cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5dv41ns5t
title: Data from: Adrenomedullin ameliorates pulmonary fibrosis by regulating TGF-β-Smads signaling and myofibroblast differentiation

description: Pulmonary fibrosis is an irreversible, potentially fatal disease.
 Adrenomedullin (AM) is a multifunctional peptide whose activity is
 regulated by receptor activity-modifying protein 2 (RAMP2). In the present
 study, we used the bleomycin (BLM)-induced mouse pulmonary fibrosis model
 to investigate the pathophysiological significance of the AM-RAMP2 system
 in the lung. In heterozygous AM knockout mice (AM+/-), hydroxyproline
 content and Ashcroft scores reflecting the fibrosis severity were
 significantly higher than in wild-type mice (WT). During the acute phase
 after BLM administration, FACS analysis showed significant increases in
 eosinophil, monocyte, and neutrophil infiltration into the lungs of AM+/-.
 During the chronic phase, fibrosis-related molecules were upregulated in
 AM+/-. Notably, nearly identical changes were observed in RAMP2+/-. AM
 administration reduced fibrosis severity. In the lungs of BLM-administered
 AM+/-, the activation level of Smad3, a receptor-activated Smad, was
 higher than in WT. In addition, Smad7, an antagonistic Smad, was
 downregulated and microRNA 21, which targets Smad7, was upregulated
 compared to WT. Isolated AM+/- lung fibroblasts showed less proliferation
 and migration capacity than WT fibroblasts. Stimulation with TGF-β
 increased the numbers of α-SMA-positive myofibroblasts, which were more
 prominent among AM+/- cells. TGF-β-stimulated AM+/- myofibroblasts were
 larger and exhibited greater contractility and extracellular matrix
 production than WT cells. These cells were α-SMA (+), F-actin (+) and
 Ki-67(-) and appeared to be nonproliferating myofibroblasts
 (non-p-MyoFbs), which contribute to the severity of fibrosis. Our findings
 suggest that in addition to suppressing inflammation, the AM-RAMP2 system
 ameliorates pulmonary fibrosis by suppressing TGF-β-Smad3 signaling,
 microRNA-21 activity and differentiation into non-p-MyoFbs.
DOI: 10.5061/dryad.6q573n5zf
title: Atmospheric boundary layer intensive sounding data at Cangzhou site

description: This dataset is obtained from a field experiment of intensive GPS (Global
 Positioning System) boundary layer sounding carried out in
 Cangzhou (38.3°N, 116.84°E), from 26 November to 26 December
 2019. Eight soundings were taken in each day, at 02:00, 05:00, 08:00,
 11:00, 14:00, 17:00, 20:00 and 23:00 BJT (i.e., UTC + 8). GPS radiosonde
 (Beijing Changzhi Sci & Tech Co. Ltd., China) was used to obtain
 profiles of wind, temperature, humidity and PM2.5 mass concentration with
 a vertical resolution of approximately 3-5 m (1 s interval in
 time).  The ABL height was derived via the bulk
 Richardson number method.
DOI: 10.5061/dryad.dfn2z3515
title: Nuclear and mitochondrial genome of the mediterranean corn borer Sesamia nonagrioides

description: This dataset contains the assembly and annotation of the mitochondrial
 genome and of the nuclear genome of the Mediterranean corn borer (Sesamia
 nonagrioides, Noctuidae, Lepidoptera), a major pest of maize in Europe and
 Africa. The DNA used to generate this assembly was extracted from a pool
 of inbred males and females third instar larvae. The assembly is based on
 short- and long-read sequencing. The complete mitochondrial genome is
 15,330 bp and contains all expected 13 and 24 protein-coding and RNA
 genes, respectively. The nuclear assembly is 1,021 Mbp, composed of 2,553
 scaffolds and it has an N50 of 1,105 kbp. A total of 17,230 protein-coding
 genes were predicted, including 15,776 with InterPro domains. These genome
 assemblies provide a solid molecular basis to study insect genome
 evolution and to further develop biocontrol strategies against S.
 nonagrioides.
DOI: 10.5061/dryad.m63xsj41x
title: Camera trap data: Density dependence of daily activity in three ungulate species

description: Daily activity in herbivores reflects a balance between finding food and
 safety. The safety-in-numbers theory predicts that living in higher
 population densities increases safety, which should affect this balance.
 High-density populations are thus expected to show a more even
 distribution of activity – i.e. spread – and higher activity levels across
 the day. We tested these predictions for three ungulate species; red deer
 (Cervus elaphus), roe deer (Capreolus capreolus) and wild boar (Sus
 scrofa). We used camera traps to measure the level and spread of activity
 across ten forest sites at the Veluwe, the Netherlands, that widely range
 in ungulate density. Food availability and hunting levels were included as
 covariates. Daily activity was more evenly distributed when population
 density was higher for all three species. Both deer species showed
 relatively more feeding activity in broad daylight and wild boar during
 dusk.  Activity level increased with population density
 only for wild boar. Food availability and hunting showed no correlation
 with activity patterns. These findings indicate that ungulate activity is
 to some degree density dependent. However, while these patterns might
 result from larger populations feeling safer as the safety-in-numbers
 theory states, we cannot rule out that they are the outcome of greater
 intraspecific competition for food, forcing animals to forage during
 suboptimal times of the day. Overall, this study demonstrates
 that wild ungulates adjust their activity spread and level based on their
 population size.
DOI: 10.5061/dryad.1ns1rn8t6
title: Significant differentially expressed genes (DEG) for midgut tissue from bees maintained for four hours at 35°C or 45°C

description: Honey bee colonies in the United States have suffered from increased
 die-off in the last few years with a complex set of interacting stresses
 playing a key role. With changing climate, an increase in the frequency of
 severe weather events, such as heat waves, is anticipated. Understanding
 how these changes may contribute to stress in honey bees is crucial.
 Individual honey bees appear to have a high capacity to endure thermal
 stress. One reason for this high-level endurance is likely their robust
 HSR which contributes to thermotolerance at the cellular level. However,
 less is known about other mechanisms of thermotolerance, especially those
 operating at the tissue level. To elucidate other determinants of this
 resilience in this species, we used thermal stress coupled with RNAseq and
 identified broad transcriptional remodeling of a number of key signaling
 pathways in the honey bee, including those pathways known to be involved
 in digestive tract regeneration in the fruit fly such as the Hippo and
 JAK/STAT pathways. We also observe cell death and shedding of epithelial
 cells, which likely leads to induction of this regenerative
 transcriptional program. We found that thermal stress affects many of
 these pathways in other tissues, suggesting a shared program of damage
 response. This study provides important foundational characterization of
 the tissue damage response program in this key pollinating species. In
 addition, our data suggest that a robust regeneration program may also be
 a critical contributor to thermotolerance at the tissue level, a
 possibility which warrants further exploration in this and other species.
description: Honey bees were fed sucose solution Containing 0.5% DMSO) at
 either 35 ∘C  or 45 ∘C  for 4 hours. Midguts were removed, stored in
 RNAlater, and RNA was harvested using Trizol reagent. RNA was submitted to
 additional quality control analysis before mRNA was enriched by polyA
 selection. Llibrary preparation was performed using a NEBNext Ultra RNA
 library preparation kit. Sequencing was then performed using Illumina
 HiSeq platform.
DOI: 10.5061/dryad.sqv9s4n3q
title: Individual-based simulations of genome evolution and ancestry: the GENOMEADMIXR R package

description: Hybridization between populations or species results in a mosaic of the
 two parental genomes. This and other types of genome admixture have
 received increasing attention for their implications in speciation, human
 evolution, Evolve and Resequence (E&R) and genetic mapping.
 However, a thorough understanding of how local ancestry changes after
 admixture, and how selection affects patterns of local ancestry remains
 elusive. The complexity of these questions limits analytical treatment,
 but these scenarios are specifically suitable for simulation. Here, we
 present the R package GenomeAdmixR, which uses an individual-based model
 to simulate genomic patterns following admixture forward in time.
 GenomeAdmixR provides user-friendly functions to set up and analyze
 simulations under evolutionary scenarios with selection, linkage and
 migration. We show the flexible functionality of the GenomeAdmixR workflow
 by demonstrating 1) how to design an E&R simulation using
 GenomeAdmixR and 2) how to use GenomeAdmixR to verify analytical
 expectations following from the theory of junctions. GenomeAdmixR provides
 a mechanistic approach to explore expected genome responses to realistic
 admixture scenarios. With this package, we aim to aid researchers in
 testing specific hypotheses based on empirical findings involving admixing
 populations.
description: README Included here is the code used to
 create figures 2 and 3 in the main text, but also code to reproduce the
 two examples (E&R and junctions) in the main text. Furthermore, we
 have included the  R package GenomeAdmixR as tar ball.
 - the file Supplementary Material 2.1 includes all the
 supplementary analysis as referred to in the main text.
 - the R scripts Figure_2_ancestry.R and Figure_2_sequence.R
 perform the simulations necessary for Figure 2 and generate the required
 plots. - the R script code_figure_3.R re-creates figure
 3. - The R script scripts_figure_4.R re-creates the
 E&R scenario, and explores both models. At the end of the script,
 the figures used in Figure 3 in the main text are created.
 - The zip file 'Junctions.zip' contains 1) code to
 simulate many replicates for all parameter values used (simulate_data.R)
 and 2) code to create Figure 4 in the main text (plot_figure.R), which
 uses the files created by simulate_data.R
DOI: 10.5061/dryad.qv9s4mwdj
title: Raw radiocarbon dates and stable carbon isotope values for individual bone specimens from Madagascar's Central Highlands.

description: This commentary has no abstract. 
description: This dataset summarizes published radiocarbon and δ13C data, and
 also includes new, previously unpublished data for lemurs, hippos, and a
 euplerid carnivoran from the Central Highlands. Collagen was isolated by
 soaking samples in 0.5 N HCl at 4°C, rinsing in ultrapure water, soaking
 samples in 0.01 N NaOH, rinsing again in ultrapure water, gelatinizing in
 0.01 N HCl at ca. 70°C, filtering through 1.5 micrometer glass fiber
 filters, and freeze drying. Stable isotope values were obtained at the
 Stable Isotope Lab at the University of Cincinnati and radiocarbon dates
 were obtained at the Lawrence Livermore National Lab. We corrected data by
 -1.2‰ to account for isotopic changes in atmospheric CO2 following the
 industrial revolution (The Suess Effect).
DOI: 10.5061/dryad.wstqjq2kt
title: Supplementary data for article: Central insulin modulates dopamine signaling in the human striatum

description: Objective: Activity in the dopaminergic pathways of the brain is highly
 sensitive to body weight and metabolic states. Animal studies show that
 dopamine neurons are important targets for the metabolic hormone insulin
 with abolished effects in the insulin resistant state, leading to
 increases in body weight and food intake. In humans, the influence of
 central acting insulin on dopamine and effects of their interplay are
 still elusive. Research Design and Methods: We investigated whether
 central administered insulin influences dopaminergic activity in striatal
 regions and whole-brain neural activity. Using a PET/MRI hybrid scanner,
 we simultaneously performed [11C]-raclopride-PET and resting state fMRI in
 10 healthy normal weight men after application of intranasal insulin or
 placebo on two separate days in a randomized, placebo-controlled, blinded,
 crossover trial. Results: In response to central insulin compared to
 placebo administration, we observed greater [11C]-raclopride binding
 potential (BPnd) in the bilateral ventral and dorsal striatum. This
 suggests an insulin-induced reduction in synaptic dopamine levels.
 Resting-state striatal activity was lower 15 and 30 min after nasal
 insulin compared to placebo. Functional connectivity of the
 mesocorticolimbic circuitry associated with differences in dopamine
 levels: individuals with a stronger insulin-induced effect on dopamine
 levels showed a stronger increase in functional connectivity 45 min after
 intranasal insulin.­ Conclusions: This study indicates that central
 insulin modulates dopaminergic tone in the striatum, which may affect
 regional brain activity and connectivity. Our results deepen the
 understanding of the insulin-dopamine interaction and the complex network
 that underlies the regulation of whole-body metabolism.
description: The readme file contains an explanation of each of the variables
 in the dataset and its measurement units. Information on how the
 measurements were done can be found in the associated manuscript
 referenced above.
DOI: 10.5061/dryad.3n5tb2rh2
title: Geographical variation in the bill-flower fit in a plant-pollinator interaction in western Mexico

description: Few studies have examined geographical variation in traits involved in
 biotic interactions, although such variation is likely key in the
 evolution of interactions. The fit between hummingbird bills and the
 flowers they feed on suggests mutual selection pressures. We tested for
 geographical variation in the pollinator – flower fit in the Mexican
 hermit Phaethornis mexicanus and Heliconia spp. flowers by analyzing the
 morphospaces of the interacting species and the ways they vary. To analyze
 the geographical variation in the morphology of P. mexicanus and Heliconia
 spp. flowers, we grouped samples into three operational geographic units
 (OGUs). Within each OGU, we assessed pollinator-flower specificity by
 analyzing floral resource preference, and morphological data using
 correlations and principal component analysis. Our data on floral
 preferences and morphology indicate geographical variation in the P.
 mexicanus – Heliconia interaction in all of the OGUs. Heliconia was the
 preferred floral resource (83% of the samples), suggesting a preference
 for these flowers as a food source. We also detected morphological overlap
 between the bill of P. mexicanus and the corollas of both Heliconia
 species, at least in the two westernmost OGUs. That P. mexicanus
 morphology tracked variation in the different Heliconia spp. across the
 hummingbird’s range suggests that the specificity of the hummingbird –
 plant interaction exerts a significant selection pressure on hummingbird
 morphology. The morphological overlap observed in the two northernmost
 OGUs is probably due to the evolution of a close biotic interaction, which
 is reflected in the high correlation values in the morphological
 characters involved.
description: File: PhaethornisHeliconia2.xlsx Database
 including basic data for analyses (Datasheet: Database)
 Explanation for the columns (Datasheet: Field
 explanation) File: PhaethornisHeliconiaR.txt
 R Manuscript for data analyses (boxplots, Statistical
 tests)
DOI: 10.5061/dryad.37pvmcvk4
title: Data for: Sodium addition increases leaf herbivory and fungal damage across four grasslands

description: 1. Sodium (Na) is an essential element for all animals, but not plants.
 Soil Na supplies vary geographically. Animals that primarily consume
 plants thus have the potential to be Na limited and plants that uptake Na
 may be subject to higher rates of herbivory, but their high Na content
 also may attract beneficial partners such as pollinators and seed
 dispersers. 2. To test for the effects of Na biogeochemistry on herbivory,
 we conducted distributed Na press experiments in four North American
 grasslands. 3. Na addition increased soil and plant Na concentrations at
 all sites. Grasses in Na addition plots had significantly higher herbivore
 damage by leaf miners and fungal pathogens than those in control plots.
 Forbs with higher foliar Na concentrations had significantly more chewing
 insect herbivore and fungal damage. 4. While no pattern was evident across
 all species, several forb species had higher Na concentrations in
 inflorescences compared to leaves, suggesting they may allocate Na to
 attract beneficial partners. 5. The uptake of sodium by plants, and animal
 responses, has implications for the salinification in the Anthropocene.
 Increased use of road salt, irrigation with saline groundwater, rising sea
 levels, and increasing temperatures and evapotranspiration rates with
 climate change can all increase inputs of sodium into terrestrial
 ecosystems. 6. Our results suggest increasing terrestrial sodium
 availability will benefit insect herbivores and plant fungal pathogens.
DOI: 10.6078/d1ph79
title: Data for: Human food use increases plant geographic ranges in the Sonoran Desert

description: Aim. Climate is usually regarded as the main determinant of plant species’
 distributions. However, past human use of species for food also may have
 influenced distributions. We hypothesized that human-mediated dispersal
 has resulted in food plants occupying more of their potential geographic
 range. We also hypothesized that key ecological traits could predispose a
 species to occupy more of its potential climatic geographic range and be
 selected by humans for food. Location. The Sonoran Desert of southwestern
 North America. Time period. Present day. Major taxa studied. Food plants.
 Methods. We used ethnobotanical and data from large botanical
 ecoinformatics databases to estimate realized (dispersal- and
 climate-constrained) and potential (climate-constrained) ranges for food
 plants and their used and un-used congeners. Results. We found that food
 plants fill more of their potential geographic ranges than their un-used
 congeners. We also found that succulence and annual growth interacted with
 food usage to increase range filling. Main conclusions. Human food use has
 expanded the distribution of many plant species in the Sonoran Desert.
description: Please see main <em>Global Ecology and Biogeography
 </em>article for details of data collection and
 processing.
description: <b>File S1</b>. A full plant list of Sonoran Desert
 food plants and congeners based on phylogenetic publications. (CSV
 format) <b>File S2.</b> Range filling
 statistics estimated from species distribution models for all species in
 the dataset, combined with information on species distribution modeling
 parameters and data sample sizes. Model results are presented for 25 and
 50 km grain size. (CSV format) <b>File
 S3.</b> Trait values for all species in the dataset. (CSV
 format) <b>File S4.</b> R code to replicate
 all data gathering steps, statistical analyses, and figures in this study.
 (TXT format) Please see README enclosed in
 <strong>File S4</strong> for usage instructions.
DOI: 10.5061/dryad.7wm37pvsm
title: Biophysical properties governing septin assembly

description: Septin filaments build structures such as rings, lattices and gauzes that
 serve as platforms for localizing signaling and organizing cell membranes.
 How cells control the geometry of septin assemblies in poorly understood.
  We show here that septins are isodesmic polymers, in contrast to
 cooperative polymerization exhibited by F-actin and
 microtubules.  We constructed a physical model to analyze and
 interpret how septin assemblies change in the presence of regulators in
 yeast extracts.  Notably filaments differ in length and curvature
 in yeast extract compared to pure protein indicating cellular regulators
 modulate intrinsic biophysical features.  Combining analysis of
 extracts from regulatory mutants with simulations, we found increased
 filament flexibility and reduced filament fragmentation promote assembly
 of septin rings, whereas reduced flexibility in crowded environments
 promotes local filament alignment. This work demonstrates how tuning of
 intrinsic features of septin filament assembly by regulatory proteins
 yields a diverse array of structures observed in cells.
description: Images were acquired via TIRF microscopy after incubating
 septins/extracts on planar supported lipid bilayers. Images were prepared
 using FIJI/ImageJ.
DOI: 10.5061/dryad.v41ns1rvt
title: Neighboring edges: interacting edge effects of linear disturbances on vegetation in treed fens

description: The influence of edges on forest biodiversity is an important
 environmental effect associated with habitat fragmentation, as edge
 effects can further reduce the remaining ‘interior’ habitat. However,
 extrapolating the influence of edges across the broader landscape has been
 difficult, especially regarding how to treat multiple edges in close
 proximity, where edge effects might interact. In this study, we examined
 the interaction of edge effects for multiple edges from a dense network of
 narrow (3-8 m wide) and low-severity linear disturbances called ‘seismic
 lines’. Seismic lines are created during oil and gas exploration and are
 responsible for severe dissection of boreal forests in western Canada.
 Specifically, our objectives were to: (1) to compare the edge influence of
 “wide” (~8 m) and “narrow” (~3 m) seismic lines; and (2) to determine
 whether edges in close proximity show interaction of edge influences, i.e.
 do multiple narrow seismic lines have a stronger or weaker edge influence
 than a single narrow seismic line. We sampled vegetation along transects
 perpendicular to seismic lines in treed moderate-rich and poor fens. We
 used randomization tests of edge influence to calculate the magnitude and
 distance of edge effects. In moderate-rich fens, we found a positive edge
 influence on understory diversity from both wide and narrow seismic lines.
 We also found a weakening edge interaction on diversity, i.e., single
 narrow seismic lines had a stronger edge influence on diversity than
 multiple narrow seismic lines. In treed poor fens, multiple narrow seismic
 lines had a negative edge effect on tree density, understory abundance,
 richness, and composition. In addition, we found strengthening edge
 interactions in treed poor fens on tree density, graminoid cover, and
 understory composition. Our results show how assessing the edge influence
 of multiple disturbances can provide a better understanding of the
 cumulative effects of habitat fragmentation.
description: Data was collected in poor and moderate-rich treed fens in
 Northern Alberta (S. of Fort McMurray). 
description: Linetype is for the three different treatments (F2D = single wide
 treatment, F3D = single narrow treatment, L3D = multiple narrow treatment)
 and their corresponding edge aspect (S = south-facing edge). 
 Plots SLA and SLB are the 2 seismic line plots
 Ecosite: PF = poor fen, MRF = moderate-rich fen. 
 SL.width = seismic line width.