cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zs7h44j7s
title: Data from: 11C-PK11195-PET brain imaging of the mitochondrial translocator protein in mitochondrial disease

description: Objective: To explore the possibilities of radioligands against the
 mitochondrial outer membrane protein TSPO as biomarkers for mitochondrial
 disease, we performed positron emission tomography (PET)-MR brain imaging
 with [11C]PK11195 in 14 patients with genetically confirmed mitochondrial
 disease and 33 matched controls.   
 Methods: A case-control study of PET-MR imaging with the TSPO
 radioligand [11C]PK11195.  Results: 46% of symptomatic
 patients had volumes of abnormal radiotracer binding greater than the
 95th percentile in controls. [11C]PK11195 binding was
 generally greater in grey matter and significantly decreased in white
 matter. This was most striking in patients with
 nuclear TYMP or mitochondrial
 m.3243A&gt;G MT-TL1 mutations, in keeping with differences in
 mitochondrial density seen post mortem. Some regional binding
 patterns corresponded to clinical presentation and underlying mutation,
 even in the absence of structural changes on MRI. This was most obvious
 for the cerebellum, where patients with ataxia had decreased binding in
 the cerebellar cortex, but not necessarily volume loss. Overall, there was
 a positive correlation between aberrant [11C]PK11195 binding and clinical
 severity.  Conclusion: These findings endorse the use of PET
 imaging with TSPO radioligands as a non-invasive in
 vivo biomarker of mitochondrial pathology. Classification of
 Evidence: This study provides Class III evidence that PET-MR
 brain imaging with TSPO radioligands identifies mitochondrial pathology.
DOI: 10.5061/dryad.zs7h44j7t
title: Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic

description: Files included in this data package includes data, scripts and a
 simulation program to replicate simulations of genetic divergence patterns
 and comparision with observations, as described in the paper. Filename:
 content coastalcoddata.csv: genotypes and metadata, described in detail
 below IBD.dat: data, pairwise observed Fst among cod samples
 report_pairwise_Fst_Vikingbank.R: R-script to extract relevant data from
 IBD.dat connectivity_matrix.txt: output from oceanographic modelling, for
 simulations popfile.dat: population data, for simulations simmat: compiled
 simulation program (linux 64 bit, dynamically linked) simmat.c: C source
 code for simmat simulation program simloop.R: R-script for running
 simulations (R.scripts uses the R computing environment:
 https://www.r-project.org/) The coastalcoddata.csv file contains SNP
 genotypes and metadata for individual cod (one line per individual),
 coastal cod as well as reference samples: Column name: Explanation
 RefSamp: 0 = coastal cod sample, 1 = North Sea reference sample, 2 = NEAC
 reference sample Region: County (prior to 2020 county revision) Locality:
 Name of sample locality Year: Year of sampling Lat: Latitude of sample
 locality Long: Longitude of sample locality SampleID: Internal ID og
 sample locality and year IndividualID: Individual number Otype: Otolith
 type of individual (1 = certain CC/NS, 2 = uncertain CC/NS, 4 = uncertain
 NEAC, 5 = certain NEAC, where NS=North Sea cod, CC=coastalcod, NEAC=North
 East Arctic cod) Missing: Number of missing genotypes for individual
 cgpGmoS1026 (and so on): SNP genotype in Genepop 3-digit format (missing
 genotype =000000)  
description: SNP genotyping, ocenographic modelling, computer simulations
description: Genotype and position data from coastalcoddata.csv are used to
 calculate pairwise genetic divergence (Fst) and geographic distances
 (Dist) among samples, including all individuals or after removal of
 suspect NEAC individuals (w/otolith types 4 or 5). The calculated values
 are reported in the IDB.dat file as Fst (all individuals) and Fst.NCC
 (excluding suspect NEAC), respectively, with lower (CL025) and upper
 (CL975) Confidence Limits based on Jackknifing over loci.
 Computer simulations are run from inside R by calling simloop.R
 which in turn calls report_pairwise_Fst_Vikingbank.R and starts the
 simulation program simmat. The latter program is provided both as an
 executable program (linux 64 bit, dynamically linked) and as a source code
 file (simmat.c: C source) and may need to be recompiled for the intended
 computer system. Programs and scripts have been tested for the linux
 operating system only (Fedora distribution:
 https://getfedora.org/).
DOI: 10.5061/dryad.b2rbnzsdt
title: Shrub density effects on the community structure and composition of a desert animal community

description: Positive interactions between shrubs and animals are frequent in desert
 ecosystems. Shrub canopies can provide refuge to some animal species from
 predators and shelter from stressful environmental conditions by
 ameliorating high temperatures through lowering the amplitude of
 variation. Consequently, there have been many contrasts of shrub versus
 open effects; however, we extend this approach further by testing these
 effects on a gradient of shrub densities in the Carrizo National Monument,
 California. We tested the hypothesis that shrub density is a
 landscape-level predictor of vertebrate community composition and
 structure. We used camera traps, transects, and focal observations to
 estimate animal density and composition, alongside the deployment of
 temperature sensors. Plots were established within shrub patches ranging
 from 0 to 12 shrubs per 10m radius. Plots with relatively higher shrub
 densities had increased the abundance and richness of vertebrate animal
 species. Temperature and residual dry matter were also important mediators
 of animal density and richness. Shrub cover was also an important driver
 of animal communities but we propose that shrub density is a more rapid
 proxy for vegetation effects in deserts relevant to wildlife
 conservationists, and managers.
DOI: 10.5061/dryad.v6wwpzgvh
title: Differences in thermal tolerance between parental species could fuel thermal adaptation in hybrid wood ants

description: Genetic variability is essential for adaptation and could be acquired via
 hybridization with a closely related lineage. We use ants to investigate
 thermal adaptation and the link between temperature and genetic variation
 arising from hybridization. We test for differences in cold and heat
 tolerance between Finnish Formica polyctena and Formica aquilonia wood
 ants and their naturally occurring hybrids. Using workers, we find the
 parental individuals differ in both cold and heat tolerances and express
 thermal limits which reflect their global distributions. Hybrids however
 cannot combine thermal tolerance of parental species as they are equally
 heat-tolerant to F. polyctena , but not equally cold-tolerant to F.
 aquilonia . We then focus on a single hybrid population to investigate the
 relationship between temperature variation and genetic variation across 16
 years using reproductive individuals. Based on the thermal tolerance
 results, we expected the frequency of putative F. polyctena alleles to
 increase in warm years and F. aquilonia alleles to increase in cold years.
 We find support for this in hybrid males but not in hybrid females. These
 results contribute to understanding the outcomes of hybridization, that
 may be sex-specific or depend on the environment. Furthermore, genetic
 variability resulting from hybridization could help hybrid wood ants cope
 with changing thermal conditions.
description: The purification of total DNA was performed with DNeasy Tissue
 kits (Qiagen) following the manufacturer’s spin-column protocol for
 insects. Samples were genotyped based on previous genetic studies using
 nine microsatellite markers (Fe7, Fe17, Fy3, Fe19, Fe13, Fy15, Fy12, Fl29,
 and Fy13) and PCR conditions determined in earlier studies (Kulmuni et
 al., 2010; Beresford et al., 2017). Total DNA was amplified with
 polymerase chain reactions (PCR) in Veriti 96-well Thermal Cycler (Applied
 Biosystems) with fluorescent labelling. Genotypes were resolved by
 capillary electrophoresis with a 3730 DNA Analyzer (Applied Biosystems)
 using 500 ROX size standard. Lastly, genotypes were scored with GENEMAPPER
 version 4.0 (Applied Biosystems). As genotypes were compared to samples
 genotyped in an earlier study on the same system (Beresford et al., 2017)
 we used three reference samples of known genotypes in every PCR reaction
 to control for variation potentially introduced by different PCR and DNA
 Analyzer machines.
DOI: 10.15468/dl.uh4r5z
title: Occurrence Download

description: A dataset containing 2803 records in GBIF matching the query:
SELECT
 '455' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= 113.8874202948881
 AND decimalLongitude &lt;= 125.88796183592417
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 2803 records were derived from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002810-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g1jwstqqg
title: Data from: Botany is the root and the future of invasion biology

description: This dataset was used to create Figure 1 within the linked On the Nature
 of Things article. The article describes how botanists have historically
 contributed to the field of invasion biology and why botanists should be
 an important contributor in the coming years. To make this point, we
 compared the relative frequencies of google ngrams containing the words
 'invasive species', 'invasive plants', or the sum of
 frequencies from several different animal taxa including: ‘invasive
 insects’, ‘invasive animals’, ‘invasive fish’, ‘invasive birds’, ‘invasive
 amphibians’, and ‘invasive mammals’ from 1958-2019. We also evaluated
 similar searches that used the words 'exotic',
 'foreign' or 'weed' in the place of
 'invasive'. This dataset contains the results of these searches
 with each row representing a separate year and with each column
 representing a separate search term. Our findings from this dataset
 support our conclusion that plants have been important model systems in
 invasion biology as they are the most highly cited the taxonomic group in
 our search. Results were similar when using 'exotic',
 'foreign', but were an order of magnitude higher when using
 'weed' as this term is widely used in the public vernacular
 outside of the research community. This dataset may be of use to anyone
 interested in the history of invasion biology.
description: Please see Readme file.
DOI: 10.15468/dl.hd2crz
title: Occurrence Download

description: A dataset containing 1497 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Anas formosa",
 "Year 2000-2026"
 ]
}

 The dataset includes 1497 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002813-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vmcvdncs2
title: Source data for: Human monoclonal antibodies against Staphylococcus aureus surface antigens recognize in vitro biofilm and in vivo implant infections

description: Implant-associated Staphylococcus aureus infections are difficult to treat
 because of biofilm formation. Bacteria in a biofilm are often insensitive
 to antibiotics and host immunity. Monoclonal antibodies (mAbs) could
 provide an alternative approach to improve the diagnosis and potential
  treatment of biofilm-related infections. Here we show that mAbs
 targeting common surface components of S. aureus can recognize clinically
 relevant biofilm types. The mAbs were also shown to bind a collection of
 clinical isolates derived from different biofilm-associated infections
 (endocarditis, prosthetic joint, catheter). We identify two groups of
 antibodies: one group that uniquely binds S. aureus in biofilm state and
 one that recognizes S. aureus in both biofilm and planktonic state.
 Furthermore, we show that a mAb recognizing wall teichoic acid (WTA; clone
 4497) specifically localizes to a subcutaneously implanted pre-colonized
 catheter in mice. In conclusion, we demonstrate the capacity of several
 human mAbs to detect S. aureus biofilms in vitro and in vivo.
description: Methods are included in the related preprint manuscript (https://doi.org/10.1101/2021.02.09.429966)
description: The dataset "flow cytometry.zip" contains the
 supporting data (.fsc files) used to analyze binding of monoclonal
 antibodies to <em>Staphylococcus aureus </em>in planktonic
 state using flow cytometry. An .xlsx file containing the samples
 corresponding to each .fsc file is included in each separate
 folder. The dataset "Z stacks confocal.zip"
 contains the supporting data used to analyze binding of monoclonal
 antibodies to <em>Staphylococcus aureus </em>biofilm using
 confocal microscopy. It contains all Z-stacks (.lif files) analyzed in
 this study. The dataset "Mice.zip" contains
 the supporting data used to analyze localization of monoclonal antibodies
 to subcutaneous implants in a mouse model. It contains unprocessed
 SPECT/CT scans (.nii files) of the first set of mice at 24, 72 and 120h
 post injection of [<sup>111</sup>In]In-4497-IgG1 (spcific
 antibody) or [<sup>111</sup>In]In-Palivizumab (ctrl antibody).
 For each scan, this data set also contains volumes of interests (.voi
 files) and corresponding statistics (.voistat files) used for
 analysis. The file "de Vor_data for
 graphs.zip" contains plate reader data used to analyze binding of
 monoclonal antibodies to <em>Staphylococcus aureus
 </em>biofilm and contains all processed data used to generate the
 graphs in the manuscript.
DOI: 10.5061/dryad.866t1g1q6
title: Direct and indirect disturbance impacts in forests

description: Human and natural disturbances are key drivers of change in forest
 ecosystems. Yet, the direct and indirect mechanisms which underpin these
 changes remain poorly understood at the ecosystem level. Here, using
 structural equation modelling across a 150+ year chronosequence, we
 disentangle the direct and indirect effects of major disturbances in a
 temperate forest ecosystem. We show that wildfires, logging and post-fire
 (salvage) logging can affect plant and microbial communities and abiotic
 soil properties both directly and indirectly through plant-soil-microbial
 interactions. We quantified 68 direct and indirect disturbance effects
 across these components, with the majority resulting in ecosystem-wide
 adverse effects. Indirect disturbance effects accounted for 43% of total
 disturbance effects, with some amplifying or partially mitigating direct
 disturbance effects. Overall, human disturbances were associated with more
 negative effects than natural disturbances. Our analyses provide novel
 insights into the multifaceted dynamics of forest disturbances and the
 mechanisms which underpin their relative impacts.
description: Please see https://doi.org/10.1111/ele.13741 for detailed methods.
description: Please see the below table for further detail on provided data<br> Variable (column) Description Bacteria_chao1_0-10cm Chao1 diversity measures Bacteria_chao1_20-30cm Chao1 diversity measures Symbiotrophic_fungi_chao1_0-10cm Chao1 diversity measures Symbiotrophic_fungi_chao1_20-30cm Chao1 diversity measures Saprotrophic_fungi_chao1_0-10cm Chao1 diversity measures Saprotrophic_fungi_chao1_20-30cm Chao1 diversity measures All_fungi_chao1_0-10cm Chao1 diversity measures All_fungi_chao1_20-30cm Chao1 diversity measures Nitrate_0-10cm Nitrate nitrogen (mg/kg) Nitrate_20-30cm Nitrate nitrogen (mg/kg) Phosphorus_0-10cm Phosphorus (colwell) (mg/kg) Phosphorus_20-30cm Phosphorus (colwell) (mg/kg) Potassium_0-10cm Potassium (colwell) (mg/kg) Potassium_20-30cm Potassium (colwell) (mg/kg) Organic.carbon_0-10cm Organic carbon (%) Organic.carbon_20-30cm Organic carbon (%) pH (CaCl2)_0-10cm pH (CaCl2) pH (CaCl2)_20-30cm pH (CaCl2) Acacia (prop) proportion cover Eucalyptus (prop) proportion cover Tree (prop) proportion cover Shrub (prop) proportion cover Treefern (prop) proportion cover Slope Slope (m) Elevation Elevation (m) Time_since_last_disturbance Time since last disturbance (years) No.Fires Number of fires  Clearcut logging 1=yes, 0=no Salvage logging 1=yes, 0=no Thinning 1=yes, 0=no
DOI: 10.5061/dryad.msbcc2fxk
title: Data from: Identifying ‘vital attributes’ for assessing disturbance-recovery potential of seafloor communities

description: Soft-sediment macrofaunal community data used
 in "Identifying ‘vital attributes’ for assessing
 disturbance-recovery potential of seafloor communities" in Ecology
 and Evolution. Data is macrofauna community data from two soft-sediment
 disturbance recovery experiments conducted in the Tvärminne-Hanko
 Archipelago in the Baltic Sea, and Kawau Bay in New Zealand.
description: Methods for data collection are detailed in "Identifying
 ‘vital attributes’ for assessing disturbance-recovery potential of
 seafloor communities" in <em>Ecology and
 Evolution.</em>
DOI: 10.5068/d16q39
title: Mechanisms of reduced interspecific interference between territorial species

description: Interspecific territoriality has complex ecological and evolutionary
 consequences. Species that interact aggressively often exhibit spatial or
 temporal shifts in activity that reduce the frequency of costly
 encounters. We analyzed data collected over a 13-year period on 50
 populations of rubyspot damselflies (Hetaerina spp.) to examine how rates
 of interspecific fighting covary with fine-scale habitat partitioning and
 to test for agonistic character displacement in microhabitat preferences.
 In most sympatric species, interspecific fights occur less frequently than
 expected based on the species’ relative densities. Incorporating
 measurements of spatial segregation and species discrimination into the
 calculation of expected frequencies accounted for most of the reduction in
 interspecific fighting (subtle differences in microhabitat preferences
 could account for the rest). In 23 of 25 sympatric population pairs, we
 found multivariate differences between species in territory microhabitat
 (perch height, stream width, current speed, and canopy cover). As
 predicted by the agonistic character displacement hypothesis, sympatric
 species that respond more aggressively to each other in direct encounters
 differ more in microhabitat use and have higher levels of spatial
 segregation. Previous work established that species with the lowest levels
 of interspecific fighting have diverged in territory signals and
 competitor recognition through agonistic character displacement. In the
 other species pairs, interspecific aggression appears to be maintained as
 an adaptive response to reproductive interference, but interspecific
 fighting is still costly. We now have robust evidence that evolved shifts
 in microhabitat preferences also reduce the frequency of interspecific
 fighting.
description: Data were collected from field observations and experiments (see
 main text for details). Raw data was transcribed and organized into a
 format that could be analyzed by software including Excel and R.
description: The first tab of the Excel file is a "readme" tab with
 notes about the other tabs and column headers.
DOI: 10.5061/dryad.59zw3r26j
title: Data from: Signatures of north-eastern expansion and multiple refugia: Genomic phylogeography of the Pine Barrens Treefrog, Hyla andersonii (Anura: Hylidae)

description: Range fragmentation poses challenges for species persistence over time and
 may be caused by both historical and contemporary processes. We combined
 genomic data, phylogeographic model testing, and paleoclimate niche
 modeling to infer the evolutionary history of the Pine Barrens Treefrog
 (Hyla andersonii), a seepage bog specialist, in eastern North America to
 better understand the historical context of its fragmented distribution.
 We sampled H. andersonii populations across the three disjunct
 regions of the species’ range: Alabama/Florida (AF), the Carolinas (CL),
 and New Jersey (NJ). Phylogenetic relationships within H.
 andersonii were consistent between the nuclear species tree and
 mitochondrial analyses, indicating divergence between AF and CL/NJ
 (Atlantic clade) ~0.9 million years ago and divergence of the NJ clade
 ~0.15 mya. Several predictions of northeastern expansion along the
 Atlantic coast were supported by phylogeographic analyses. Model testing
 using genome-wide SNP data and species distribution models both provided
 evidence for multiple disjunct refugia. This comprehensive phylogeographic
 study of H. andersonii demonstrates a long history of range fragmentation
 within an endemic coastal plain species and highlights the influence of
 historical climate change on the current distribution of species and their
 genetic diversity.
description: Tissue samples were collected by hand from adult frogs and total
 genomic DNA was purified from toe clips. Samples were processed using
 anchored hybrid enrichment (Pseudacris v.1 probe set). Mitochondrial
 genomes were assembled as sequencing 'bycatch'. Nuclear and
 mitochondrial assemblies were separately aligned in MAFFT v.7.023b. Two
 nuclear datasets were generated: one with sequence alignments and one with
 extracted single nucleotide polymorphisms (SNPs). Divergence times were
 estimated in BEAST v.1.10.1 using the mitochondrial alignment. Nuclear
 phylogenetic relationships were estimated in SVDQuartets and ASTRAL. Tests
 for northeastern expansion and estimates of ancestor location, dispersal
 rate, and migration direction were done in PhyloMapper using mitochondrial
 data. The R package 'delimitR' tested phylogeographic models
 using the nuclear SNP data. Species distribution models were also
 generated using Maxent for contemporary and three historical time points;
 however, no GPS coordinates are provided publicly (request directly from
 the corresponding author).
description: ReadMe file included that describes all files. Aligned datasets
 (one mitochondrial and two nuclear) as input files to BEAST, SVDQuarterts,
 and ASTRAL. Input files for Phylomapper and delimitR are also included.
 Only input files for MaxEnt are not included (request directly from the
 corresponding author).