cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q2bvq83nm
title: Genome-wide methylation in the panmictic European eel (Anguilla anguilla)

description: The role of methylation in adaptive, developmental and speciation
 processes has attracted considerable interest, but interpretation of
 results is complicated by diffuse boundaries between genetic and
 non-genetic variation. We studied whole genome genetic and methylation
 variation in the European eel, distributed from subarctic to subtropical
 environments, but with panmixia precluding genetically based local
 adaptation beyond single-generation responses. Overall methylation was
 70.9%, with hypomethylation predominantly found in promoters and first
 exons. Redundancy analyses involving juvenile glass eels showed 0.06% and
 0.03% of the variance at SNPs to be explained by localities and
 environmental variables, respectively, with GO terms of genes associated
 with outliers primarily involving neural system functioning. For CpGs
 2.98% and 1.36% of variance was explained by localities and environmental
 variables. Differentially methylated regions particularly included genes
 involved in developmental processes, with hox clusters featuring
 prominently. Life stage (adult versus glass eels) was the most important
 source of inter-individual variation in methylation, likely reflecting
 both ageing and developmental processes. Demethylation of transposable
 elements relative to pure European eel was observed in European X American
 eel hybrids, possibly representing postzygotic barriers in this system
 characterized by prolonged speciation and ongoing gene flow. Whereas the
 genetic data are consistent with a role of single-generation selective
 responses, the methylation results underpin the importance of epigenetics
 in the life cycle of eels and suggests interactions between local
 environments, development and phenotypic variation mediated by methylation
 variation. Eels are remarkable by having retained eight hox clusters, and
 the results suggest important roles of methylation at hox genes for
 adaptive processes.
DOI: 10.22008/promice/data/ice_discharge/d/v02/jauwia
title: README.txt

description: README. Git hash: 0f04be7b
DOI: 10.22008/promice/data/ice_discharge/d/v02/dc9khw
title: region_coverage.csv

description: Regional coverage. Git hash: 0f04be7b
DOI: 10.22008/promice/data/ice_discharge/d/v02/dguwf1
title: region_D.csv

description: Regional discharge. Git hash: 0f04be7b
DOI: 10.22008/promice/data/ice_discharge/d/v02/koj2g0
title: region_err.csv

description: Regional error. Git hash: 0f04be7b
DOI: 10.22008/promice/data/ice_discharge/d/v02/mrujyh
title: region.nc

description: Regional discharge, coverage, and error. Git hash: 0f04be7b
DOI: 10.22008/promice/data/ice_discharge/d/v02/j82rby
title: sector_coverage.csv

description: Sector coverage. Git hash: 0f04be7b
DOI: 10.22008/promice/data/ice_discharge/d/v02/8w6uxz
title: sector_D.csv

description: Sector discharge. Git hash: 0f04be7b
DOI: 10.22008/promice/data/ice_discharge/d/v02/gsu2te
title: sector_err.csv

description: Sector error. Git hash: 0f04be7b
DOI: 10.5061/dryad.qrfj6q5js
title: Desert tortoise scat microsatellite results

description: Sampling fecal droppings (scat) to genetically identify individual animals
 is an established method for monitoring mammal populations and could be
 highly useful for monitoring reptile populations. Whereas existing
 protocols for obtaining DNA from reptile scat focus on analyses of whole,
 fresh scat deposited during animal handling, the collection of scat
 naturally deposited by reptiles in situ, as required for non-invasive
 population monitoring, requires protocols to extract highly degraded DNA.
 Using surface swabs from such scats can reduce logistical challenges,
 ecological impacts, and zoonotic risks. We report on three related but
 independently designed studies of DNA analyses from scat swabs of
 herbivorous reptiles under natural desert conditions: two free-ranging
 desert tortoise species (Agassiz's desert tortoise, Gopherus
 agassizii, California, US, and Morafka's desert tortoise, G.
 morafkai, Arizona, US) and the common chuckwalla (Sauromalus atar)
 (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise
 species with the same set of 16 microsatellites and chuckwalla samples
 with four mtDNA markers; studies also varied in swab preservation medium
 and DNA extraction method. Microsatellite amplification success, defined
 as ≥9 loci with amplification varied by species: 15% of samples for
 Agassiz's desert tortoise and 42% Morafka's desert tortoise. For
 chuckwallas, we successfully amplified and sequenced 50% of samples.
 Fragments up to 400 bp for tortoises and 980 bp for chuckwallas were
 successfully recovered from scat swab samples. This study demonstrates
 that genotypes can successfully be obtained from swabs of herbivorous
 reptile scat collected in the field under natural environmental conditions
 and emphasizes that repeat amplifications are necessary for estimating
 population genetic parameters.
DOI: 10.22008/promice/data/ice_discharge/d/v02/c0mooh
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: 0f04be7b
DOI: 10.22008/promice/data/ice_discharge/d/v02/biuqvy
title: gate_coverage.csv

description: Gate coverage. Git hash: e461cbb1
DOI: 10.15468/dl.8ruzng
title: Occurrence Download

description: A dataset containing 214 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Asia",
 "Country is Japan",
 "TaxonKey is Morchella"
 ]
}

 The dataset includes 214 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003154-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22008/promice/data/ice_discharge/d/v02/ysvxiw
title: gate_D.csv

description: Gate discharge. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/b7zpho
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/lt79ou
title: gate_err.csv

description: Gate errors. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/pfbdys
title: GIS_coverage.csv

description: Greenland coverage. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/t6iaw9
title: GIS_D.csv

description: Greenland discharge. Git hash: e461cbb1
DOI: 10.5061/dryad.6hdr7sr3p
title: Dodonaphy - a Software using Hyperbolic Space for Bayesian Phylogenetic Inference

description: Bayesian inference for phylogenetics is a gold standard for computing
 distributions of phylogenies. It faces the challenging problem of moving
 throughout the high-dimensional space of trees. However, hyperbolic space
 offers a low dimensional representation of tree-like data. In this paper,
 we embed genomic sequences into hyperbolic space and perform hyperbolic
 Markov Chain Monte Carlo for Bayesian inference. The posterior probability
 is computed by decoding a neighbour joining tree from proposed embedding
 locations. We empirically demonstrate the fidelity of this method on eight
 data sets. The sampled posterior distribution recovers the splits and
 branch lengths to a high degree. We investigated the effects of curvature
 and embedding dimension on the Markov Chain's performance. Finally,
 we discuss the prospects for adapting this method to navigate tree space
 with gradients. This software embeds phylogenetic taxa in hyerbolic space
 to perform Bayesian inference. Version 1.0.0 includes a Markov Chain Monte
 Carlo (MCMC) that we compared to the state-of-art on eight datasets
 (previously published elsewhere). This package is implemented in Python3.9
 with a simle command line interface provided.
DOI: 10.22008/promice/data/ice_discharge/d/v02/wv3nc1
title: GIS_err.csv

description: Greenland error. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/hh6pk1
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: e461cbb1
DOI: 10.5061/dryad.x95x69pms
title: The use of environmental DNA to monitor impacted coastal estuaries

description: Environmental DNA (eDNA) metabarcoding is increasingly being used to
 assess community composition in coastal ecosystems. In this study, we
 chose to examine temporal and spatial changes in the aquatic community of
 Manly Lagoon – one of the most heavily developed and polluted estuaries in
 eastern Australia. Based on metabarcoding of the 16S mitochondrial gene
 (for fish) and the 18S nuclear gene (for macroinvertebrates), we
 identified seasonal differences in fish and macroinvertebrate community
 composition as well as species richness, which correlated, in some cases,
 with environmental parameters (sea surface temperature and freshwater
 input). Moreover, given the greater taxonomic resolution of fish versus
 macroinvertebrate assignments, we identified several known migratory fish
 species of management importance that contributed significantly to the
 overall patterns observed. Overall, our data support the use of eDNA
 metabarcoding to track fish assemblages shifting in response to
 environmental drivers in polluted estuaries with increased sampling and
 consultation with historical data.
description: We here provide the raw sequencing data files in fastq format
 along with an excel spreadsheet listing the sequencing run, assay, sample
 ID, forward and reverse tags, as well as forward and reverse primers
 required for demultiplexing and quality filtering ("Sequencing run,
 assay, sample ID, tags, and primers.xlsx") used in the following
 paper: DiBattista, J.D., Riley, I.J., Fowler, A.M.,
 Reader, S., Hay, A., Parkinson, K., and Hobbs, J.-P.A. (in press) The use
 of environmental DNA to monitor impacted coastal estuaries. Marine
 Pollution Bulletin.
 https://doi.org/10.1016/j.marpolbul.2022.113860
DOI: 10.22008/promice/data/ice_discharge/d/v02/unkiri
title: region_coverage.csv

description: Regional coverage. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/2agpwl
title: region_D.csv

description: Regional discharge. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/x37mjt
title: region_err.csv

description: Regional error. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/wpaeil
title: region.nc

description: Regional discharge, coverage, and error. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/i2hqip
title: sector_coverage.csv

description: Sector coverage. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/0lcfxl
title: sector_D.csv

description: Sector discharge. Git hash: e461cbb1
DOI: 10.5284/1139297
title: Excavation at Clifford's Tower

description: null
DOI: 10.22008/promice/data/ice_discharge/d/v02/laif8e
title: sector_err.csv

description: Sector error. Git hash: e461cbb1
DOI: 10.22008/promice/data/ice_discharge/d/v02/h1ckoj
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: e461cbb1
DOI: 10.5061/dryad.5dv41ns88
title: Arbuscular mycorrhizal fungi improve the growth and drought tolerance of Cinnamomum migao by enhancing physio-biochemical responses

description: Drought is the main limiting factor for plant growth in karst
 areas with a fragile ecological environment. Cinnamomum
 migao H. W. Li is an endemic medicinal woody plant present in the
 karst areas of southwestern China, and it is endangered due to poor
 drought tolerance. Arbuscular mycorrhizal fungi (AMF) are known
 to enhance the drought tolerance of plants. However, few studies
 have examined the contribution of AMF in improving the drought
 tolerance of Cinnamomum
 migao seedlings. Therefore, we conducted a series of
 experiments to determine whether
 a single inoculation and coinoculation of AMF
 (Claroideoglomus lamellosum and Claroideoglomus etunicatum)
 enhanced the drought tolerance of Cinnamomum
 migao. Further, we compared the effects of single inoculation and
 coinoculation with different inoculum sizes (20, 40, 60,
 and 100 g; four replicates per treatment) on mycorrhizal
 colonization rate, plant growth, photosynthetic parameters, antioxidant
 enzyme activity, and malondialdehyde (MDA) and osmoregulatory substance
 contents. The results showed that compared with
 nonmycorrhizal plants, AMF colonization
 significantly improved plant growing status; net photosynthetic
 rate; superoxide dismutase, catalase, and
 peroxidase activities; and soluble sugar, soluble
 protein, and proline contents. Further, AMF colonization
 increased relative water content and reduced MDA content in
 cells. These combined cumulative effects of
 AMF symbiosis ultimately enhanced the drought
 tolerance of seedlings and were closely related
 to the inoculum size. With an increase in inoculum size, the
 growth rate and drought tolerance of plants first increased and
 then decreased. The damage caused by drought stress could be reduced by
 inoculating 40–60 g of AMF, and the effect of co-inoculation was
 significantly better than that of single inoculation at 60 g of AMF, while
 the effect was opposite at 40 g of AMF. Additionally, the interaction
 between AMF and inoculum sizes had a significant effect
 on drought tolerance. In conclusion, the inoculation of the AMF
 Claroideoglomus lamellosum and Claroideoglomus
 etunicatum improved photosynthesis, activated
 antioxidant enzymes, regulated cell osmotic state, and
 enhanced the drought tolerance of Cinnamomum
 migao, enabling its growth in fragile ecological environments.
DOI: 10.22008/promice/data/ice_discharge/d/v02
title: Greenland Ice Sheet solid ice discharge from 1986 through last month: Discharge

description: Greenland Ice Sheet solid ice discharge from 1986 through last month Recent update includes PROMICE Ice Velocity (200m resolution), and baseline thickness has been updated to the 2020 DEM from Winstrup et al in review see github issue: #44 and related datasets. Before using the data you should check for any open/active issue tagged WARNING
DOI: 10.15468/dl.5nebhx
title: Occurrence Download

description: A dataset containing 525417 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Riparia diluta (Sharpe & Wyatt, 1893), Riparia riparia (Linnaeus, 1758), Irena puella (Latham, 1790), Lanius borealis Vieillot, 1808, Lanius bucephalus Temminck & Schlegel, 1845, Lanius collurio Linnaeus, 1758, Lanius collurioides Lesson, 1831, Lanius cristatus Linnaeus, 1758, Lanius excubitor Linnaeus, 1758, Lanius giganteus Przevalski, 1887, Lanius isabellinus Hemprich & Ehrenberg, 1833, Lanius minor Gmelin, 1788, Lanius phoenicuroides (Schalow, 1875), Lanius schach Linnaeus, 1758, Lanius sphenocercus Cabanis, 1873, Lanius tephronotus (Vigors, 1831), Lanius tigrinus Drapiez, 1828, Lanius vittatus Valenciennes, 1826, Minla cyanouroptera (Hodgson, 1837), Actinodura egertoni Gould, 1836, Actinodura morrisoniana Ogilvie-Grant, 1906, Actinodura nipalensis (Hodgson, 1836), Actinodura ramsayi Walden, 1875, Actinodura souliei Oustalet, 1897, Minla strigula (Hodgson, 1837), Actinodura waldeni Godwin-Austen, 1874, Cutia nipalensis Hodgson, 1837, Garrulax canorus (Linnaeus, 1758), Garrulax castanotis (Ogilvie-Grant, 1899), Garrulax leucolophus (Hardwicke, 1816), Garrulax maesi (Oustalet, 1890), Garrulax merulinus Blyth, 1851, Garrulax monileger (Hodgson, 1836), Garrulax strepitans Blyth, 1855, Garrulax taewanus Swinhoe, 1859, Garrulax striatus (Vigors, 1831), Heterophasia auricularis (Swinhoe, 1864), Heterophasia capistrata (Vigors, 1831), Heterophasia desgodinsi (Oustalet, 1877))",
 "Geometry POLYGON((73.5208333 16.6625,135.0791667 16.6625,135.0791667 53.5541667,73.5208333 53.5541667,73.5208333 16.6625))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is one of (China, Hong Kong, Macao, Chinese Taipei)"
 ]
}

 The dataset includes 525417 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017425-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.36qzng
title: Occurrence Download

description: A dataset containing 13417 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Arthrobacter Conn & Dimmick, 1947"
 ]
}

 The dataset includes 13417 records from 332 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017458-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3fuuac
title: Occurrence Download

description: A dataset containing 1568025 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Motacilla flava Linnaeus, 1758)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 1568025 records from 2704 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017432-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10419310
title: Sound-Frameworks: James Wilkie - Survey Interview

description: This is a transcription of a survey interview that took place within the project Sound-Frameworks: Collaborative Frameworks for Integrating Sound Within Urban Design and Planning Processes.

Sound-Frameworks is an action-led research project that explores the role of sound in urban design and city planning. The project is led by the artist and researcher Dr. Sven Anderson and hosted by Theatrum Mundi, a non-profit organisation that expands the craft of city-making through collaboration with artists.

Central to this project is a focus on how urban sonic experience can serve as a driver for design in the public realm. The public realm constitutes the integral connective tissue that defines the contemporary cityscape, within which different individuals, communities and institutions engage with each other through cooperation and conflict. Sound has remained a neglected dimension of this domain, generally coming into consideration only within late stages of design through efforts to ameliorate the impact of environmental noise. As the densification of urban territories accelerates, the role of sonic experience as an essential factor to be addressed by urban designers must be reassessed.

Sound-Frameworks explores new methodologies for integrating sound in urban design through the production of three inter-related resources:

1. A sound in practice survey2. A publication on best practice guidelines in this field3. An online tool to guide the integration of sound in the design of the public realm

Drawing from environmental acoustics, spatial planning, contemporary sound studies, the project initiates a framework to extend regional, national and international objectives for integrated city planning and contribute to public realm initiatives in Europe and beyond.

Sound-Frameworks has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101032632.

Sound-Frameworks is hosted by Theatrum Mundi (UK) and supported by partnerships with Arup (UK), UrbanIdentity (CH), Struer Kommune (DK), the University of Oxford Faculty of Music (UK) and the Sound Studies Lab at the University of Copenhagen (DK). 

Sound-Frameworks: https://www.soundframeworks.orgTheatrum Mundi: https://www.theatrum-mundi.orgSven Anderson: https://www.svenanderson.net
DOI: 10.15468/dl.jj4nec
title: Occurrence Download

description: A dataset containing 351 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Meghimatium pictum (Stoliczka, 1873)"
 ]
}

 The dataset includes 351 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012041-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.equnpm
title: Occurrence Download

description: A dataset containing 3039206 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is Tanzania, United Republic of",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3039206 records from 1351 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012027-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8f8h5y
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Talismania antillarum (Goode & Bean, 1896)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((36.2225 24.1647,35.9648 24.4806,35.9648 19.8496,37.7519 19.8496,37.7005 20.2556,37.7935 21.209,37.3891 21.7756,37.3588 22.2459,36.8499 22.7968,36.6611 23.2461,36.1736 23.4033,36.31 23.7463,36.2225 24.1647))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012040-250525065834625/datasets/export for details.
DOI: 10.15468/dl.gp23mt
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "DatasetKey is one of (INSDC Sequences, Natural History Museum (London) Collection Specimens, UWIZM Molluscs, International Barcode of Life project (iBOL), Terrestrial Mollusc Survey of Trinidad & Tobago from 2014-2017)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ovachlamys fulgens (Gude, 1900)"
 ]
}

 The dataset includes 22 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012042-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.