cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6gj64
title: Data from: Piscivore addition causes a trophic cascade within and across ecosystem boundaries

description: The addition of predators can play a key role in structuring ecological
 communities through both consumptive and non-consumptive effects. Stocking
 of piscivorous fish in lakes and similar experimental introductions have
 provided fundamental evidence in support of trophic cascade theory. Yet,
 the impact of piscivore addition on cross ecosystem subsidies and
 meso-predator resource use has not been well studied. Here, we use a
 replicated pond experiment to document the trophic impacts of a piscivore,
 cutthroat trout Onchorhynchus clarkii, on aquatic communities already
 containing a meso-predatory fish (threespine stickleback Gasterosteus
 aculeatus) and neighbouring terrestrial ecosystems. We find that piscivore
 addition led to a trophic cascade that extended across an ecosystem
 boundary: trout addition increased the biomass and average size of insects
 emerging into the terrestrial system. Piscivores caused a diet shift in
 stickleback, a non-consumptive effect that was likely mainly responsible
 for the increase in emerging insect biomass. We additionally show that
 heterogeneity in the strength of the pelagic trophic cascade was more
 closely correlated with the magnitude of diet shift (reflecting a
 non-consumptive effect) than decreases in stickleback abundance (a
 consumptive effect). Taken together, our experiment demonstrates that the
 addition of a piscivore causes a trophic cascade that can extend beyond
 the aquatic system and suggests that non-consumptive effects may more
 strongly influence the strength of a trophic cascade than has been
 previously recognized.
description: Piscivore_addition_zooplanktonData_160323Zooplankton data collecting for the study as described in Rudman et al. 2016.Piscivore_addition_phytoplanktonData_160323Phytoplankton data used collected from experiment described by Rudman et al. 2016.Piscivore_addition_EmergingInsects_160323Emerging insect data from Rudman et al. 2016.Piscivore_addition_CascadeCorrelates_160323Data file with calculated strength of trophic cascade, measure of consumptive, and non-consumptive effects from Rudman et al. 2016.Piscivore_addition_sticklebackDiet_160323Stickleback diet data from Rudman et al. 2016.
DOI: 10.82209/qkg3-kr25
title: Performance of selected models for the recognition of 16 named entities in plasma physics research articles: Multiple LSTM-CRF evaluates 0.58 F1 score on the Plasma Physics dataset for the nested named entity recognition task.
DOI: 10.5061/dryad.sm454
title: Data from: The price of being seen to be just: an intention signalling strategy for indirect reciprocity

description: Cooperation among strangers is a marked characteristic of human sociality.
 One prominent evolutionary explanation for this form of human cooperation
 is indirect reciprocity, whereby each individual selectively helps people
 with a ‘good’ reputation, but not those with a ‘bad’ reputation. Some
 evolutionary analyses have underscored the importance of second-order
 reputation information (the reputation of a current partner's
 previous partner) for indirect reciprocity as it allows players to
 discriminate justified ‘good’ defectors, who selectively deny giving help
 to ‘bad’ partners, from unjustified ‘bad’ defectors. Nevertheless, it is
 not clear whether people in fact make use of second-order information in
 indirect reciprocity settings. As an alternative, we propose the intention
 signalling strategy, whereby defectors are given the option to abandon a
 resource as a means of expunging their ‘bad’ reputation. Our model
 deviates from traditional modelling approaches in the indirect reciprocity
 literature in a crucial way—we show that first-order information is
 sufficient to maintain cooperation if players are given an option to
 signal their intention. Importantly, our model is robust against invasion
 by both unconditionally cooperative and uncooperative strategies, a first
 step towards demonstrating its viability as an evolutionarily stable
 strategy. Furthermore, in two behavioural experiments, when participants
 were given the option to abandon a resource so as to mend a tarnished
 reputation, participants not only spontaneously began to use this option,
 they also interpreted others' use of this option as a signal of
 cooperative intent.
description: Experimental
 DataBehavioural Data from
 Experiments 1 and 2.Tanaka_ExperimentalData.xlsx
DOI: 10.5061/dryad.3jr62
title: Data from: Modelled drift patterns of fish larvae link coastal morphology to seabird colony distribution

description: Colonial breeding is an evolutionary puzzle, as the benefits of breeding
 in high densities are still not fully explained. Although the dynamics of
 existing colonies are increasingly understood, few studies have addressed
 the initial formation of colonies, and empirical tests are rare. Using a
 high-resolution larval drift model, we here document that the distribution
 of seabird colonies along the Norwegian coast can be explained by
 variations in the availability and predictability of fish larvae. The
 modelled variability in concentration of fish larvae is, in turn,
 predicted by the topography of the continental shelf and coastline. The
 advection of fish larvae along the coast translates small-scale
 topographic characteristics into a macroecological pattern, viz. the
 spatial distribution of top-predator breeding sites. Our findings provide
 empirical corroboration of the hypothesis that seabird colonies are
 founded in locations that minimise travel distances between breeding and
 foraging locations, thereby enabling optimal foraging by central-place
 foragers.
description: Grid cell
 characteristicsDescription of the
 characteristics of the coastal grid cells used in
 simulationsgridcell.csvGeneric particle abundancesGridded spatial data of particle abundances according to the generic larval drift modelgeneric.csvCod larvae abundancesGridded spatial data of abundances of Northeast Arctic cod eggs and larvae according to the larval drift modelcod.csvHerring larvae abundancesGridded spatial data of abundances of Norwegian spring-spawning herring larvae according to the larval drift modelherring.csv
DOI: 10.5061/dryad.r1s8g
title: Data from: Model-based inference for estimating shifts in species distribution, area occupied and centre of gravity

description: Changing climate is already impacting the spatial distribution of many
 taxa, including bees, plants, birds, butterflies and fishes. A common goal
 is to detect range shifts in response to climate change, including changes
 in the centre of the population's distribution (the centre of
 gravity, COG), population boundaries and area occupied. Conventional
 estimators, such as the abundance-weighted average (AWA) estimator for
 COG, confound range shifts with changes in the spatial distribution of
 available survey data and may be biased when the distribution of survey
 data shifts over time. AWA also does not estimate the standard error of
 COG in individual years and cannot incorporate data from multiple survey
 designs. To explicitly account for changes in the spatial distribution of
 survey effort, we propose an alternative species distribution function
 (SDF) estimator. The SDF approach involves calculating distribution
 metrics, including COG, population boundary and area occupied, directly
 from the predicted species distribution or density function. We illustrate
 the SDF approach using a spatiotemporal model that is available as an r
 package. Using simulated data, we confirm that the SDF substantially
 decreases bias in COG estimates relative to the AWA estimator. We then
 illustrate the method by analysing data from two data sets spanning
 1977–2013 for 18 marine fishes along the U.S. West Coast. In our case
 study, the SDF estimator shows significant northward shifts for six of 18
 species (with southward shifts for only 2), where two species
 (darkblotched and greenstriped rockfishes) have both a northward shift and
 a decreased area occupied. Pelagic species (e.g. Pacific hake and spiny
 dogfish) have more variable distribution than bottom-associated species.
 We also find substantial differences between AWA and SDF estimates of COG
 that are likely caused by shifts in sampling distribution (which affect
 the AWA but not the SDF estimator). We caution that common estimators for
 range shift can yield inappropriate inference whenever sampling designs
 have shifted over time. We conclude by suggesting further improvements in
 model-based approaches to analysing climate impacts, including methods
 addressing the impact of local and regional temperature changes on species
 distribution.
description: AFSC triennial and NWFSC
 annual shelf-slope bottom trawl surveys
 (spatially-restricted)A subset of locations
 and species obtained from the Alaska Fisheries Science Center triennial
 shelf survey (1977-2004) and Northwest Fisheries Science Center annual
 shelf-slope survey (2003-2013). Please see ReadMe.txt for more
 detailsArchive.csv
DOI: 10.5061/dryad.ph81h
title: Data from: High-throughput screening of inorganic compounds for dielectric and optical properties to enable the discovery of novel materials

description: Dielectrics are an important class of materials that are ubiquitous in
 modern electronic applications. Even though their properties are important
 for the performance of devices, the number of compounds with known
 dielectric constant is on the order of a few hundred. Here, we use Density
 Functional Perturbation Theory as a way to screen for the dielectric
 constant and refractive index of materials in a fast and computationally
 efficient way. Our results form the largest database to date, containing
 the full dielectric tensor for 1,056 compounds. Details regarding the
 computational methodology and technical validation are presented along
 with the format of our publicly available data. In addition, we integrate
 our dataset with the Materials Project allowing users easy access to
 material properties. Finally, we explain how our dataset and calculation
 methodology can be used in the search for novel dielectric compounds.
description: Dielectric tensors and
 refractive indicesThe data provided are in
 the form of a human-readable JSON file. The file contains the dielectric
 tensors and refractive index values for 1,056 inorganic compounds,
 calculated using Density Functional Perturbation
 Theory.dielectric_tensors_and_refractive_indices_v3.json
DOI: 10.5061/dryad.9r0gv
title: Data from: Avoidance of windfarms by harbour seals is limited to pile driving activities

description: As part of global efforts to reduce dependence on carbon-based energy
 sources there has been a rapid increase in the installation of renewable
 energy devices. The installation and operation of these devices can result
 in conflicts with wildlife. In the marine environment, mammals may avoid
 wind farms that are under construction or operating. Such avoidance may
 lead to more time spent travelling or displacement from key habitats. A
 paucity of data on at-sea movements of marine mammals around wind farms
 limits our understanding of the nature of their potential impacts. Here,
 we present the results of a telemetry study on harbour seals Phoca
 vitulina in The Wash, south-east England, an area where wind farms are
 being constructed using impact pile driving. We investigated whether seals
 avoid wind farms during operation, construction in its entirety, or during
 piling activity. The study was carried out using historical telemetry data
 collected prior to any wind farm development and telemetry data collected
 in 2012 during the construction of one wind farm and the operation of
 another. Within an operational wind farm, there was a close-to-significant
 increase in seal usage compared to prior to wind farm development.
 However, the wind farm was at the edge of a large area of increased usage,
 so the presence of the wind farm was unlikely to be the cause. There was
 no significant displacement during construction as a whole. However,
 during piling, seal usage (abundance) was significantly reduced up to 25
 km from the piling activity; within 25 km of the centre of the wind farm,
 there was a 19 to 83% (95% confidence intervals) decrease in usage
 compared to during breaks in piling, equating to a mean estimated
 displacement of 440 individuals. This amounts to significant displacement
 starting from predicted received levels of between 166 and 178 dB re 1
 μPa(p-p). Displacement was limited to piling activity; within 2 h of
 cessation of pile driving, seals were distributed as per the non-piling
 scenario. Synthesis and applications. Our spatial and temporal
 quantification of avoidance of wind farms by harbour seals is critical to
 reduce uncertainty and increase robustness in environmental impact
 assessments of future developments. Specifically, the results will allow
 policymakers to produce industry guidance on the likelihood of
 displacement of seals in response to pile driving; the relationship
 between sound levels and avoidance rates; and the duration of any
 avoidance, thus allowing far more accurate environmental assessments to be
 carried out during the consenting process. Further, our results can be
 used to inform mitigation strategies in terms of both the sound levels
 likely to cause displacement and what temporal patterns of piling would
 minimize the magnitude of the energetic impacts of displacement.
description: Wash_diagWash_diag.xlsx is the historic location data (pre windfarm construction) for the 19 individuals used in the analysis described in Russell et al.
DOI: 10.5061/dryad.nb41c
title: Data from: Approach-induced biases in human information sampling

description: IInformation sampling is often biased towards seeking evidence that
 confirms one’s prior beliefs. Despite such biases being a pervasive
 feature of human behavior, their underlying causes remain unclear. Many
 accounts of these biases appeal to limitations of human hypothesis testing
 and cognition, de facto evoking notions of bounded rationality, but
 neglect more basic aspects of behavioral control. Here, we investigated a
 potential role for Pavlovian approach in biasing which information humans
 will choose to sample. We collected a large novel dataset from 32,445
 human subjects, making over 3 million decisions, who played a gambling
 task designed to measure the latent causes and extent of
 information-sampling biases. We identified three novel approach-related
 biases, formalized by comparing subject behavior to a dynamic programming
 model of optimal information gathering. These biases reflected the amount
 of information sampled (“positive evidence approach”), the selection of
 which information to sample (“sampling the favorite”), and the interaction
 between information sampling and subsequent choices (“rejecting unsampled
 options”). The prevalence of all three biases was related to a Pavlovian
 approach-avoid parameter quantified within an entirely independent
 economic decision task. Our large dataset also revealed that individual
 differences in the amount of information gathered are a stable trait
 across multiple gameplays and can be related to demographic measures,
 including age and educational attainment. As well as revealing limitations
 in cognitive processing, our findings suggest information sampling biases
 reflect the expression of primitive, yet potentially ecologically
 adaptive, behavioral repertoires. One such behavior is sampling from
 options that will eventually be chosen, even when other sources of
 information are more pertinent for guiding future action.
description: Raw data, scripts and
 model codeArchive containing
 MATLAB analysis .m code, code for computational model, and raw .mat data.
 Please read the associated readme file.Hunt_infotask.zip
DOI: 10.5061/dryad.n70c7
title: Data from: Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi

description: Recent studies of humans, dogs and rodents have started to discover the
 genetic underpinnings of high altitude adaptations, yet amphibians have
 received little attention in this respect. To identify possible signatures
 of adaptation to altitude, we performed a genome scan of 15 557 single
 nucleotide polymorphisms (SNPs) obtained with restriction site-associated
 DNA sequencing of pooled samples from 11 populations of Andrew's toad
 (Bufo andrewsi) from the edge of the Tibetan Plateau, spanning an
 altitudinal gradient from 1690 to 2768 m.a.s.l. We discovered significant
 geographic differentiation among all sites, with an average FST = 0.023
 across all SNPs. Apart from clear patterns of isolation by distance, we
 discovered numerous outlier SNPs showing strong associations with
 variation in altitude (1394 SNPs), average annual temperature (1859 SNPs)
 or both (1051 SNPs). Levels and patterns of genetic differentiation in
 these SNPs were consistent with the hypothesis that they have been subject
 to directional selection and reflect adaptation to altitudinal variation
 among the study sites. Genes with footprints of selection were
 significantly enriched in binding and metabolic processes. Several genes
 potentially related to high altitude adaptation were identified, although
 the identity and functional significance of most genomic targets of
 selection remain unknown. In general, the results provide genomic support
 for results of earlier common garden and low coverage genetic studies that
 have uncovered substantial adaptive differentiation along altitudinal and
 latitudinal gradients in amphibians.
description: Andrew's toad
 pooled RAD-seq dataThe file includes
 reference sequences used for alignment, SNPs identified with PoPoolation2
 and their FST values of all population pairs, and genepop format data of
 SNPs identified with PoPoolation2. The command line used for SNP calling
 with PoPoolation2 could be found in README.txt.Andrew_toad_Pool_RAD-seq.tar.gz
DOI: 10.5061/dryad.1mh30
title: Data from: Ediacaran distributions in space and time: testing assemblage concepts of earliest macroscopic body fossils

description: The mid-late Ediacaran Period (~579–541 Ma) is characterized by globally
 distributed marine soft-bodied organisms of unclear phylogenetic
 affinities colloquially called the “Ediacara biota.” Despite an absence of
 systematic agreement, previous workers have tested for underlying factors
 that may control the occurrence of Ediacaran macrofossils in space and
 time. Three taxonomically distinct “assemblages,” termed the Avalon, White
 Sea, and Nama, were identified and informally incorporated into Ediacaran
 biostratigraphy. After ~15 years of new fossil discoveries and taxonomic
 revision, we retest the validity of these assemblages using a
 comprehensive database of Ediacaran macrofossil occurrences. Using
 multivariate analysis, we also test the degree to which taphonomy, time,
 and paleoenvironment explain the taxonomic composition of these
 assemblages. We find that: (1) the three assemblages remain distinct
 taxonomic groupings; (2) there is little support for a large-scale
 litho-taphonomic bias present in the Ediacaran; and (3) there is
 significant chronostratigraphic overlap between the taxonomically and
 geographically distinct Avalonian and White Sea assemblages ca. 560–557
 Ma. Furthermore, both assemblages show narrow bathymetric ranges,
 reinforcing that they were paleoenvironmental–ecological biotopes and
 spatially restricted in marine settings. Meanwhile, the Nama assemblage
 appears to be a unique faunal stage, defined by a global loss of
 diversity, coincident with a noted expansion of bathymetrically
 unrestricted, long-ranging Ediacara taxa. These data reinforce that
 Ediacaran biodiversity and stratigraphic ranges of its representative taxa
 must first statistically account for varying likelihood of preservation at
 a local scale to ultimately aggregate the Ediacaran macrofossil record
 into a global biostratigraphic context.
description: Ediacaran distributions
 in space and time_supplementaryDatabase tables of
 Ediacaran fossil occurrences, with additional tables describing the
 formatting of the database and a catalogue of geochronological data
 associated with fossiliferous Ediacaran strata. Also included are
 subsequent statistical analyses of the data-set using hierarchical cluster
 analysis and confidence intervals.Boag_supplementary_accepted.docx
DOI: 10.5061/dryad.7dj7t
title: Data from: Common genetic variation in ETV6 is associated with colorectal cancer susceptibility

description: Genome-wide association studies (GWAS) have identified multiple
 susceptibility loci for colorectal cancer, but much of heritability
 remains unexplained. To identify additional susceptibility loci for
 colorectal cancer, here we perform a GWAS in 1,023 cases and 1,306
 controls and replicate the findings in seven independent samples from
 China, comprising 5,317 cases and 6,887 controls. We find a variant at
 12p13.2 associated with colorectal cancer risk (rs2238126 in ETV6, P =
 2.67 × 10-10). We replicate this association in an additional 1,046 cases
 and 1,076 controls of European ancestry (P = 0.034). The G allele of
 rs2238126 confers earlier age at onset of colorectal cancer (P = 1.98 ×
 10-6) and reduces the binding affinity of transcriptional enhancer MAX.
 The mRNA level of ETV6 is significantly lower in colorectal tumors than in
 paired normal tissues. Our findings highlight the potential importance of
 genetic variation in ETV6 conferring susceptibility to colorectal cancer.
description: CRC GWAS
 dataWe performed a
 genome-wide association studies (GWAS) and replicated the findings in
 seven independent samples from China. In the GWAS stage, 2,364 samples
 were enrolled from the Cancer Center of Nanjing Medical University.
 Genotyping for the GWAS stage was conducted using Illumina Human Omni
 ZhongHua Bead Chips for 900,015 SNPs. Individual-level genotype calls are
 in original file format as PLINK binary format.Colorectal_cancer_
 data.zip