cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1g1jwsv0v
title: Data from: A warmer environment can reduce sociability in an ectotherm

description: The costs and benefits of being social vary with environmental conditions,
 so individuals must weigh the balance between these trade-offs in response
 to changes in the environment. Temperature is a salient environmental
 factor that may play a key role in altering the costs and benefits of
 sociality through its effects on food availability, predator abundance,
 and other ecological parameters. In ectotherms, changes in temperature
 also have direct effects on physiological traits linked to social
 behaviour, such as metabolic rate and locomotor performance. In light of
 climate change, it is therefore important to understand the potential
 effects of temperature on sociality. Here, we took advantage of a ‘natural
 experiment’ of threespine sticklebacks from contrasting thermal
 environments in Iceland: geothermally warmed water bodies (warm habitats)
 and adjacent ambient-temperature water bodies (cold habitats) that were
 either linked (sympatric) or physically distinct (allopatric). We first
 measured the sociability of wild-caught adult fish from warm and cold
 habitats after acclimation to a low and a high temperature. At both
 acclimation temperatures, fish from the allopatric warm habitat were less
 social than those from the allopatric cold habitat, whereas fish from
 sympatric warm and cold habitats showed no differences in sociability. To
 determine whether differences in sociability between thermal habitats in
 the allopatric population were heritable, we used a common garden breeding
 design where individuals from the warm and the cold habitat were reared at
 a low or high temperature for two generations. We found that sociability
 was indeed heritable but also influenced by rearing temperature,
 suggesting that thermal conditions during early life can play an important
 role in influencing social behaviour in adulthood. By providing the first
 evidence for a causal effect of rearing temperature on social behaviour,
 our study provides novel insights into how a warming world may influence
 sociality in animal populations.
DOI: 10.5061/dryad.ttdz08m2f
title: Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping

description: Genetic research is a key component to modern wildlife conservation, but
 it is contingent on the collection of reliable and high-quality genetic
 samples. Invasive genetic sampling techniques have potential to negatively
 impact individuals, which may be prohibitive when working with threatened
 and endangered species. Prior to sample collection, project managers must
 try to balance the negative impact on individuals included in the study
 with the demand for DNA and the difficulty of obtaining samples. Although
 established methods for blood and tissue collection in reptiles meet the
 need for high-quantity and quality DNA, they inherently require longer
 handling times and more skill to obtain. Thus, non-invasive DNA collection
 methods, such as cloacal swabs, may be preferred when animal welfare is a
 priority. Cloacal swabs are quicker, easier, require less training and
 reduce handling time. To evaluate cloacal swabbing as an alternative to
 collecting blood, we obtained both cloacal and blood swabs. We extracted
 DNA from cloacal and blood cells that were collected from 23 Timber
 Rattlesnakes (Crotalus horridus). We assessed DNA by purity (A260/A280),
 concentration, and microsatellite genotyping. Our results show
 high-quality DNA can be obtained from both cloacal swabs and blood
 samples, but quality and concentration of DNA was significantly lower from
 cloacal swabs. Further, degradation and contamination affects the
 performance of cloacal DNA when compared to blood DNA in
 microsatellite-based genotyping. Although we recommend collecting blood
 samples whenever possible to obtain the highest-quality DNA, cloacal swabs
 represent a viable alternative for genetic sampling when using
 microsatellite loci as genetic markers.
description: DNA and microsatellite summary data and code used for
 analysis.
description: Data analyzed using R.
DOI: 10.15463/3nbjsdbajwqr3fsq
title: XML-TEI zum Liv-, est- und kurländischen Urkundenbuch: Band 4, 1. Abteilung: 1394-1413

description: Im Rahmen des Projekts zur kritischen Edition der Bände I 15 (1484–1488) und I 16 (1489–1494) des „Liv-, Est- und Kurländischen Urkundenbuchs“ werden von sämtlichen Bänden, sowohl den neuen als auch den alten, durchsuchbare PDF-Dateien mit Digitalisaten und Volltexten wie auch Forschungsdaten im Format XML-TEI hergestellt.
description: Das XML-TEI wurde durch die Firma textloop auf der Grundlage eines Retrodigitalisats des fraglichen Urkundenbuchs erstellt.
description: StructureConformsTo: XML-TEI basiert auf dem DTA-Basisschema, erweitert um notwendige Anpassungen/Erweiterungen nach der vom DTA empfohlenen Methode des Chaining-ODDs-Mechanismus.
Konkret wurden folgende Erweiterungen vorgenommen:
1. Um die für das Urkundenbuch typischen Textblöcke innerhalb eines Documents typisieren zu können, wurden zusätzliche Attributwerte für @type eingeführt
"document" = für das Dokument, enthält meist Regest, diplomatische
Beschreibung und Urkundentext
"abstract"= Regest
"diplDesc"= Diplomatische Beschreibung
"edText" = Text der Urkunde

2. Für das Attribut @rendition wurde der Attributwert "#n" hinzugefügt, über den im Urkundenbuch recte/normale Textpassagen innerhalb von kursiv gesetzten Textblöcken ausgewiesen werden. Alle sonstigen Attributwerte für @rendition sind DTA standardkonform.
description: ResourceDimension: 7278 Zeilen
description: CharacterEncoding: UTF-8
description: Latein
DOI: 10.5061/dryad.fttdz08wv
title: Compensatory recruitment unlikely in high elevation amphibian populations challenged with disease

description: Population-level variation in host responses to disease can be observed
 across a wide array of host-pathogen systems. Some host populations are
 extirpated, some persist at lower densities or abundances, and others
 rebound to pre-disease levels. Understanding the causes of this variation,
 and the mechanisms of successful persistence, can serve as vital
 information for species conservation. One such mechanism of population
 persistence that has gained support in the amphibian Batrachochytrium
 dendrobatidis (Bd) host-pathogen system is the demographic process of
 compensatory recruitment. Host populations may persist by increasing
 recruitment to compensate for reduced survival due to infection, thus
 limiting the negative effects of the disease on population trajectories.
 However, high-elevation amphibian populations are inherently vulnerable to
 stochastic processes and may be limited in their ability to exhibit
 compensatory recruitment relative to lower-elevation populations. We use
 long-term mark-recapture data from five populations of boreal toads
 (Anaxyrus boreas boreas), across an elevational gradient in Colorado,
 before and after pathogen arrival to assess whether populations can
 persist with Bd via compensatory recruitment. Prior to Bd arrival, we
 found a life history tradeoff between survival and recruitment across
 elevations, where high-elevation toads have high survival but lower
 recruitment and vice versa at lower elevations. Bd arrival had a strong
 negative effect on apparent annual survival and recruitment, and led to
 negative population growth rates and dramatically reduced host abundances.
 The data did not support the occurrence of compensatory recruitment.
 Synthesis and applications. Our unique dataset suggests that demographic
 responses to pathogens may be environmentally (i.e., elevationally)
 context-dependent and highlights the value of long-term monitoring. We
 recommend that practitioners verify that potential persistence mechanisms
 occur across multiple populations and relevant environmental gradients to
 counter any assumptions of the mechanism existing species-wide.
 Quantifying any variation in population responses to disease will aid in
 understanding the bounds of such persistence mechanisms, and identify
 particularly vulnerable populations where mechanisms are non-existent.
description: See Supporting Information in Hardy et al.
description: Any program that can open .csv files.
DOI: 10.5061/dryad.8sf7m0cs9
title: A regime shift in Southeast Greenland marine ecosystem

description: Two major oceanographic changes have recently propagated through several
 trophic levels in coastal areas of Southeast Greenland (SEG). Firstly, the
 amount of drift-ice exported from the Fram Strait and transported with the
 East Greenland Current (EGC) has decreased significantly over the past two
 decades, and a main tipping element (summer sea ice) has virtually
 disappeared since 2003 leading to a regime shift in oceanographic and
 ecological conditions in the region. The following 20-year period with low
 or no coastal sea ice is unique in the 200-year history of ice
 observations in the region, and the regime shift is also obvious in the
 volume of ice export through the Fram Strait after 2013. In the same
 period the temperature of the EGC south of 73.5N has increased
 significantly (&gt;2oC) since 1980. Secondly, the warm Irminger
 Current, that advects warm, saline Atlantic Water into the region, has
 become warmer since 1990. The lack of pack ice in summer together with a
 warming ocean generated cascading effects on the ecosystem in SEG that are
 manifested in a changed fish fauna with an influx of boreal species in the
 south and the subarctic capelin further north. At higher trophic levels
 there has been an increase in the abundance of several boreal cetaceans
 (humpback, fin, killer and pilot whales and dolphins) that are either new
 to this area or occur in historically large numbers. It is estimated that
 the new cetacean species in SEG are responsible for an annual predation
 level of 700.000 tonnes of fish. In addition, predation on krill species
 is estimated at &gt;1.500.000 tonnes mainly consumed by the fin
 whales. Simultaneously there has been a reduction in the abundance and
 catches of narwhals and walrus in SEG and it is suggested that these
 species have been impacted by the habitat changes. 
description: It is processed data from remote sensing, shore based observation
 and catch statistics
description: Files can be accessed using Excel or R.
DOI: 10.5285/4b2dee26-0c3a-42d1-8b1f-6797945f1526
title: Processed model output from an Amundsen Sea MITgcm configuration forced by ERA5 1979-2021

description: This dataset includes post-processed model output from an Amundsen Sea regional configuration of MITgcm. The model use ocean, sea ice and ice shelf components. The model is forced by ERA5 from the years 1979-2021, with the exception of 1996 for which ERA Interim is used. The data is used for figures in the research paper "Wind-driven coastal polynya variability drives decadal ice-shelf melt variability in the Amundsen Sea" by Michael Haigh, Paul Holland and Thomas Caton Harrison.

Creation of the dataset was funded by the NERC project "Drivers of Oceanic Change in the Amundsen Sea", NE/T012803/1.
description: The data was produced using checkpoint 67s of MITgcm in an Amundsen Sea configuration. The data is post-processed model output and is presented in figures in the associated research paper.

The model utilises a grid with 0.1° longitudinal grid spacing. The vertical direction is discretised into 50 levels, with thinnest levels (10 m) near the ocean surface and thickest levels (200 m) near the ocean floor.
DOI: 10.5061/dryad.ns1rn8pwz
title: Data for: Excitatory and inhibitory D-serine binding to the NMDA receptor

description: N-methyl-D-aspartate receptors (NMDARs) uniquely require binding of two
 different neurotransmitter agonists for synaptic transmission. D-serine
 and glycine bind to one subunit, GluN1, while glutamate binds to the
 other, GluN2. These agonists bind to the receptor’s bi-lobed
 ligand-binding domains (LBDs), which close around the agonist during
 receptor activation. To better understand the unexplored mechanisms by
 which D-serine contributes to receptor activation, we performed
 multi-microsecond molecular dynamics simulations of the GluN1/GluN2A LBD
 dimer with free D-serine and glutamate agonists. Surprisingly, we observed
 D-serine binding to both GluN1 and GluN2A LBDs, suggesting that D-serine
 competes with glutamate for binding to GluN2A. This mechanism is confirmed
 by our electrophysiology experiments, which show that D-serine is indeed
 inhibitory at high concentrations. Although free energy calculations
 indicate that D-serine stabilizes the closed GluN2A LBD, its inhibitory
 behavior suggests that it either does not remain bound long enough or does
 not generate sufficient force for ion channel gating. We developed a
 workflow using pathway similarity analysis to identify groups of residues
 working together to promote binding. These conformation-dependent pathways
 were not significantly impacted by the presence of N-linked glycans, which
 act primarily by interacting with the LBD bottom lobe to stabilize the
 closed LBD.
description: The data included here come from all-atom equilibrium molecular
 dynamics simulations, umbrella sampling simulations, and TEVC
 electrophysiology experiments. We have included the processed trajectories
 (stripped of waters and ions) from equilibrium molecular dynamics
 simulations performed on the Anton 2 supercomputer.
description: Jupyter is required to visualize and run the included code.
 Notebooks were pre-run using python/3.9.2. Microsoft Excel and open-source
 equivalents can be used to view the electrophysiology data. 
 For each trajectory, load in the PSF file and then the DCD file
 into a molecular visualization software application such as VMD or
 PyMOL.
DOI: 10.5061/dryad.x0k6djhp4
title: Nanopore sequencing data analysis using Microsoft Azure cloud computing service

description: Genetic information provides insights into the exome, genome, epigenetics
 and structural organisation of the organism. Given the enormous amount of
 genetic information, scientists are able to perform mammoth tasks to
 improve the standard of health care such as determining genetic influences
 on outcome of allogeneic transplantation. Cloud-based computing has
 increasingly become a key choice for many scientists, engineers and
 institutions as it offers on-demand network access and users can
 conveniently rent rather than buy all required computing resources. With
 the positive advancements of cloud computing and nanopore sequencing data
 output, we were motivated to develop an automated and scalable analysis
 pipeline utilizing cloud infrastructure in Microsoft Azure to accelerate
 HLA genotyping service and improve the efficiency of the workflow at lower
 cost. In this study, we describe (i) the selection process for suitable
 virtual machine sizes for computing resources to balance between the best
 performance versus cost-effectiveness; (ii) the building of Docker
 containers to include all tools in the cloud computational environment;
 (iii) the comparison of HLA genotype concordance between the in-house
 manual method and the automated cloud-based pipeline to assess data
 accuracy. In conclusion, the Microsoft Azure cloud-based data analysis
 pipeline was shown to meet all the key imperatives for performance, cost,
 usability, simplicity and accuracy. Importantly, the pipeline allows for
 the ongoing maintenance and testing of version changes before
 implementation. This pipeline is suitable for data analysis from MinION
 sequencing platforms and could be adopted for other data analysis
 application processes.
description: Manual analysis performed onsite versus Automated analysis
 performed by Azure cloud server.
DOI: 10.5061/dryad.8w9ghx3qt
title: Fitness costs associated with a GABA receptor mutation conferring dieldrin resistance in Aedes albopictus

description: Understanding the dynamics of insecticide resistance genes in mosquito
 populations is pivotal for a sustainable use of insecticides. Dieldrin
 resistance in Aedes albopictus is conferred by the alanine to serine
 substitution (A302S or RdlR allele) in the γ-aminobutyric acid (GABA)
 receptor encoded by the Rdl gene. On Reunion Island, dieldrin resistance
 was initially reported in natural Ae. albopictus populations sampled in
 2008 despite the ban of dieldrin since 1994. To monitor insecticide
 resistance in Ae. albopictus on the island and to identify its drivers, we
 measured (i) the frequency of resistance alleles in 19 distinct natural
 populations collected between 2016 and 2017, (ii) fitness costs associated
 with dieldrin resistance in laboratory-controlled experiments, and (iii)
 the resistance conferred by RdlR to fipronil, an insecticide widely used
 on the island and reported to cross-react with RdlR. The results show a
 persistence of RdlR in Ae. albopictus natural populations at low
 frequencies. Among the measured life history traits, mortality in
 pre-imaginal stages, adults’ survival as well as the proportion of
 egg-laying females were significantly affected in resistant mosquitoes.
 Finally, bioassays revealed resistance of RdlR mosquitoes to fipronil,
 suggesting that the use of fipronil in natura could select for the RdlR
 allele. This study shows that dieldrin resistance is persistent in natural
 mosquito populations likely as a result of combined effects between
 fitness costs associated with RdlR and selection exerted by cross-reacting
 environmental insecticides such as fipronil.
DOI: 10.15463/ostdata-bsb-bbhhmzqpsb
title: Ein Foto-Korpus von Linguistic Landscapes in der Republik Moldau
title: A Photo Corpus of Linguistic Landscapes in the Republic of Moldova
DOI: 10.5061/dryad.51c59zwc3
title: Lpnet: Reconstructing phylogenetic networks from distances using integer linear programming

description: We present Lpnet, a variant of the widely used Neighbor-net method that
 approximates pairwise distances between taxa by a circular phylogenetic
 network. We first apply standard methods to construct a binary
 phylogenetic tree and then use integer linear programming to compute
 optimal circular orderings that agree with all tree splits. This approach
 achieves an improved approximation of the input distance for the clear
 majority of experiments that we have run for simulated and real data. We
 release an implementation in R that can handle up to 94 taxa and usually
 needs about one minute on a standard computer for 80 taxa. For larger taxa
 sets, we include a top-down heuristic which also tends to perform better
 than Neighbor-net.
description: Two parts of data were used in our paper about Lpnet
 algorithm. Random matrix: 10000
 distance matrixes for 30 taxa which use random numbers between 0 and 1
 from the uniform distribution as pairwise distances. And then, we add the
 smallest constant to all distances to guarantee the triangle inequality in
 every distance matrix. We provide 10000 distance matrixes.
 Simulation sequences: We randomly generate
 10000 trees for 30 taxa by using the function sim.taxa from the R package
 TreeSimGM. We let the parameter waiting time until speciation for sim.taxa
 be exponentially distributed and normalize the maximum pairwise distance
 to 1 for every simulation tree. Then we use the software Dawg to simulate
 DNA sequences of length 10000bp from the simulation trees under
 Jukes-Cantor model. We provide origin simulation trees, distance matrixes,
 and simulation sequences.
description: We upload .txt files which can be opened with any text
 editor.
DOI: 10.5061/dryad.2fqz612sk
title: Microbial autotrophy explains large-scale soil CO2 fixation

description: Microbial communities play critical roles in fixing carbon from the
 atmosphere and fixing it in the soils. However, the large-scale variations
 and drivers of these microbial communities remain poorly understood. Here,
 we conducted a large-scale survey across China and found that soil
 autotrophic organisms are critical for explaining CO2 fluxes from the
 atmosphere to soils. In particular, we showed that large-scale variations
 in CO2 fixation rates are highly correlated to those in autotrophic
 bacteria and phototrophic protists. Paddy soils, supporting a larger
 proportion of obligate bacterial and protist autotrophs, display four-fold
 of CO2 fixation rates over upland and forest soils. Precipitation and pH,
 together with key ecological clusters of autotrophic microbes, also played
 important roles in controlling CO2 fixation. Our work provides a novel
 quantification on the contribution of terrestrial autotrophic microbes to
 soil CO2 fixation processes at a large scale, with implications for global
 carbon regulation under climate change.
DOI: 10.5061/dryad.h70rxwdnb
title: Raw data for: Novel food resources and conservation of ecological interactions between the Andean Araucaria and the Austral parakeet

description: In fragile ecosystems, the introduction of exotic species could alter some
 ecological processes. The Austral parakeet (Enicognathus ferrugineous)
 shows close ecological and evolutionary relationships with the Andean
 Araucaria (Araucaria araucana), so any alteration in these interactions
 may have negative consequences for both partners and for ecosystem
 functioning and structure. We conducted extensive roadside surveys to
 estimate the abundance of parakeets in the northern Patagonian Andes over
 four years and recorded the food plants consumed by foraging flocks. The
 use of native habitats and humanized areas like villages and farms was
 influenced by Araucaria seed crop. In masting years, the large seed crop
 allowed a massive use of this resource during the non-breeding season, and
 even during the breeding season. The exploitation of exotic plants was
 minor in the masting year, but became predominant in non-masting years,
 especially during the non-breeding season. This feeding switch towards
 exotic plants primarily arose because the low Araucaria seed crop in
 non-masting years is entirely consumed just after production by domestic
 and wild exotic mammals living in Araucaria forests year-round, thus
 forcing the displacement of parakeets towards anthropic habitats to
 exploit exotic plants. Given the degradation of the remaining Andean
 Araucaria forests due to the impact of exotic mammals on the ecological
 interaction between Araucaria and Austral parakeets, ambitious programs to
 exclude or reduce the density of these alien mammals, including livestock,
 are warranted. 
description: Please refer to the Methods section and
 Supplementary Information of the published article.
description: This data repository consists on the following
 files: ·       Word document containing information on each
 file and instructions for use
 (<strong>README.docx</strong>). ·       Excel document containing raw data concerning
 the feeding flocks of <em>Enicognathus ferrugineous</em>,
 comprising number of individuals (including single foraging individuals
 and groups of variable size), plant species, item exploited in the case of
 Araucaria, and habitat
 (<strong>Feeding_Flocks_Raw_data.xlsx</strong>) ·       Excel document containing raw data for abundance(individuals/km) of <em>Enicognathus ferrugineous</em> obtained during roadside surveys (<strong>Abundance_Raw_data.xlsx</strong>)
DOI: 10.15463/ostdata-zqtdgsbclo
title: Forschungsdatenkollektion Rigas Handel 1883-1933