet network. Specifically, this dataset
 contains a trained U-net (convolutional neural network) which was trained
 for the purpose of segmenting noncontrast thoracic computed tomography
 images. 
description: We collected noncontrast thoracic CT images from our institution
 and manually segmented them. We then trained a U-Net (with the Pytorch
 framework) to perform semantic segmentation. The final state of the
 trained network is contained in this dataset.
description: This repository contains a .pth file which is the complete set of
 trained weights for the neural network. A repository of Python code
 contained at https://github.com/ucsd-fcrl/unet_deploy may be a useful
 starting point for using this U-Net.
DOI: 10.5068/d1h102
title: Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the US.

description: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has
 caused a global disruption to human health and activity. Being able to
 trace the early outbreak of SARS-CoV-2 within a locality will inform
 public health measures and provide insights to contain or prevent the
 viral transmission to save lives. Investigation of the transmission
 history requires efficient sequencing methods and analytic strategy, which
 can be generally useful in the study of viral outbreaks. Los Angeles (LA)
 County has sustained a large outbreak of severe acute respiratory syndrome
 coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we
 carried out surveillance viral genome sequencing to determine 142 viral
 genomes from unique patients seeking care at UCLA Health System. 86 of
 these genomes are from samples collected before April 19, 2020. We found
 that the early outbreak in LA, as in other international air travel hubs,
 was seeded by multiple introductions of strains from Asia and Europe. We
 identified a US-specific strain, B.1.43, which has been found
 predominantly in California and Washington State. While samples from LA
 County carry the ancestral B.1.43 genome, viral genomes from neighboring
 counties in California and from counties in Washington State carry
 additional mutations, suggesting a potential origin of B.1.43 in Southern
 California. We quantified the transmission rate of SARS-CoV-2 over time,
 and found evidence that the public health measures put in place in LA
 County to control the virus were effective at preventing transmission, but
 may have been undermined by the many introductions of SARS-CoV-2 into the
 region. Our work demonstrates that genome sequencing can be a powerful
 tool for investigating outbreaks and informing the public health response.
 Our results reinforce the critical need for the U.S. to have coordinated
 inter-state responses to the pandemic.
DOI: 10.5061/dryad.7d7wm37vk
title: Collins Pine and FIA Comparison

description: The overwhelming majority of information on historical forest conditions
 in the western North America comes from public lands, which may provide an
 incomplete description of historical landscapes. Historical data
 from privately-owned lands could help inform large-scale forest
 restoration efforts across ownerships. In this study we made use of an
 archive containing extensive timber survey data collected in the early
 1920’s from privately owned forestland. We then used contemporary
 FIA data to compare changes in tree density, basal area, and pine
 dominance with historical conditions. With this dataset provided,
 we subset FIA data from plots within the region of our historical timber
 inventory that showed similar biophysical environments as our
 historical dataset. The climatic and topographic data provided here were
 extracted from those FIA plots and from the locations of the historical
 timber survey. We subsequently used those extractions in random
 forest modeling and regression tree analysis to produce our final results
 reported in our manuscrip. Our specific objectives with this study were
 (1) describe the range of historical forest conditions across the survey
 area and compare that to contemporary forest conditions,
 (2) investigate the influence of biophysical factors on observed
 variability in historical and contemporary forest conditions and (3)
 predict historical forest conditions across a large spatial domain using
 modeled relationships with biophysical variables.
DOI: 10.5061/dryad.7d7wm37vm
title: Data from: Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.)

description: Variation in genetic diversity across species ranges has long been
 recognized as highly informative for assessing populations’ resilience and
 adaptive potential. The spatial distribution of genetic diversity within
 populations, referred to as fine-scale spatial genetic structure (FSGS),
 also carries information about recent demographic changes, yet it has
 rarely been connected to range scale processes. We studied eight silver
 fir (Abies alba Mill.) population pairs (sites), growing at high and low
 elevations, representative of the main genetic lineages of the species. A
 total of 1368 adult trees and 540 seedlings were genotyped using 137 and
 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a
 clear east-west isolation-by-distance pattern consistent with the
 post-glacial colonization history of the species. Genetic differentiation
 among sites (FCT=0.148) was an order of magnitude greater than between
 elevations within sites (FSC=0.031), nevertheless high elevation
 populations consistently exhibited a stronger FSGS. Structural equation
 modeling revealed that elevation and, to a lesser extent, post-glacial
 colonization history, but not climatic and habitat variables, were the
 best predictors of FSGS across populations. These results suggest that
 high elevation habitats have been colonized more recently across the
 species range. Additionally, paternity analysis revealed a high
 reproductive skew among adults and a stronger FSGS in seedlings than in
 adults, suggesting that FSGS may conserve the signature of demographic
 changes for several generations. Our results emphasize that spatial
 patterns of genetic diversity within populations provide information about
 demographic history complementary to non-spatial statistics, and could be
 used for genetic diversity monitoring, especially in forest trees.
description: See the section 'Data sets' in the Materials and
 Methods of the manuscript.
DOI: 10.5061/dryad.jm63xsjbc
title: Acoustic characteristics of four frog species

description: Human activities worldwide are increasingly releasing low-frequency noise
 into the environment. Anthropogenic noise imposes a novel stress for wild
 animals and has become an increasing global concern. Many animals have
 been found to mitigate noise disturbance by modifying their acoustic
 parameters, yet the calling behaviours of species that breed near airports
 have not been explored in detail, especially for amphibians. Here, we
 measured the environmental noise of a swamp close to the runway at Haikou
 Meilan Airport in China. We also recorded the calls of four anuran species
 that reproduce in this swamp, and we measured the sound pressure levels of
 each focal species. These frogs vary in their call amplitude and possess
 disparate spectral and temporal traits. We show that two frog species
 characterized by lower frequency calls increase their call frequency when
 an airplane takes off. Moreover, three anuran species characterized by
 higher call rates significantly reduce their call rates (or call efforts)
 in response to airplane flyby. These results suggest that animals’
 behavioural adaptation to human-made noise may be species specific.
 Because call frequency and call effort have close relationships with
 reproductive success, we deduce that such noise-induced behaviour
 adjustments may influence the fitness of taxa that depend on communication
 by sound.
DOI: 10.6084/m9.figshare.31166733
title: Experimental Data from Osteoblasts Exert a Pro-Tumorigenic Effect on Breast Cancer Spheroids in a CXCR2 Dependent Manner In 2D And 3D Bone Mimetic Cultures

description: Spreadsheet with data for figures and supplem
DOI: 10.6084/m9.figshare.31166733.v1
title: Experimental Data from Osteoblasts Exert a Pro-Tumorigenic Effect on Breast Cancer Spheroids in a CXCR2 Dependent Manner In 2D And 3D Bone Mimetic Cultures

description: Spreadsheet with data for figures and supplem
DOI: 10.5061/dryad.rr4xgxd8j
title: Data for: Flying through gaps – How does a bird deal with the problem and what costs are there?

description: Animals flying in the wild often show remarkable abilities to negotiate
 obstacles and narrow openings in complex environments. Impressive as these
 abilities are, this must result in costs in terms of impaired flight
 performance. In this study, I used a budgerigar as model for studying
 these costs. The bird was filmed in stereo when flying through a wide
 range of gap widths from well above wingspan down to a mere 1/4 of
 wingspan. 3D flight trajectories were acquired and speed, wingbeat
 frequency and accelerations/decelerations were calculated. The bird used
 two different wing-postures to get through the gaps and could use very
 small safety margins (down to 6mm on either side) but preferred to use
 larger when gap width allowed. When gaps were smaller than wingspan flight
 speed was reduced with reducing gap width down to half for the smallest
 and wingbeat frequency was increased. I conclude that flying through gaps
 potentially comes with multiple types of cost to a bird of which the main
 may be: i) reduced flight speed increases the flight duration and hence
 the energy consumption to get from point A to B, ii) the underlying
 U-shaped speed to power relationship means further cost from reduced
 flight speed, and associated with it iii) elevated wingbeat frequency
 includes a third direct cost.
description: Stereo filming and 3D trajectory calculations. The dataset
 contains digitized coordinates and the code included can be used to re-run
 all calculations that was done for during the analysis for the
 study.
description: Analysis of the coordinate files is done by running the
 matlab-script "Analyse_flights.m". It will allow the user to
 specify the files to analyse and will ask for the files (calibration file,
 frames to analyse and reference plate position) it needs in order to run
 analysis. All required files are included in the folders with the
 coordinates. The reference plate positions (called Plate points SX)
 contain three points on the calibration plate in horizontal orientation in
 the first frame and this will define the coordinate system to put it into
 real world. The Matlab file
 "Analyse_WT_distance.m" will run the calculations of the
 wing-tip distances using the same coordinates files as with the speed
 analysis. "Plot_all_speeds_over_time.m" will
 calculate accelerations and plot all together. See
 "Read Me.txt" for more details.
DOI: 10.5061/dryad.rxwdbrv8r
title: Complex adaptive architecture underlies adaptation to quantitative host resistance in a fungal plant pathogen

description: Plant pathogens often adapt to plant genetic resistance so
 characterization of the architecture underlying such an adaptation is
 required to understand the adaptive potential of pathogen populations.
 Erosion of banana quantitative resistance to a major leaf disease caused
 by polygenic adaptation of the causal agent, the fungus Pseudocercospora
 fijiensis, was recently identified in the northern Caribbean region.
 Genome scan and quantitative genetics approaches were combined to
 investigate the adaptive architecture underlying this adaptation.
 Thirty-two genomic regions showing host selection footprints were
 identified by pool sequencing of isolates collected from seven plantation
 pairs of two cultivars with different levels of quantitative resistance.
 Individual sequencing and phenotyping of isolates from one pair revealed
 significant and variable levels of correlation between haplotypes in 17 of
 these regions with a quantitative trait of pathogenicity (the diseased
 leaf area). The multilocus pattern of haplotypes detected in the 17
 regions was found to be highly variable across all the population pairs
 studied. These results suggest complex adaptive architecture underlying
 plant pathogen adaptation to quantitative resistance with a polygenic
 basis, redundancy, and a low level of parallel evolution between pathogen
 populations. Candidate genes involved in quantitative pathogenicity and
 host adaptation of P. fijiensis were identified in genomic regions by
 combining annotation analysis with available biological data.
description: See Materials and Methods of the article
description: This repository contains the data and code required to reproduce
 analyses reported in the associated paper. Raw Illumina
 sequences (FastQ files) for all individuals and pools are available from
 the NCBI Sequence Read Archive under BioProject n°PRJNA783739 (Adaptation to quantitative resistance of Banana in the fungus Pseudocercospora fijiensis causing black leaf streak disease). See the README.txt file for more details.
DOI: 10.15468/dl.jctrks
title: Occurrence Download

description: A dataset containing 9233 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ammotragus lervia"
 ]
}

 The dataset includes 9233 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002876-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.