cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2280gb5tt
title: Data from: Harvest and density-dependent predation drive long-term population decline in a northern ungulate

description: The relative effect of top-down versus bottom-up forces in regulating and
 limiting wildlife populations is an important theme in ecology. Untangling
 these effects is critical for a basic understanding of trophic dynamics
 and effective management. We examined the drivers of moose (Alces alces)
 population growth by integrating two independent sources of observations
 within a hierarchical Bayesian population model. This analysis used one of
 the largest existing spatiotemporal datasets on ungulate population
 dynamics globally. We documented a 20% population decline over the period
 examined. Moose population growth was negatively density-dependent.
 Although the mechanisms producing density-dependent suppression of
 population growth could not be determined, the relatively low densities at
 which moose populations were documented suggests it could be due primarily
 to density-dependent predation. Predation primarily limited population
 growth, except at low density, where it was regulating. Harvest appeared
 to be largely additive and contributed to population declines. Our
 results, highlight how population dynamics are context dependent and vary
 strongly across gradients in climate, forest type, and predator abundance.
 These results help clarify long-standing questions in population ecology
 and highlight the complex relationships between natural and human-caused
 mortality in driving ungulate population dynamics.
description: See the manuscript for details on how the dataset was collected
 and processed.
description: Data is found here on Dryad (moose_data_dryad.RData), but the R
 scripts (run_jags_model.R and gompertz_jags.R) are found on Zenodo (https://doi.org/10.5281/zenodo.6030027). See the README.txt for a description of all 3 files.
DOI: 10.5061/dryad.zs7h44jbr
title: Data from: The genetic basis of variation in sexual aggression: evolution versus social plasticity

description: Male sexual aggression towards females is a form of sexual conflict that
 can result in increased fitness for males through forced copulations or
 coercive matings at the cost of female lifetime fitness. We used male
 fruit flies (Drosophila melanogaster) as a model system to uncover the
 genomic contributions to variation in forced copulation, both due to
 standing variation in a wild population, and due to plastic changes
 associated with variation in social experience. We used RNAseq to analyze
 whole-transcriptome differential expression in male head tissue associated
 with evolved changes in forced copulation from lineages previously
 selected for high and low forced copulation rate (Dukas et al., 2020), and
 in male flies with varying forced copulation rates due to social
 experience. We identified hundreds of genes associated with evolved and
 plastic variation in forced copulation, however only a small proportion
 (27 genes) showed consistent differential expression due to both modes of
 variation. We confirmed this trend of low concordance in gene expression
 effects across broader sets of genes significant in either the evolved or
 plastic analyses using multivariate approaches. The gene ontology terms
 neuropeptide hormone activity and serotonin receptor activity were
 significantly enriched in the set of significant genes. Of 7 genes chosen
 for RNAi knockdown validation tests, knockdowns of 4 genes showed the
 expected effect on forced copulation behaviours. Taken together, our
 results provide important information about the apparently independent
 genetic architectures that underlie natural variation in sexual aggression
 due to evolution and plasticity.
description: Please see attached README file for
 information about the data sets and experiment-specific notes on missing
 values.
DOI: 10.5061/dryad.66t1g1k3v
title: Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level

description: Single-stranded breaks (SSBs) are the most frequent DNA lesions
 threatening genomic integrity. A highly kinked DNA structure in complex
 with human PARP-1 domains led to the proposal that SSB sensing in
 Eukaryotes relies on dynamics of both the broken DNA double helix and
 PARP-1’s multi-domain organization. Here, we directly probe this
 fundamental yet poorly understood process at the single-molecule level.
 Quantitative smFRET and structural ensemble calculations reveal how
 PARP-1’s N-terminal zinc fingers convert DNA SSBs from a largely
 unperturbed conformation, via an intermediate state into the highly kinked
 DNA conformation. Our data suggest an induced fit mechanism via a
 multi-domain assembly cascade that drives SSB sensing and stimulates an
 interplay with the scaffold protein XRCC1 orchestrating subsequent DNA
 repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib
 shifts the equilibrium towards the unkinked DNA conformation, whereas the
 inhibitor EB47 stabilizes the kinked state.
DOI: 10.15468/dl.n979v3
title: Occurrence Download

description: A dataset containing 7346 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Castanea mollissima"
 ]
}

 The dataset includes 7346 records from 219 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003058-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wstqjq2p3
title: Data and scripts from: Exploratory analysis of multi-trait coadaptations in the light of population history

description: During the process of range expansion, populations encounter a variety of
 environments. They respond to the local environments by modifying their
 mutually interacting traits. Common approaches of landscape analysis
 include first focusing on the genes that undergo diversifying selection or
 directional selection in response to environmental variation. To
 understand the whole history of populations, it is ideal to capture the
 history of their range expansion with reference to the series of
 surrounding environments and to infer the multi-trait coadaptation. To
 this end, we propose a complementary approach; it is an exploratory
 analysis using up-to-date methods that integrates population genetic
 features and features of selection on multiple traits. First, we conduct
 correspondence analysis of site frequency spectra, traits and environments
 with auxiliary information of population-specific fixation index (FST).
 This visualizes the structure and the ages of populations and helps infer
 the history of range expansion, encountered environmental changes and
 selection on multiple traits. Next, we further investigate the inferred
 history using an admixture graph that describes the population split and
 admixture. Finally, principal component analysis of the selection on
 edge-by-trait (SET) matrix identifies multi-trait coadaptation and the
 associated edges of the admixture graph. We introduce a newly defined
 factor loadings of environmental variables in order to identify the
 environmental factors that caused the coadaptation. A numerical simulation
 of one-dimensional stepping-stone population expansion showed that the
 exploratory analysis reconstructed the pattern of the environmental
 selection that was missed by analysis of individual traits. Analysis of a
 public dataset of natural populations of black cottonwood in northwestern
 America identified the first principal component (PC) coadaptation of
 photosynthesis- vs growth-related traits responding to the geographical
 clines of temperature and daylength. The second PC coadaptation of
 volume-related traits suggested that soil condition was a limiting factor
 for above-ground environmental selection.
DOI: 10.5061/dryad.ksn02v763
title: Data for: Habitat diversity, resource availability, and island age in the species-area relationship

description: Aim: The island species-area relationship (ISAR) and its theoretical
 justifications assume the area of islands to be homogeneous across an
 archipelago, which is generally not the case. We compare the performance
 of models that adjust or substitute for island area with measures of
 habitat diversity, island age, and resource availability to account for
 the violation of this assumption. We further compare the performance of
 models for two taxonomic groups. Location: Five hotspot archipelagos
 (Azores, Galapagos, Hawaii, Cape Verde, Canary Islands). Taxa: Vascular
 plants and birds. Methods: We used the mathematical framework of the power
 law to compare relevant models, treating the one containing only area as a
 null model against which others were compared. Data was collated from the
 GIFT database and from the literature. Models were compared using linear
 regression within archipelagos and via mixed effect models with
 archipelago as a random effect. Results: Weighting of island area by
 habitat diversity and resource availability systematically improved
 statistical significance and model fits versus the area only power law.
 Models including island age did not show the same systematic improvement
 in model fits. For vascular plants, weighting islands by resource
 availability (energy and water) performed better than weighting by habitat
 diversity, although for birds these weightings performed equally well.
 Main Conclusions: Given that islands within archipelagos are fairly
 uniform in climate, topography, and geology, it is worth accounting for
 this in ISARs. Our results suggest that, for islands in volcanic hotspot
 archipelagos this is best done by using direct measures of habitat
 diversity and resource availability rather than using island age as a
 proxy. Because weighting area by habitat diversity and resource
 availability produced better predictors of species diversity, the proposed
 approach may be particularly valuable in conservation science.
description: Data was collected from published sources and the current upload
 is collected analysis relating to the paper JBI-21-0522. Regression
 analysis was performed using R packages. 
description: Required software: R  (preferrably R studio).
DOI: 10.5061/dryad.w9ghx3fr7
title: Effect of heterogeneous substrate adhesivity of follower cells on speed and tension profile of leader cells in primary keratocyte collective cell migration

description: In single keratocyte motility, membrane tension is reported to be high at
 cell-fronts and believed to establish front coherence. To understand role
 of membrane mechanics in collective cell migration, we study membrane
 height fluctuations in cell sheets from fish scales using interference
 reflection microscopy (IRM). We report the monolayer to have cells lacking
 substrate adhesion and show that such “non-sticky” cells can form bridges
 between leader cells and far-away follower cells. Do such interactions
 alter motility and membrane mechanics in such leaders? We find
 non-significant, but reduced speed for leaders with “non-sticky” followers
 in comparison to other leaders. Cells show high phenotypic variability in
 their membrane fluctuation tension profiles. On average, this tension is
 found to be lower at cell fronts than the mid-section. However, leaders
 with non-sticky followers are more prone to display higher tension at
 their front and have a negative correlation between cell speed and
 front-mid tension difference. We, thus, conclude that intracellular
 tension gradients are heterogeneous in cell sheets and substrate
 adhesivity of followers can control the coupling of the gradient to cell
 speed.
DOI: 10.5061/dryad.msbcc2g0t
title: Dataset for complete sputum smear monitoring among adults with pulmonary tuberculosis in central Uganda: evidence from a retrospective cohort study

description: People with bacteriologically confirmed pulmonary tuberculosis (TB)
 require sputum smear monitoring at 2, 5, and 6 months to establish
 treatment outcomes. We retrospectively reviewed and abstracted data for
 416 persons with bacteriologically confirmed pulmonary TB initiated on
 treatment between January 2017 and December 2019 across 11 large TB units
 in Masaka district in central Uganda. The dataset includes variables on
 health facility attributes and clinical factors. We defined complete
 sputum smear monitoring was measured as the receipt of three sputum smear
 microscopy tests at 2, 5, and 6 months of TB treatment.
description: We collected data for participants aged ≥15 years diagnosed with
 bacteriologically confirmed pulmonary TB and who were started on treatment
 between January 2017 and December 2019. Data were abstracted from TB unit
 registers used a standardized data abstraction tool, with the sequence of
 variables organized following that in the registers. We used trained
 trained research assistants to collect the data.
description: The variable names are written using short words and responses
 are indicated in a more meaningful way.
DOI: 10.5061/dryad.5qfttdz7f
title: MALDI-TOF MS spectra and sequence data of collagen of modern and archaeological flatfish from European waters

description: MALDI-TOF MS spectra, LC-MS/MS datafiles, and Mascot MZID files of modern
 bone collagen of 18 species of Pleuronectiformes as reference spectra that
 were used to develop peptide biomarkers for ZooMS (Zooarchaeology by Mass
 Spectrometry). Details on the samples used can be found in the file
 "Reference spectra information.csv". Further information on the
 method and results can be found in the manuscript. The file names contain
 the type of data file and the species name.  MALDI-TOF MS of 202
 archaeological samples for Zooarchaeology by Mass Spectrometry (ZooMS)
 from three case study sites from around the North Sea: Barreau
 Saint-George ferroviaire in northern France, and 16-22 Coppergate and Blue
 Bridge Lane from York in the United Kingdom. Details on the samples can be
 found in the supplementary information of the manuscript. Further
 information on the method can be found in the manuscript. The file names
 are labeled with the sample ID number and the triplicate number (out of
 3).
description: Details can be found in the manuscript.
DOI: 10.5061/dryad.1rn8pk0w6
title: Data for: More than what they eat: Uncoupled biophysical constraints underlie geographic patterns of herbivory

description: Data used in Lynn et al. 2022 at Ecography. The first dataset contains
 data from published studies used for the main analyses of the paper. The
 second dataset is from Lynn and Fridley 2019 in Journal of Plant Ecology
 used for figure 3. The abstract from the paper is: Herbivory rates have
 classically been hypothesized to decrease from the tropics towards higher
 latitudes because the more benign abiotic conditions in tropical systems
 foster greater ecosystem complexity including greater intensity of biotic
 interactions. However, attempts to quantify latitudinal patterns of
 herbivory often fail to support this hypothesis. While biases have been
 offered as explanations for null results, here, we argue that framing the
 question of latitudinal variation in herbivory around nutrient and
 energetic constraints of insect herbivores and plants may provide
 mechanistic explanations of latitudinal herbivory patterns. As a case
 study, we focused on sodium as an uncoupled nutrient between herbivore and
 plant communities: sodium is a key limiting micronutrient for herbivore
 neural and muscular development while present at orders of magnitude lower
 concentrations in plants. We compared sodium deposition with latitude,
 mean annual temperature (MAT), and actual evapotranspiration (measure of
 primary productivity; AET) in their ability to predict consumed percentage
 leaf area from published datasets. Leaf percent herbivory increased with
 sodium deposition and MAT and decreased with latitude but was unrelated to
 AET. Sodium had comparable effect size and predictive ability to either
 MAT or latitude. Additionally, herbivory was highest in locales with both
 high sodium deposition and high MAT. Our hypothesis that geographic
 variation in herbivory is driven by an interaction of unrestrictive
 temperature environments (high MAT) and limiting nutrient supply to
 herbivores (high sodium deposition) was strongly supported. We propose
 that greater generality, predictability, and theoretical development on
 geographic variation in herbivory will arise from a refocus on the
 biophysical constraints (e.g., productivity, micronutrient availability,
 leaf mass consumed) that ultimately control consumer interactions rather
 than latitude per se. This refocus is likely to open new
 hypotheses for the evolution of defense syndromes across plant populations
 and communities based on the specific geography of limiting nutrients.
description: See the manuscript.
description: The paper and supplementary material contains details on how the
 data was collected and handled to be usable in our analyses. We claim no
 rights to the data, as all of it was taken from openly available
 datasets.
DOI: 10.5061/dryad.wh70rxwpz
title: Consilience across multiple, independent genomic data sets reveals species in a complex with limited phenotypic variation

description: Species delimitation in the genomic era has focused predominantly on the
 application of multiple analytical methodologies to a single massive
 parallel sequencing (MPS) data set, rather than leveraging the unique but
 complementary insights provided by different classes of MPS data. In this
 study we demonstrate how the use of two independent MPS data sets, a
 sequence capture data set and a single nucleotide polymorphism (SNP) data
 set generated via genotyping-by-sequencing, enables the resolution of
 species in three complexes belonging to the grass genus Ehrharta, whose
 strong population structure and subtle morphological variation limit the
 effectiveness of traditional species delimitation approaches. Sequence
 capture data are used to construct a comprehensive phylogenetic tree of
 Ehrharta and to resolve population relationships within the focal clades,
 while SNP data are used to detect patterns of gene pool sharing across
 populations, using a novel approach that visualises multiple values of K.
 Given that the two genomic data sets are fully independent, the strong
 congruence in the clusters they resolve provides powerful ratification of
 species boundaries in all three complexes studied. Our approach is also
 able to resolve a number of single-population species and a probable
 hybrid species, both which would be difficult to detect and characterize
 using a single MPS data set. Overall, the data reveal the existence of 11
 and five species in the E. setacea and E. rehmannii complexes, with the E.
 ramosa complex requiring further sampling before species limits are
 finalized. Despite phenotypic differentiation being generally subtle, true
 crypsis is limited to just a few species pairs and triplets. We conclude
 that, in the absence of strong morphological differentiation, the use of
 multiple, independent genomic data sets is necessary in order to provide
 the cross-data set corroboration that is foundational to an integrative
 taxonomic approach.
description: Please see the README document ("README_.txt"), the
 supplementary methods (SUPPLEMENTARY METHODS & FIGURES.docx) and
 the accompanying article:  Wootton, L.M., Forest, F., Verboom, G.A., 2022.
 Consilience across multiple, independent genomic data sets reveals species
 in a complex with limited phenotypic variation.
DOI: 10.5061/dryad.sn02v6x60
title: The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis

description: Rationale: The role of the pulmonary microbiome in sarcoidosis is
 unknown.Objectives: The objectives of the current study was to:
 1) Examine whether the pulmonary fungal and bacterial microbiota
 differed in patients with sarcoidosis compared with controls. 2) Examine
 whether there was an association between the microbiota and levels of the
 antimicrobial peptides (AMPs) in protected bronchoalveolar lavage (PBAL),
 indicating an interaction with the innate immune
 response.Methods: 35 sarcoidosis patients and 35 healthy controls
 underwent bronchoscopy and were sampled with oral wash (OW), protected BAL
 (PBAL) and left protected sterile brushes (LPSB).  The
 fungal ITS1 region and the V3V4 region of the bacterial 16SrDNA gene were
 sequenced. Bioinformatic analyses were performed with QIIME 2. The AMPs
 secretory leucocyte protease inhibitor (SLPI) and human beta defensins 1
 and 2 (hBD-1 & hBD-2), were measured in PBAL by enzyme linked
 immunosorbent assay (ELISA).Measurements and Main
 Results: Aspergillus dominated the PBAL samples in
 sarcoidosis. Differences in bacterial taxonomy were minor. There was no
 significant difference in fungal alpha diversity between sarcoidosis and
 controls, but the bacterial  alpha diversity in
 sarcoidosis was significantly lower in OW (p=0.047) and PBAL (p=0.03)
 compared with controls. The beta diversity for sarcoidosis compared with
 controls differed for both fungi and bacteria. AMP levels were
 significantly lower in sarcoidosis compared to controls (SLPI &
 hBD-1: p&lt;0.01). No significant correlations were found
 between a-diversity and AMPs.Conclusions: The pulmonary
 fungal and bacterial microbiota in sarcoidosis differed from controls,
 with lower antimicrobial peptides levels in sarcoidosis.
description: The dataset is part of the larger Bergen COPD Microbiome Study
 ("MicroCOPD") and Bergen ILD Microbiome Study
 ("MicroILD").  Processing details can be viewed in the paper
 & its supplement.
description: See the uploaded README.txt.
DOI: 10.5061/dryad.1c59zw3x3
title: Calculating bond dissociation energies of X-H (X = C, N, O, S) bonds of aromatic systems via DFT: A detailed comparison of methods

description: In this study, the bond dissociation energy (BDE) values of X-H (X = C, N,
 O, S) bonds of aromatic compounds were computed by using 17 different DFT
 functionals, namely M08-HX, M06-2X, M05-2X, M06, M05, BMK, MPW1B95, B1B95,
 B98, B97-2, LC-wPBE, B3LYP, cam-B3LYP, B2PLYP, MPWB1K, BB1K, BB95, within
 the basis set range 6-31G(d), 6-31+G(d), 6-31+G(d,p), 6-311G(d,p) and
 6-311++G(d,p). The results show that the 6-31G(d) is the most convenient
 basis set to perform the BDE calculations with sufficient accuracy
 compared to the relevant experimental BDEs. The M06-2X, M05-2X, and M08-HX
 functionals gave highly accurate BDE values (with the average mean
 unsigned error MUE = 1.2-1.5 kcal/mol), performing better than the other
 functionals. The results suggest that the M06-2X, M05-2X, and M08-HX
 density functionals in the combined DFT/6-311+G(3df,2p)//B3LYP/6-31G(d)
 model chemistry offer the best method for calculating BDEs of ArX-H (X =
 C, N, O, S) bonds.
description: The dataset was collected during the Gaussian 16 suite of
 programs at The University of Danang - University of Technology and
 Education, Vietnam, and La Trobe University, Australia. In this approach,
 the geometry is optimized, and zero-point energy corrections are
 calculated with the same model chemistry for all compounds, followed by
 single-point calculations of BDE values with a range of model chemistries.
 Consistently, geometry optimizations and frequency calculations were first
 carried out using B3LYP functional with the 6-31G(d) basis set that was
 shown before to be the best for this task. Then the single-point energies
 were calculated using 17 different functionals and the 6-311+G(3df,2p)
 basis set, followed by comparing calculated and experimental BDE
 values.
description: The data here contains all relevant necessary data to reproduce
 all results in the paper.
DOI: 10.5281/zenodo.18391427
title: Datalog dataset