cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tg60c4s
title: Data from: Enhancement of optical force acting on vesicles via the binding of gold nanoparticles

description: Here we found that gold nanoparticles (AuNPs) enhance the optical force
 acting on vesicles prepared from phospholipids via hydrophobic and
 electrostatic interactions. A laser beam was introduced into a cuvette
 filled with a suspension of vesicles and it accelerated them in its
 propagation direction via a scattering force. The addition of the AuNPs
 exponentially increased the velocity of the vesicles as their
 concentration increased, but polystyrene particles had no significant
 impact on velocity in the presence of AuNPs. To elucidate the mechanism of
 the increased velocity, the surface charges in the vesicles and the AuNPs
 were controlled; the surface charges of the vesicles were varied via the
 use of anionic, cationic and neutral phospholipids, whereas AuNPs with
 positive and negative charges were synthesized by coating with citrate ion
 and 4-dimethylaminopyridine, respectively. All vesicles increased the
 velocity at different degrees depending on the surface charge. The
 vesicles were accelerated more efficiently when their charges were
 opposite those of the AuNPs. These results suggested that hydrophobic and
 electrostatic interactions between the vesicles and the AuNPs enhanced the
 optical force. By accounting for the binding constant between the vesicles
 and the AuNPs, we proposed a model for the relationship between the
 concentration of the AuNPs and the velocity of the vesicles. Consequently,
 the increased velocity of the vesicles was attributed to the light
 scattering that was enhanced when AuNPs were adsorbed onto the vesicles.
description: Movie-S1Vesicle accelerated by an optical force.RSOS_YTThe excel file includes all data in Figures 2 and 3.The excel file includes all data in Figures 2 and 3.
DOI: 10.5061/dryad.d1t59pp
title: Data from: Nɛ-acetyl lysine derivatives with zinc binding groups as novel HDAC inhibitors

description: HDAC inhibitors have been developed very rapidly in clinical trials and
 even in approvals for treating several cancers. However, there are few
 reported HDAC inhibitors designed from Nε-acetyl lysine. In current study,
 we raised a novel design, which is about Nε-acetyl lysine analogues
 containing amide acetyl groups with the hybridization of ZBG groups as
 novel HDAC inhibitors.
description: NMR
 spectrumsCarbon and Proton NMR
 spectrums
DOI: 10.57967/hf/7656
title: lunar-image-crater-segmentation-global-v1
DOI: 10.5061/dryad.h1c0b52
title: Data from: The strategic reference gene: an organismal theory of inclusive fitness

description: How to define and use the concept of inclusive fitness is a contentious
 topic in evolutionary theory. Inclusive fitness can be used to calculate
 selection on a focal gene, but it is also applied to whole organisms.
 Individuals are then predicted to appear designed as if to maximise their
 inclusive fitness, provided that certain conditions are met (formally when
 interactions between individuals are ‘additive’). Here we argue that
 applying the concept of inclusive fitness to organisms is justified under
 far broader conditions than previously shown, but only if it is
 appropriately defined. Specifically, we propose that organisms should
 maximise the sum of their offspring (including any accrued due to the
 behaviour/phenotype of relatives), plus any effects on their relatives’
 offspring production, weighted by relatedness. In contrast, most
 theoreticians have argued that a focal individual’s inclusive fitness
 should exclude any offspring accrued due to the behaviour of relatives.
 Our approach is based on the notion that long-term evolution follows the
 genome’s ‘majority interest’ of building coherent bodies that are
 efficient ‘vehicles’ for gene propagation. A gene favoured by selection
 that reduces the propagation of unlinked genes at other loci (e.g. meiotic
 segregation distorters that lower sperm production) is eventually
 neutralised by counter-selection for modifiers throughout the rest of the
 genome. Most phenotypes will therefore appear as if designed to maximise
 the propagation of any given gene in a focal individual and its relatives.
description: one locus
 modelmain code for one locus
 modelone_locus_model.mrun_one_locus_modelhigher-level code that uses the one-locus model to produce figure S1multilocus_modelmain code for multilocus simulationsrun_multilocus_modelhigher-level code that uses the multilocus model to produce figures S2-S4correlationfunction to calculate phenotypic correlationcorrtest.m
DOI: 10.5061/dryad.q80p8j4
title: Data from: Cambrian rhynchonelliform nisusioid brachiopods: phylogeny and distribution

description: A comprehensive review and phylogenetic analysis of genera and species
 presently assigned to the rhynchonelliform superfamily Nisusioidea and
 family Nisusiidae suggests that this short-lived but important group of
 brachiopods first appeared in peri-Gondwana during the second half of the
 Cambrian Series 2, before going extinct by the end of Drumian time.
 Nisusiides achieved their maximum morphological disparity and geographical
 distribution during Wuliuan age, and most likely Laurentia was the major
 center of dispersal. The new phylogenetic analysis suggests an early
 separation between the lineages of spinose and non-spinose nisusiids. The
 non-spinose nisusiids probably evolved in Laurentia by the end of Cambrian
 Series 4. The new nisusiid genus Bellistrophia is described. The new
 species Nisusia multicostata represents the first documented
 rhynchonelliform (kutorginide) brachiopod from the Miaolingian (Drumian)
 of Alborz Mountains.
description: Table 1.
 MatrixMatrix of 28
 morphological characters recognized in 22 species of the Family Nisusiidae
 and two species of Kutorginidae listed in the text.nisusia.tntTable 3. List of the characters and character sets used in the phylogenetic analysis:List of the characters and character sets used in the phylogenetic analysis.characters.docx
DOI: 10.5061/dryad.s7j17qp
title: Data from: Parser extraction of triples in unstructured text

description: The web contains vast repositories of unstructured text. We investigate
 the opportunity for building a knowledge graph from these text sources. We
 generate a set of triples which can be used in knowledge gathering and
 integration. We define the architecture of a language compiler for
 processing subject-predicate-object triples using the OpenNLP parser. We
 implement a depth-first search traversal on the POS tagged syntactic tree
 appending predicate and object information. A parser enables higher
 precision and higher recall extractions of syntactic relationships across
 conjunction boundaries. We are able to extract 2-2.5 times the correct
 extractions of ReVerb. The extractions are used in a variety of semantic
 web applications and question answering. We verify extraction of 50,000
 triples on the ClueWeb dataset.
description: Parser Extraction of
 Triples in Unstructured TextThe web contains vast
 repositories of unstructured text. We investigate the opportunity for
 building a knowledge graph from these text sources. We generate a set of
 triples which can be used in knowledge gathering and integration. We
 define the architecture of a language compiler for processing
 subject-predicate-object triples using the OpenNLP parser. We implement a
 depth-first search traversal on the POS tagged syntactic tree appending
 predicate and object information. A parser enables higher precision and
 higher recall extractions of syntactic relationships across conjunction
 boundaries. We are able to extract 2-2.5 times the correct extractions of
 ReVerb. The extractions are used in a variety of semantic web applications
 and question answering. We verify extraction of 50,000 triples on the
 ClueWeb dataset.
DOI: 10.5061/dryad.t429r75
title: Data from: Population bottlenecks have shaped the genetic variation of Ailanthus altissima (Mill.) Swingle in an area of early introduction

description: Ailanthus altissima is a common tree species of the European non-native
 flora. In Eastern Austria, Ailanthus has both a long tradition, dating
 back to the late 18th century, and a high frequency of occurrence. Here,
 we apply molecular markers from the nuclear and chloroplast DNA in order
 to study the origin, as well as the clonal and genetic structure of the
 species in forest stands of this region. Our results indicate a single
 area of origin for all our study populations from the north-eastern part
 of the native range, in agreement with historical reports. Within
 populations, vegetative reproduction has resulted in extensive clonal
 structures at some sites. Long presence and repeated vegetative
 recruitment might have led to expansion of clones in areas of early
 introduction. In addition, limited mate availability may also have
 promoted vegetative reproduction. Tests for recent bottlenecks were
 significant in almost all stands, possibly reflecting founder effects
 since the introduction of Ailanthus in our study area. Among populations,
 we found a very pronounced and significant genetic structure, which did
 not follow a spatial pattern. We argue that founder effects due to
 population establishment with a low number of propagules – whether
 naturally or artificially – have caused genetic drift and a structured
 gene pool. The lack of spatial pattern or isolation-by-distance suggests
 that seed transfer by humans might have been a major factor shaping the
 genetic variation of Ailanthus in Eastern Austria.
description: Genotypic data from 10
 populations of Ailanthus altissima in Eastern AustriaThe file contains
 genotypic data of 298 trees from 10 populations of Ailanthus altissima in
 eastern Austria. Samples were collected in the field and genotyped
 according to the methods described in the cited research. The file
 contains genotypes of five (5) microsatellite loci scored using fragment
 length analysis (Aa22, Aa69, Aa75, Aa76 and Aa82) and further twelve (12)
 microsatellite loci scored based on an SSR-GBS approach (loci loci HT2,
 HT7, HT9, HT10, HT16, HT19, HT22, HT24, HT27, HT30, HT31 and HT35).
 Genotypes of the same population assigned to a particular multilocus
 lineage (MLL) are marked with a capital letter (from
 A-F).Ailanthus_Eastern_Austria_data.csv
DOI: 10.5061/dryad.g085g05
title: Data from: Mechanisms underlying predator-driven biotic resistance against introduced barnacles on the Pacific coast of Hokkaido, Japan

description: Introduced species are a major threat to coastal ecosystems worldwide.
 Thus, understanding biotic resistance (i.e. the ability of native species
 to limit introduced species) is a central goal of invasion biology. This
 paper examines mechanisms underlying biotic resistance. Consumption can
 limit introduced prey provided that native predators prefer such prey.
 Furthermore, predator nonconsumptive effects (NCEs), mediated through
 predator-released cues perceived by prey, can limit prey recruitment, a
 key demographic process for prey populations. However, information on
 predator NCEs is largely absent in the context of recruitment in
 introduced prey. Working on the Pacific coast of Hokkaido (Japan), we
 addressed this knowledge gap using native predatory dogwhelks (Nucella
 lima) that prey on native barnacles (Chthamalus dalli) and introduced
 barnacles (Balanus glandula). We experimentally examined dogwhelk
 preferences for barnacles in the laboratory and dogwhelk NCEs on barnacle
 recruitment in the field. We found that N. lima preferred B. glandula over
 C. dalli, likely as B. glandula prey is more profitable, as suggested by
 previous findings in congeneric dogwhelks. Moreover, we found that N. lima
 NCEs limited recruit density in C. dalli and B. glandula, likely as
 barnacle larvae moved away from dogwhelk cues to reduce future predation
 risk. Our study suggests that predator prey preferences and predator
 nonconsumptive limitation of prey recruitment are two mechanisms that can
 contribute to predator-driven biotic resistance against introduced prey.
description: Barnacle recruit
 densityBarnacle recruit
 densityBarnacle_recruit_density.xlsxPredator preference for preyPredator preference for preyPredator_preference_for_prey.xlsx
DOI: 10.5061/dryad.tj06js8
title: Data from: Parallel Miocene dispersal events explain the cosmopolitan distribution of the Hypogymnioid lichens

description: Aim: Contemporary species’ distributions are shaped by both geography and
 historical events, such as extinction, diversification in specific areas
 and long-distance dispersals. In the most diverse family of lichen-forming
 fungi, Parmeliaceae, the Hypogymnioid clade, is an example of an
 evolutionary lineage comprised of species occurring in temperate to
 subpolar regions in both hemispheres. Here, we elucidate the timing of
 diversification events and the impact of historical events on the species
 distribution in this lineage. Location: Worldwide. Taxon: Genera
 Arctoparmelia, Brodoa, Hypogymnia and Pseudevernia (Parmeliaceae).
 Methods: Our sampling focused on the most diverse genus of the clade,
 Hypogymnia, including ca. 70% of the described species. We reconstructed
 phylogenetic relationships using a multi-locus dataset, estimated
 divergence times, and inferred ancestral distributions. Results: Our
 analyses suggest that the ancestor of the Hypogymnioid clade occurred in
 the Holarctic. In each of the four genera, all recovered as monophyletic
 here, diversification have occurred largely during the Miocene and
 Pliocene. A number of currently accepted species did not form monophyletic
 groups, especially in cases where specimens were collected from distinct
 geographic areas, with multiple, distinct clades corresponding to the
 geographic region of origin. Our results suggest that only a very few
 species in the Hypogymnioid clade have cosmopolitan distributions, all of
 which reproduces using vegetative propagules including both symbiotic
 partners. Main conclusions: While the diversification occurred
 predominantly in the Northern Hemisphere during the Miocene, a
 long-distance dispersal event from the Northern to the Southern
 Hemisphere, resulted in diversification of a clade of species largely
 restricted to the Southern Hemisphere. Similar to other groups in this
 diverse family, our study highlights the need for re-evaluation of species
 boundaries among members of the Hypogymnioid clade.
description: Hypogymnioid-5
 genes_alignment
DOI: 10.5061/dryad.25s5j4g
title: Data from: Personal information about danger trumps social information from avian alarm calls

description: Information about predators can mean the difference between life and
 death, but prey face the challenge of integrating personal information
 about predators with social information from the alarm calls of others.
 This challenge might even affect the structure of interspecific
 information networks: species vary in response to alarm calls, potentially
 because different foraging ecologies constrain the acquisition of personal
 information. However, the hypothesis that constrained personal information
 explains a greater response to alarm calls has not been experimentally
 tested. We used a within-species test to compare the antipredator
 responses of New Holland honeyeaters, Phylidonyris novaehollandiae, during
 contrasting foraging behaviour. Compared to perched birds, which hawk for
 insects and have a broad view, those foraging on flowers were slower to
 spot gliding model predators, showing that foraging behaviour can affect
 predator detection. Furthermore, nectar-foraging birds were more likely to
 flee to alarm call playbacks. Birds also assessed social information
 relevance: more distant calls, and those from another species, prompted
 fewer flights and slower reaction times. Overall, birds made flexible
 decisions about danger by integrating personal and social information,
 while weighing information relevance. These findings support the idea that
 a strategic balance of personal and social information could affect
 community function.
description: Data
 Set
DOI: 10.5061/dryad.5j5gh63
title: Data from: Individual variation in the social plasticity of water dragons

description: Individuals should alter when they socially associate with conspecifics to
 avoid potentially costly interactions. Moreover, individuals may vary in
 their propensity to use information about conspecifics when making such
 social decisions. However, surprisingly little is known about either the
 determinants of, or individual variation in, such ‘social plasticity’. We
 show here that eastern water dragons (Intellegama lesueurii lesueurii) may
 simultaneously use information from different components of their social
 environment when deciding whether or not to socially associate. In
 particular, we found that individuals altered when they socially
 associated according to levels of potential conflict and competition in
 their social environment; both sexes socially associated more at higher
 local density than would be expected under increased random encounters.
 Further, females were more likely to socially associate during the
 breeding season, and when there were more males and/or conspecifics whom
 they typically avoided in their social environment. This suggests that
 females may seek safety in numbers when the potential for intra-sexual
 conflict or sexual harassment is high. Using a behavioural reaction-norm
 framework, we also provide novel evidence to show that individuals vary in
 the extent and direction of their social plasticity, and that males varied
 more than females. Our study thus implies that individuals use multiple
 cues in their environment when deciding to socially associate, and that
 the resulting social plasticity varies between the sexes and between
 individuals.
description: Data from: Individual
 variation in the social plasticity of water dragonsData.xlsx
DOI: 10.5061/dryad.3m24c84
title: Data from: Prey colour biases in jumping spiders (Habronattus brunneus) differ across populations

description: Predators often avoid aposematic prey as a result of aversions to
 particular prey signals (e.g., bright colours and noxious odours). These
 aversions may be flexible, that is, they can be reinforced or extinguished
 with experience. As such, we might expect populations to differ in their
 biases against certain prey characteristics (e.g., colour or pattern)
 depending on the prey available in the community. Here, we tested whether
 the jumping spider, Habronattus brunneus(Salticidae), exhibits colour
 biases against red prey using choice tests with novel (artificially
 coloured) prey, and then went on to examine how these biases differ across
 four geographically distinct focal populations. We then conducted
 preliminary field surveys at each of these four sites to explore
 differences in habitat type and prey availability. Overall, we found that
 field‐caught H. brunneusexhibited a bias against the colour red (compared
 with black) when tested with artificially coloured prey in the laboratory.
 However, the degree of colour bias varied among our four focal populations
 (with two populations exhibiting strong biases against red and two showing
 no colour biases). Preliminary habitat and prey surveys suggest that these
 populations also differed in both habitat structure (percentage of grass,
 leaf litter and bare ground) and prey availability across many taxa,
 suggesting that the spiders from each population may have been exposed to,
 and had experiences with, different potential prey. We discuss how prey
 availability may influence colour biases in predators, as well as how
 predator experience may shape the evolution of prey colour signals.
description: Colour bias experiments,
 prey and habitat surveysThe Excel data file
 includes four sheets. First, "Colour biases" includes the data
 for choice tests with artificially coloured prey. Here, individual spiders
 have a unique ID. Second, "Surveys- habitat data" lists the
 habitat composition (proportion of grass, leaves, bare ground/dirt) of
 randomly-selected quadrats in our four focal sites. Third, "Surveys-
 prey data (all)" includes all prey sampled using three methods (leaf
 litter sifting, sticky traps, and sweep netting) across our four focal
 sites. Prey identification and rationale for taxa groupings is discussed
 in Powell et al. (2019). Finally, the fourth sheet, "Surveys, prey
 data (analyzed)" includes only the subset of prey data that was
 included our analyses following the methods described in Powell et al.
 (2019). Note that sweep net data is scaled for transect length as
 described in in Powell et al. (2019). Please contact corresponding author,
 Erin Powell (erin.powell94@gmail.com), for further inquiries regarding
 specific analyses.Powell_et_al_Ethology_2019.xlsx
DOI: 10.5061/dryad.p0g4t96
title: Data from: Seasonal ecosystem metabolism across shallow benthic habitats measured by aquatic eddy covariance

description: This submission consists of 40 eddy covariance datasets collected from six
 shallow sites in the Baltic Sea over an 18 month period. Hourly fluxes
 were extracted from the high-density data streams and were used to compute
 daily rates of benthic metabolism (gross primary production (GPP),
 respiration (R), and net ecosystem metabolism (NEM); in mmol O2 m-2 d-1).
 These were converted to C assuming an O2 : C of 1.0 for GPP and R. A
 description of the flux data processing protocol is given in the
 manuscript. These datasets were used to compute annual rates of GPP, R,
 and NEM at each habitat site. The annual rates were then used to
 investigate (i) phototrophic biomass turnover rates, by comparing the GPP
 rates with standing phototrophic biomass measurements, and (ii) the
 regional importance of benthic metabolism, by upscaling the annual rates
 to habitat distribution maps. This dataset includes all data on standing
 biomass and habitat extent.
description: Attard et al. LO
 LettersDaily benthic metabolism
 rates, annual integrated rates, biomass turnover rates, and spatial
 upscaling estimates presented in Attard et al. LO
 LettersMetadata template_Attard
 et alMetadata template for
 Attard et al. LO Letters dataset