cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.15dv41p24
title: Data from: Flying high: Sampling savanna vegetation with UAV-lidar

description: The flexibility of UAV-lidar remote sensing offers a myriad of new
 opportunities for savanna ecology, enabling researchers to measure
 vegetation structure at a variety of temporal and spatial scales. However,
 this flexibility also increases the number of customizable variables, such
 as flight altitude, pattern, and sensor parameters, that, when adjusted,
 can impact data quality as well as the applicability of a dataset to a
 specific research interest. To better understand the impacts that UAV
 flight patterns and sensor parameters have on vegetation metrics, we
 compared 7 lidar point clouds collected with a Riegl VUX-1LR over a 300 x
 300 m area in the Kruger National Park, South Africa. We varied the
 altitude (60 m above ground, 100 m, 180 m, and 300 m) and sampling pattern
 (slowing the flight speed, increasing the overlap between flightlines, and
 flying a crosshatch pattern), and compared a variety of vertical
 vegetation metrics related to height and fractional cover. Comparing
 vegetation metrics from acquisitions with different flight patterns and
 sensor parameters, we found that both flight altitude and pattern had
 significant impacts on derived structure metrics, with variation in
 altitude causing the largest impacts. Flying higher resulted in lower
 point cloud heights, leading to a consistent downward trend in percentile
 height metrics and fractional cover. The magnitude and direction of these
 trends also varied depending on the vegetation type sampled (trees,
 shrubs, or grasses), showing that the structure and composition of savanna
 vegetation can interact with the lidar signal and alter derived metrics.
 While there were statistically significant differences in metrics among
 acquisitions, the average differences were often on the order of a few
 centimeters or less, which shows great promise for future comparison
 studies.We discuss how these results apply in practice, explaining the
 potential trade-offs of flying at higher altitudes and alternating flight
 pattern. We highlight how flight and sensor parameters can be geared
 toward specific ecological applications and vegetation types, and we
 explore future opportunities for optimizing UAV-lidar sampling designs in
 savannas.
description: The point cloud files (LAS files) were denoised and classified
 (Default: Class 1, Ground: 2, Noise: 7, HighScanAngles: 10) using the
 Terrasolid software suite. The point clouds can be input into the
 <em>VoxelMetrics</em> pipeline in Lidar-Notebooks (https://github.com/pbb2291/Lidar-Notebooks) to recreate all of the metrics reported in Boucher et al. (2023; <em>Flying High: Sampling Savanna Vegetation with UAV-lidar</em>). The CHM and DTM raster files (GeoTIFF files) used in Boucher et al. (2023) are also available for download.
DOI: 10.5061/dryad.ffbg79d06
title: Host population effects on ectomycorrhizal fungi

description: Geographic distinctions in the affinity of tree populations for select
 ectomycorrhizal fungi (EMF) may occur where strong edaphic pressures act
 on fungal communities and their hosts. We examine this premise for
 Pseudotsuga menziesii var. menziesii of southwest British Columbia, using
 ten native seedlots collected from a range of mean annual precipitation
 (MAP), as a proxy for podzolization extent and phosphorus (P)
 deficiencies, and evaluated in contrasting low P and high P soils. After
 two growing seasons, seedling biomass in the high P soil dwarfed that of
 the low P soil, and better growth rates under high P were detected for
 populations from very dry and very wet origins. EMF communities on the
 high P soil displayed more symmetry among host populations than the low P
 soil (average community dissimilarity of 0.20% vs 0.39%, respectively).
 Seedling foliar P% differed slightly but significantly in relation to MAP
 of origin. EMF species richness varied significantly among host
 populations but independently of climatic parameters. There were
 significant shifts in EMF species abundance related to seedlot MAP,
 particularly on the low P soil where nonlinear relationships were found
 for Wilcoxina mikolae, Hyaloscypha finlandica, and Rhizopogon villosulus.
 Despite efforts to enhance colonization by native fungi, the predominance
 of ruderal EMF species hindered a realistic evaluation of local adaptation
 among host-fungi populations. Nevertheless, the shifting affinity in taxa
 abundance and wider community disparity on low P soil reflected the
 potential for a consequential host genetic effect related to geographical
 patterns in P availability across temperate rainforests
DOI: 10.5061/dryad.j0zpc86jr
title: Data from: Bromodomain-containing protein 4 regulates innate inflammation via modulation of alternative splicing (images and qPCR data)

description: Bromodomain-containing Protein 4 (BRD4) is a transcriptional regulator
 which coordinates gene expression programs controlling cancer biology,
 inflammation, and fibrosis. In the context of virus-infection,
 BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory
 cytokines and prevent downstream epithelial plasticity. Although the
 chromatin modifying functions of BRD4 in inducible gene expression have
 been extensively investigated, its roles in post-transcriptional
 regulation are not well understood. Given BRD4's interaction with the
 transcriptional elongation complex and spliceosome, we hypothesize that
 BRD4 is a functional regulator of mRNA processing.  To address
 this question, we combine data-independent analysis - parallel
 accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to
 achieve deep and integrated coverage of the proteomic and transcriptomic
 landscapes of human small airway epithelial cells exposed to viral
 challenge and treated with BRD4i. The transcript-level data was further
 interrogated for alternative splicing analysis, and the resulting datasets
 were correlated to identify pathways subject to post-transcriptional
 regulation. We discover that BRD4 regulates alternative splicing of key
 genes, including Interferon-related Developmental Regulator 1 (IFRD1) and
 X-Box Binding Protein 1 (XBP1), related to the innate immune response and
 the unfolded protein response.  These findings extend the
 transcriptional elongation-facilitating actions of BRD4 in control of
 post-transcriptional RNA processing in innate signaling.
description: Any image viewer/analysis software (e.g. FIJI), and excel.
DOI: 10.5061/dryad.m0cfxpp7p
title: Supplementary material: Is over-parameterization a problem for profile mixture models?

description:  All the materials are presented in the order they are referred
 to in the manuscript. At the end of this document, we include the section
 entitled Reproducibility, which explains some of the simulation
 procedures, as well as some sample command lines like used in this work to
 simulate and fit the data. Throughout this material, blank spaces are left
 on purpose.
DOI: 10.5061/dryad.zgmsbccgt
title: Effects of human and non-human predation risk on antipredator movement behaviors of an upland game bird

description: Predators can elicit antipredator behaviors in prey such as proactive and
 reactive movements, but both are rarely investigated simultaneously.
 Impacts of human predation risk on antipredator behaviors can potentially
 be greater than non-human predators, resulting in increased effects on
 populations and community structure. Therefore, we compared the influence
 of human and non-human predation risk on proactive and reactive
 antipredator movement behaviors of a commonly harvested game bird, male
 Eastern wild turkeys (Meleagris gallopavo, hereafter turkey). We used
 simultaneously collected GPS locations from 31 turkeys and 36 coyotes
 (Canis latrans) to investigate antipredator behavior of turkeys to
 coyotes. To assess antipredator behaviors by turkeys to hunters, we used
 1,661 hunting tracks collected while monitoring 109 turkeys. Specifically,
 for proactive movements, we quantified how predation risk influenced
 resource selection. To investigate reactive movements, we quantified
 changes in movement behavior of turkeys after encountering hunters and
 coyotes. Coyotes and turkeys were sympatric on the landscape as home range
 overlap was high, but lack of core area overlap, encounters, and similar
 resource selection suggested use of different areas on the landscape.
 Turkeys selected areas associated with decreased coyote risk and closer to
 hardwoods. Coyotes preferred shrubs and open areas, suggesting turkeys
 avoided coyote risk and the habitats coyotes preferred. We detected 17
 coyote and turkey contacts, and probability of a contact decreased by
 16.6% for every 100m farther from a forest edge. Turkeys did not display
 reactive movement behaviors after a direct encounter with coyotes, as step
 lengths were similar prior and after encounters, which did not differ from
 random step lengths. After the onset of hunting, turkeys selected to be
 farther away from public access points and closer to private property,
 suggesting proactive avoidance of areas associated with increased hunter
 predation risk. We detected 31 hunter and turkey contacts, step lengths
 after hunter contacts were approximately double compared to random step
 lengths. The probability of a hunter-turkey contact decreased by 5.5% for
 every 100m farther from a secondary road. Collectively, antipredator
 movement behaviors by turkeys suggest coyote risk to be low over a broad
 temporal window as we only documented proactive movement behaviors.
 Conversely, hunter risk is high for a short temporal window while hunting
 is occurring, as we documented both proactive and reactive movement
 behavior responses. Overall, we provide insight into how human-induced
 fear can cause antipredator behavioral responses greater than non-human
 fear, potentially causing changes in species distribution and community
 structure.
DOI: 10.5061/dryad.3n5tb2rn7
title: Plant functional traits predict heterogeneous distributional shifts in response to climate change

description: Climate change is causing the rapid redistribution of vegetation as plant
 species move to track their climatic optima. Despite a global trend of
 upward movement in latitude and elevation, there is extensive
 heterogeneity among species and locations, with few emerging
 generalizations. Greater generalization may be achieved by considering
 multidimensional changes in species’ distributions as well as
 incorporating ecologically relevant functional traits into studies of
 range shifts. To better understand how recent changes in climate are
 influencing the elevational distribution of plant species and how species’
 functional traits mediate distributional changes, we resampled a
 2,438-meter elevation transect spanning a distance of 16 kilometers which
 encompasses desert scrub, pinyon-juniper woodland, chaparral, and
 coniferous forest plant communities. Over the last 42 years, total
 perennial cover and species’ average cover increased at lower elevations
 and decreased at higher elevations while the average elevational
 leading-edge increased 116 m and the elevational rear edge decreased 84 m.
 Notably, these changes were mediated by species’ functional traits, where
 species exhibiting more conservative traits (lower SLA, greater δ13C,
 larger seed mass) and taller height shifted upward in their leading-edge
 range limit, average elevation, and trailing edge range limit, while
 declining in abundance at the median and trailing edge of their range.
 Species possessing more acquisitive traits (higher SLA, lower δ13C,
 smaller seed mass) and shorter height shifted downward and increased in
 abundance at their trailing edge, with increases in their total range
 size. Our results provide clear evidence that heterogeneous range dynamics
 under recent climate change can be generalized by considering ecologically
 relevant plant functional traits, and how they respond to localized
 climate exposure. Further, by documenting changes across a steep
 ecological gradient comprising a large aridity gradient, we show divergent
 patterns for plants occupying contrasting positions along the global
 spectrum of plant form and function, which provides critical insight into
 how trait-mediated changes under increasing aridity will impact ecosystem
 functioning.
description: Species occurrence and abundance data were collected using
 transects. Functional trait data were collected from the field following
 standard protocols.
DOI: 10.5061/dryad.cfxpnvx9b
title: Hurricanes affect diversification among individual life courses of a primate population

description: Extreme climatic events may influence individual-level variability in
 phenotypes, survival, and reproduction, and thereby drive the pace of
 evolution. Climate models predict increases in the frequency of intense
 hurricanes, but no study has measured their impact on individual life
 courses within animal populations. We used 45 years of demographic data of
 rhesus macaques to quantify the influence of major hurricanes on
 reproductive life courses using multiple metrics of dynamic heterogeneity
 accounting for life course variability and life history trait variances.
 To reduce intraspecific competition, individuals may explore new
 reproductive stages during years of major hurricanes, resulting in higher
 temporal variation in reproductive trajectories. Alternatively,
 individuals may opt for a single optimal life history strategy due to
 trade-offs between survival and reproduction. Our results show that
 heterogeneity in reproductive life courses increased by 4% during years of
 major hurricanes, despite a 2% reduction in the asymptotic growth rate due
 to an average decrease in mean fertility and survival, i.e. shortened life
 courses and reduced reproductive output. In agreement with this, the
 population is expected to achieve stable population dynamics faster after
 being perturbed by a hurricane (ρ = 1.512; 95% CI: 1.488, 1.538), relative
 to ordinary years (ρ = 1.482;1.475,1.490). Our work suggests that natural
 disasters force individuals into new demographic roles to potentially
 reduce competition during unfavorable environments where mean reproduction
 and survival are compromised. Variance in lifetime reproductive success
 and longevity are differently affected by hurricanes, and such variability
 is mostly driven by survival. 
description: This is demographic data from visual census collected and shared
 by the Carribean Primate Research Center from the University of Puerto
 Rico Medical Sciences Campus. 
description: All analyses were run in R Version 4.2.2.
DOI: 10.5061/dryad.pnvx0k6sj
title: Data for: Synthetic red supergiant explosion model grid for systematic characterization of Type II supernovae

description: This model grid contains 228,016 synthetic red supergiant explosion (Type
 II supernova) models. Time evolution of spectral energy distributions from
 1 Angstrom to 50,000 Angstrom (100 frequency bins in a log scale) up to
 500 days after explosion is computed in each model. We provide light
 curves for the filters of the Vera C. Rubin Observatory's Legacy
 Survey of Space and Time (LSST), Zwicky Transient Facility (ZTF), Sloan
 Digital Sky Servey (SDSS), and the Neil Gehrels Swift Observatory, but
 light curves for any photometric filters with any extinctions at any
 redshifts can be constructed based on the synthetic spectral energy
 distributions. We also provide bolometric light curves and photosphere
 information such as photospheric velocity evolution. The parameter space
 covered by the model grid is five progenitor masses (10, 12, 14, 16, and
 18 solar mass at the zero-age main sequence, solar metallicity), ten
 explosion energies (0.5e51, 1.0e51, 1.5e51, 2.0e51, 2.5e51, 3.0e51,
 3.5e51, 4.0e51, 4.5e51, and 5.0e51 erg), nine 56Ni masses (0.001, 0.01,
 0.02, 0.04, 0.06, 0.08, 0.1, 0.2, and 0.3 solar mass), nine mass-loss
 rates (10^-5.0, 10^-4.5, 10^-4.0, 10^-3.5, 10^-3.0, 10^-2.5, 10^-2.0,
 10^-1.5, and 10^-1.0 Msun/yr with a wind velocity of 10 km/s), six
 circumstellar matter radii (1e14, 2e14, 4e14, 6e14, 8e14, and 1e15 cm),
 and ten circumstellar structures (beta = 0.5, 1.0, 1.5, 2.0, 2.5, 3.0,
 3.5, 4.0, 4.5, and 5.0). 56Ni is assumed to be uniformly mixed up to the
 half mass of a hydrogen-rich envelope.
description: This model grid is constructed by the one-dimensional
 multi-frequency radiation hydrodynamics code STELLA (Blinnikov et al.
 1998, ApJ, 496, 454; Blinnikov et al. 2000, ApJ, 532, 1132; Blinnikov et
 al. 2006, A&A, 453, 229).
description: If you find any strange models, please notify the authors.
DOI: 10.5061/dryad.sbcc2frbh
title: Root functional traits determine the magnitude of the rhizosphere priming effect among eight tree species

description: Rhizosphere priming effect can accelerate or decelerate the
 decomposition of soil organic matter. Using a natural abundance
 13C tracer method allowing partitioning of native soil organic carbon
 (SOC) decomposition and plant rhizosphere respiration, we studied the
 effects of eight tree species on the strength of the rhizosphere priming.
 All tree species enhanced the rate of SOC decomposition, by 82% on
 average. Mean diameter of first-order roots and root
 exudate-derived respiration were positively correlated with the RPE,
 together explaining a large part of the observed variation in the RPE (R2
 = 0.72), whereas root branching density was negatively associated with the
 RPE. Path analyses further suggested that mean diameter of first-order
 roots was the main driver of the RPE owing to its positive direct effect
 on the RPE and its indirect effects via root exudate-derived respiration
 and root branching density. These results demonstrate that the magnitude
 of the RPE is regulated by complementary aspects of root morphology,
 architecture and physiology, implying that comprehensive approaches are
 needed to reveal the multiple mechanisms driving plant effects on the RPE.
DOI: 10.5061/dryad.0k6djhb4d
title: Diploid and haploid assemblies and annotation of monoecious shrub willow (Salix purpurea), clone ID 94003

description: The Salicaceae are dioecious perennials that utilize different sex
 determination systems. There is substantial interest in understanding the
 impacts of hybridization, speciation, and polyploidy on sex chromosome
 evolution. Here, a rare monoecious S. purpurea genotype, 94003, was
 assembled. Based on sequence alignments to dioecious and monoecious
 genomes, a 1.15 Mb sex-linked region on Chr15W was identified as absent in
 monecious plants. Inheritance of this structural variation is responsible
 for the loss of a male-suppressing function in what would otherwise be
 genetic females, resulting in monoecy or lethality, if homozygous.
description: High molecular weight DNA was extracted from 94003 using a
 protocol described by Mayjonade et al., (2016) followed by DNA clean up in
 500 μL 24:1 chloroform:isoamyl alcohol, centrifugation at 8,000 x g, and
 ethanol precipitation. Resulting DNA had a peak at 15,509 bp as determined
 by analysis on a femto pulse (Agilent). PacBio Sequencing was performed at
 the Mount Sinai Research Institute (New York, NY) to generate
 approximately 2.5 million HiFi reads and 140x HiFi read coverage. HiFi
 reads were assembled using hifiasm (Cheng et al., 2021) and aligned using
 minimap2 (Li, 2018) to the <em>S. purpurea</em> 94006 v.5.1
 reference genome to scaffold contigs (Goodstein et al., 2011; Zhou et al.,
 2020). Annotation was performed using Maker (Cantarel et al., 2008) with
 snap ab initio gene prediction. Additional high-quality DNA for Illumina
 sequencing was extracted using a Qiagen (Germantown, MD) DNeasy kit
 and paired end (2 x 150 bp) Illumina sequencing was performed at West
 Virginia University (Morgantown, WV).
description: All files can be viewed on any standard text editor (e.g. Atom,
 notepad, textedit, sublime, etc.) IGV can be used the view the genome and
 annotation in browser form with the assembly and gff3 files.
DOI: 10.34740/kaggle/dsv/14652112
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.msbcc2g33
title: Data from: Assessing the mechanisms and impacts of shrub invasion in forests: A meta-analysis

description: The encroachment of invasive shrubs in forest understories can have
 detrimental effects on native plant recruitment. As a result, removal of
 invasive species is a common practice although long-lasting success is
 rare. In order to effectively conserve and manage invaded forests, it is
 crucial to understand the mechanisms that drive shrub invasion, i.e., high
 propagule pressure, low native resistance, and exploitation of empty
 niches. To gain a deeper understanding of the invasion process in forest
 ecosystems we conducted a meta-analysis of the work done in this topic. We
 collected data on invasive species and native community performance and on
 the abiotic conditions of forest understories under low and high levels of
 shrub invasion. We analyzed data from 124 articles that yielded 377 unique
 observations. Our results revealed that while invader performance did not
 vary by the mechanism of invasion, the impact on the native community was
 significantly detrimental when invasion occurred via low biotic
 resistance, and only marginally significant via propagule pressure.
 Invasive species performance was associated with increases in light
 availability, but not with other resources (soil water, or nutrients).
 When assessing impact on native performance as a function of invasive
 performance, results were again only significant under the low biotic
 resistance mechanism. Lastly, impacts were stronger when invasion took
 place by a single invader. Synthesis and applications: Taken together,
 these results suggest that restoration efforts should focus on (i)
 increasing the presence of strong native competitors or functionally
 diverse native communities, (ii) decreasing sources of invasive shrub
 propagules while keeping the canopies closed when invasion occurs via high
 propagule pressure, (iii) avoiding management techniques that degrade or
 diminish canopy cover, and (iv) prioritizing management of forest
 understories dominated by particularly impactful invasive shrubs.