cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18383591
title: Compendium of R Scripts and Data for Lidar Feature Classification Accuracy Assessment

description: Archaeo-Lidar-Error-Quant.zip

Data and R code for assessing the relationship between underlying lidar data quality and archaeological feature classification accuracy. Logistic regression models (created in R) test whether data quality, as measured by the Digital Feature Model Confidence Map presented by Štular et al. (2021, correlates with points sampled along correctly or incorrectly identified archaeological features. Archaeological features were detected through lidar-based prospection and validated by pedestrian survey. The Confidence Map is a classification of each pixel in a DFM into six categories based on topographic and point-cloud characteristics, with 1 representing poor quality and 6 representing high quality data.

There are three folders:



R-scripts: this folder houses the R scripts used to run the multinomial logistic regression models that tested statistical relationships. The naming convention is MultinomialLogit_[buffer distance on feature line]_[% of buffer area sampled with points] (e.g., MultinomialLogit_1m_33p.R)

results: this folder houses the analysis results as .jpg and .html files. Models name, buffer distance, and sample percentage are indicated by the file name.

data: this folder houses the point data used for analysis as .csv files. Each sheet is one buffer-sample pairing, for example SamplePoints_1m_33percent.csv houses all points from the 1m buffer with 33% pixel sample.


Note: original archaeological feature vectors are not available to the public at the moment, as it is sensitive cultural heritage information. Please follow the Small Cycladic Islands Project (https://smallcycladicislandsproject.org/) for more information and updates on data availability.

The primary dataset used for analysis in published material is the 1m buffer & 33% pixel sample dataset.

DFM-Creation-and-Visualization.zip

The "DFM" and "Viz" folders store the R and Python Notebook (.ipynb) files that, respectively, were used to create original Digital Feature Models and their visualization suites. DFM creation relies on the lidR R package and the Visualizations requires ArcPy and the Relief Visualization Toolkit. File paths stored in the scripts are not universal and will require modification to function.
DOI: 10.5061/dryad.4xgxd255s
title: Evidence that more than a third of Paleozoic articulate brachiopod genera (Strophomenata) lived infaunally

description: The Strophomenata, which includes two large orders, the Strophomenida and
 Productida, was the largest group of Paleozoic brachiopods. Nearly all
 uncemented strophomenatans possessed an unusual concave brachial valve.
 Most of these animals have been considered to have lived epifaunally, but
 had they rested on the sea floor, not only would they have faced intense
 predation, but their physical instability would have been fatal. I
 conclude that nearly all strophomenatans, like similar, concavo-convex
 pectinid bivalves, lived infaunally by ejecting water to create a pit into
 which they descended, to be protected by sediment covering the concave
 valve. Strophomenatans have been discovered with this sediment preserved
 in place. If exhumed and turned upside down, a strophomenatan could have
 righted itself by squirting water. Many productides had anchoring spines,
 and some had hinge areas with stabilizing flanges. Small spines on the
 brachial valves of some productides served to trap disguising sediment.
 Evolutionary loss of hinge teeth within both the Strophomenida and
 Productida reduced the friction of valve clapping. Partly because of their
 slender shape, strophomenides were typically more vulnerable to exhumation
 than productides and ejected water less effectively. Strophomenides would
 also have been less adept than productides at righting themselves. The
 virtual disappearance of the strophomenides during the Devonian can be
 attributed to their vulnerability to intensifying benthic bulldozing and
 predation. The success of the productides during the late Paleozoic can be
 attributed to their relatively deep sequestration in the sediment and
 ability to right themselves and reburrow rapidly when exhumed and
 overturned. 
description: The data are from measurements made by the author for specimens
 at the National Museum of Natural History.
DOI: 10.5061/dryad.3tx95x6c2
title: Multiple abiotic and biotic drivers of long-term wood decomposition within and among species in semiarid inland dunes: a dual role for stem diameter

description: This is wood decomposition data conducted in an semiarid inland dune
 including mass loss, initial wood traits and k values of combinations
 between five diameter classes and four shrub species under
 different treatments including UV and litter position. We found
 that after 34 months of in situ incubation, the mass loss of buried woody
 litters was three times faster than those of suspended and
 surface woody litters (53.5 ± 2.7 %, 17.0 ± 1.0 % and 14.4± 1.2
 %, respectively). In surface and suspended positions, litter
 decomposition rates were almost equally low and most mass loss
 was during the first two years, when bark was still attached and UV
 radiation had no significant effect on woody litter mass loss.
    
description: The data were collected by in situ decomposition experiment over
 34 months of incubation. In a field manipulation experiment, we
 investigated the relative importance of litter position (sand burial
 vs surface vs suspended above the surface), UV radiation (block vs pass),
 and stem diameter class (&lt;2, 2-4, 4-8, 8-13, and 13-20 mm) on the
 mass loss of woody litters of four shrub species in an inland dune
 ecosystem in northern China. Initial bark and wood traits including bark
 thickness, bark dry matter content, wood nitrogen concentration, wood dry
 matter content, wood density were measured using standardized methods in
 the laboratory.  The <em>k</em> value for wood decomposition
 were calcuated by ordinary nonlinear regression using Olson's
 (1963) negative exponential model.
DOI: 10.15468/dl.4r3bhx
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gonorynchus gonorynchus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 10 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002218-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sbcc2fr34
title: High genomic diversity in the bank vole at the northern apex of a range expansion: the role of multiple colonizations and end-glacial refugia

description: The history of repeated northern glacial cycling and southern climatic
 stability has long dominated explanations for how genetic diversity is
 distributed within temperate species in Eurasia and North America.
 However, growing evidence indicates the importance of cryptic refugia for
 northern colonization dynamics. An excellent geographic region to assess
 this is Fennoscandia, where recolonization at the end of the last
 glaciation was restricted to specific routes and temporal windows. We used
 genomic data to analyze genetic diversity and colonization history of the
 bank vole (Myodes glareolus) throughout Europe (&gt; 800 samples) with
 Fennoscandia as the northern apex. We inferred that bank voles colonized
 Fennoscandia multiple times by two different routes; with three separate
 colonizations via a southern land-bridge route deriving from a
 ‘Carpathian’ glacial refugium and one via a north-eastern route from an
 ‘Eastern’ glacial refugium near the Ural Mts. Clustering of genome-wide
 SNPs revealed tremendous diversity in Fennoscandia, with eight genomic
 clusters: three of Carpathian origin and five Eastern. Time estimates
 revealed that the first of the Carpathian colonizations occurred before
 the Younger Dryas (YD), meaning that the first colonists survived the YD
 in Fennoscandia. Results also indicated that introgression between bank
 and northern red-backed voles (Myodes rutilus) took place in Fennoscandia
 just after end-glacial colonization. Therefore, multiple colonizations
 from the same and different cryptic refugia, temporal and spatial
 separations and interspecific introgression have shaped bank vole genetic
 variability in Fennoscandia. Together, these processes drive high genetic
 diversity at the apex of the northern expansion in this model species.
description: <strong>Genotype information for 809 individuals (6078
 SNP)</strong> Input for population genomic
 analyses (SNP after quality filtering and outlier loci removal).
 Variant Call Format file SNP.vcf.zip
DOI: 10.15468/dl.cetmrq
title: Occurrence Download

description: A dataset containing 140 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus californicus"
 ]
}

 The dataset includes 140 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002219-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.931zcrjgk
title: Separable gain control of ongoing and evoked activity in the visual cortex by serotonergic input

description: Controlling gain of cortical activity is essential to modulate weights
 between internal ongoing communication and external sensory drive. Here,
 we show that serotonergic input has separable suppressive effects on the
 gain of ongoing and evoked visual activity. We combined optogenetic
 stimulation of the dorsal raphe nucleus (DRN) with wide-field calcium
 imaging, extracellular recordings, and iontophoresis of serotonin (5-HT)
 receptor antagonists in the mouse primary visual cortex. 5-HT1A receptors
 promote divisive suppression of spontaneous activity, while 5-HT2A
 receptors act divisively on visual response gain and account for
 normalization of population responses over a range of visual contrasts in
 awake and anesthetized states. Thus, 5-HT input provides balanced but
 distinct suppressive effects on ongoing and evoked activity components
 across neuronal populations. Imbalanced 5-HT1A/2A activation, either
 through receptorspecific drug intake, genetically predisposed irregular
 5-HT receptor density, or change in sensory bombardment may enhance
 internal broadcasts and reduce sensory drive and vice versa.
description: Data are recorded from a series of optogenetic experiments
 combined with wide-field calcium imaging and multi-unit electrophysiology
 from the visual cortex of ePetCre mice in the anesthetized and the awake
 state. Also, in two sets of experiments, 5-HT1A and 5-HT2A receptors were
 blocked in vivo via iontophoretic application of these receptors antibody
 in the visual cortex. Traces of all the data that used to produce the
 figures in the manuscript are provided under the name of that figure. For
 details of the experimental paradigm please read the method section of the
 manuscript.
description: Traces of all the data that used to produce the figures in the
 manuscript are provided under the name of that figure. For details of the
 experimental paradigm please read the method section of the
 manuscript.
DOI: 10.5066/p1utdsdt
title: Maps of earthquake ground motions for the 2009 NEHRP Recommended Seismic Provisions and the 2010 ASCE/SEI 7 Standard

description: For designing buildings and other structures to safely resist earthquakes, the 2009 National Earthquake Hazards Reduction Program (NEHRP) Recommended Seismic Provisions and the 2010 American Society of Civil Engineers, Structural Engineering Institute (ASCE/SEI) 7 Standard contain maps of Risk-Targeted Maximum Considered Earthquake (MCER) spectral response accelerations, Maximum Considered Earthquake Geometric Mean (MCEG) peak ground accelerations, and long-period transition periods (TL). The MCER ground motions are also in the 2013 ASCE/SEI 41 Standard and the 2012 and 2015 editions of the International Building Code. The MCER, MCEG, and TL maps are derived from the U.S. Geological Survey (USGS) National Seismic Hazard Models and are provided in this data release in portable document format (PDF) and Geographic Information System (GIS) formats. The numbering used on the PDF maps is the same as in the above documents for cross-reference purposes. Values from these maps are typically obtained via the USGS Seismic Design Web Services. Please see the "Related External Resources" below for links to the building code reference documents, the USGS National Seismic Hazard Models used, and the corresponding USGS web services.

The underlying gridded data for the MCER and MCEG maps can be obtained from the U.S. Geological Survey data release: Gridded earthquake ground motions for the 2009 NEHRP Recommended Seismic Provisions and 2010 ASCE/SEI 7 Standard: U.S. Geological Survey data release, https://doi.org/10.5066/P90R85M7.
DOI: 10.5061/dryad.6hdr7sqx2
title: Data from: Transformation of measurement uncertainties into low-dimensional feature vector space

description: Advances in technology allow the acquisition of data with high spatial and
 temporal resolution.  These datasets are usually accompanied by
 estimates of the measurement uncertainty, which may be spatially or
 temporally varying and should be taken into consideration when making
 decisions based on the data.  At the same time, various
 transformations are commonly implemented to reduce the dimensionality of
 the datasets for post-processing, or to extract significant features.
 However, the corresponding uncertainty is not usually represented in the
 low-dimensional or feature vector space.  A method is proposed
 that maps the measurement uncertainty into the equivalent low-dimensional
 space with the aid of approximate Bayesian computation, resulting in a
 distribution that can be used to make statistical inferences. The method
 involves no assumptions about the probability distribution of the
 measurement error and is independent of the feature extraction process as
 demonstrated in three examples. In the first two examples Chebyshev
 polynomials were used to analyse structural displacements and soil
 moisture measurements; while in the third, principal component analysis
 was used to decompose global ocean temperature data. The uses of the
 method range from supporting decision making in model validation or
 confirmation, model updating or calibration and tracking changes in
 condition, such as the characterisation of the El Niño Southern
 Oscillation. 
description: Please see uploaded ReadMe file.
DOI: 10.5061/dryad.4mw6m9073
title: Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river

description: Environmental DNA (eDNA) has rapidly emerged as a promising biodiversity
 monitoring technique, proving to be a sensitive and cost‐effective method
 for species detection. Despite the increasing popularity of eDNA, several
 questions regarding its limitations remain to be addressed. We
 investigated the effect of sampling me‐ dium and time, and preservation
 methods, on fish detection performance based on eDNA metabarcoding of
 neotropical freshwater samples. Water and sediment sam‐ ples were
 collected from 11 sites along the Jequitinhonha River, Southeastern
 Brazil; sediment samples were stored in ethanol, while the same amounts of
 water per sam‐ ple (3 L) were stored in a cool box with ice, as well as by
 adding the cationic surfactant benzalkonium chloride (BAC). Sediment and
 water samples yielded a similar amount of fish MOTUs (237 vs. 239 in the
 first sampling event, and 153 vs. 142 in the second sampling event). Water
 stored in ice provided better results than those preserved in BAC (239 and
 142 vs. 194 and 71 MOTUs). While documenting the effectiveness of eDNA
 surveys as practical tools for fish biodiversity monitoring in poorly
 accessible areas, we showed that keeping water samples cooled results in
 greater eDNA recovery and taxon detection than by adding cationic
 surfactants (BAC) as sample pre‐ servatives. Furthermore, by comparing two
 sets of samples collected from the same locations at a 3‐week interval, we
 highlight the importance of conducting multiple sampling events when
 attempting to recover a realistic picture of fish assemblages in lotic
 systems.
DOI: 10.5061/dryad.cnp5hqc24
title: Positive and negative interactions jointly determine the structure of Müllerian mimetic communities

description: Negative and positive ecological interactions have opposite effects on the
 structure of ecological communities, in particular in terms of ecological
 similarity among interacting species. In nature, species belonging to the
 same guild often interact in both negative and positive ways, yet the
 interplay between interactions of different kinds in intraguild community
 dynamics remains poorly understood. Müllerian mimetic communities are
 particularly suited for investigating this interplay because positive
 (mutualistic mimicry) and negative (competition for trophic resource and
 micro-habitat) interactions are relatively easy to identify. Empirical
 research has shown that the combination of competition and mutualistic
 mimicry does not necessarily drive convergence along all dimensions of the
 ecological niche, but the determinants of such mixed result are unknown.
 Here, we analyze the structure of Müllerian mimetic communities simulated
 with an agent-based model. We show that mutualistic mimicry favours
 ecological similarity on dimensions along which similarity favours
 fine-scale co-occurrence. Co-mimetic species use similar micro-habitats,
 but do not necessarily use similar resources. Heterogeneity of resources
 among micro-habitats is necessary for ecological similarity on resource
 use among co-mimetic species to occur. We therefore highlight the
 importance of fine-scale co-occurrence if we are to understand how
 positive and negative interactions structure ecological communities.
  
description: Code Julia Code to run simulations and to
 produce the raw data: the characteristic of each individual (species;
 morph; resource used; micro-habitat used) See the README.txt file associated
 with the code for installation procedure.
DOI: 10.5061/dryad.2rbnzs7jf
title: Worldwide bird assemblages across urban-wildland gradients

description: We gathered presence/absence and abundance data from published studies and
 reports for 319 well-characterized assemblages spanning 50 cities from
 Africa, Australia, Europe, North America and South America. We focused on
 cities with comparable survey data within urban habitats and in nearby
 natural habitat. The final dataset contains almost 10,000 records for
 1507bird species, 66 of which are introduced (non-native) in at least one
 study region. Species abundance per unit area or unit time were available
 for 269 assemblages from 42 cities, comprising 1353 species. Following
 Newbold et al. (2015), we used published habitat descriptions to
 classify the intensity of human use in urban habitats
 for each assemblage: (1) highly urbanised environments mainly contain
 densely packed buildings with vegetation scarce or absent; (2) moderately
 urbanised environments are residential areas with single-family houses and
 associated gardens; and (3) little-urbanised environments have few
 buildings and abundant vegetation (e.g. urban parks). The habitats outside
 the city were assigned to either natural vegetation or rural habitat based
 on the description of the habitat given in the source paper. Standardised
 survey methods were used across habitats within each region.
description: We gathered presence/absence and abundance data from published studies and reports to characterize avian assemblages. The survey method varied across studies, but the same method was used for each habitat within a particular region, making data comparable using appropriate models.
DOI: 10.5061/dryad.76hdr7ssq
title: MHC variation is similar in little brown bats before and after white-nose syndrome outbreak

description: White-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus
 destructans (Pd), has driven alarming declines in North American
 hibernating bats, such as little brown bat (Myotis lucifugus). During
 hibernation, infected little brown bats are able to initiate anti-Pd
 immune responses, indicating pathogen-mediated selection on the major
 histocompatibility complex (MHC) genes. However, such immune responses may
 not be protective as they interrupt torpor, elevate energy costs, and
 potentially lead to higher mortality rates. To assess whether WNS drives
 selection on MHC genes, we compared the MHC DRB gene in little brown bats
 pre- (Wisconsin) and post- (Michigan, New York, Vermont, and Pennsylvania)
 WNS (detection spanning 2014-2015). We genotyped 131 individuals and found
 45 nucleotide alleles (27 amino acid alleles) indicating a maximum of 3
 loci (1-5 alleles per individual). We observed high allelic admixture and
 a lack of genetic differentiation both among sampling sites and between
 pre- and post-WNS populations, indicating no signal of selection on MHC
 genes. However, post-WNS populations exhibited decreased allelic richness,
 reflecting effects from bottleneck and drift following rapid population
 declines. We propose that mechanisms other than adaptive immunity are more
 likely driving current persistence of little brown bats in affected
 regions.
DOI: 10.5061/dryad.hhmgqnkd3
title: Gradients in richness and turnover of a forest passerine’s diet prior to breeding: a mixed model approach applied to faecal metabarcoding data

description: Little is known about the dietary richness and variation of generalist
 insectivorous species, including birds, due primarily to difficulties in
 prey identification. Using faecal metabarcoding we provide the most
 comprehensive analysis of a passerine’s diet to date, identifying the
 relative magnitudes of biogeographic, habitat and temporal trends in the
 richness and turnover in diet of Cyanistes caeruleus (blue tit) along a
 39-site, 2° latitudinal transect in Scotland. Faecal samples were
 collected during 2014-15 from adult birds roosting in nestboxes
 prior to nest building. DNA was extracted from 793 samples and we
 amplified COI and 16S minibarcodes. We identified 432 molecular
 operational taxonomic units (MOTUs) that correspond to putative dietary
 items. Most dietary items were rare, with Lepidoptera being the most
 abundant and taxon-rich prey order. We present a novel statistical
 approach for estimation of gradients and inter-sample variation in
 taxonomic richness and turnover using a generalised linear mixed model. We
 discuss the merits of this approach over existing tools and present new
 theory and methods for model-based estimation of repeatability.
 We find that dietary richness increases significantly as spring advances,
 but changes little with elevation, latitude or local tree composition. In
 comparison, dietary composition exhibits significant turnover along
 temporal and spatial gradients and among sites. Our study shows the
 promise of faecal metabarcoding for inferring the macroecology of food
 webs, but we also highlight the challenge posed by contamination and make
 recommendations of laboratory and statistical practices to
 minimise its impact on inference.