cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sqv9s4n18
title: Larvae of deep-sea invertebrates harbor low-diversity bacterial communities

description: Microbial symbionts are a common life-history character of marine
 invertebrates and their developmental stages. Communities of bacteria that
 associate with the eggs, embryos, and larvae of coastal marine
 invertebrates are species-specific and correlate with aspects of host
 biology and ecology. The richness of bacteria associated with the
 developmental stages of coastal marine invertebrates spans four orders of
 magnitude from single mutualists to 1,000s of unique taxa. If the
 developmental stages of coastal species are broadly representative of
 marine invertebrates then we may expect deep-sea species to associate with
 bacterial communities that are similar in diversity. To test this, we used
 amplicon sequencing to profile the bacterial communities of invertebrate
 larvae from multiple phyla (annelids, molluscs, crustaceans) collected
 from 2,500 to 3,670 meters depth in near-bottom waters near hydrothermal
 vents in three different regions of the Pacific Ocean (East Pacific Rise,
 Mariana Back-Arc, and Pescadero Basin). We find that larvae of deep-sea
 invertebrates associate with low-diversity bacterial communities (~30
 bacterial taxa) with little specificity between larval types. Moreover,
 the diversity of these communities is an order of magnitude lower (~11.1x)
 than that of coastal invertebrate larvae. The low diversity, lack of
 specificity, and abundance of ‘environmental’ or transient microbes in
 these communities may imply that these deep-sea invertebrate larvae
 associate with few bacterial taxa and that deep-sea invertebrate larvae do
 not have the strong reliance on specialized contributions from their
 associated bacterial communities observed for many coastal larval species.
description: Total DNA extraction
 Ampylificaiton of the 16S rRNA gene for bacteria using primers
 for the V3/V4 region Sequencing via MiSeq
DOI: 10.26183/6j3y-ek16
title: Early Language Inventory (ERLI) - Western Sydney

description: This project involves the western Sydney adaptation of the Early Language Inventory (ERLI) to support culturally responsive assessment of early communication development in Aboriginal children. Data were collected from caregivers of young children across western Sydney using an adapted ERLI vocabulary checklist that incorporated locally preferred wording and community-informed adaptation. The study generated reference patterns for receptive and expressive vocabulary development and examined how scores vary across age and percentile groups. The data provides evidence to guide early identification and clinical and educational decision-making while reflecting the linguistic and cultural contexts of the participating community.   
This document consists of a single PDF containing an adapted Western Sydney version of the Early Language Inventory (ERLI), developed to support more culturally appropriate language assessment of Aboriginal children by speech pathologists, early educators, and allied health professionals.
DOI: 10.5061/dryad.0cfxpnvzc
title: Data from: Delusions of grandeur: seed count is not a good fitness proxy under individual variation in phenology

description: The concept of fitness is central to evolutionary biology, yet it is
 difficult to define and to measure. In plant biology, fitness is often
 measured as seed count. However, under an array of circumstances, seed
 count may be a biased proxy of fitness; for example, when individuals vary
 in allocation to sexual vs. asexual reproduction. A more subtle example,
 but also likely to be important in natural populations, is when
 interindividual variation in conditions during development results in
 variation in offspring quality among seed parents. In monocarpic
 (semelparous) plants, this is expected to result from variation in
 effective season length experienced among individuals that reach
 reproductive maturity at different times. Here, we manipulate growing
 season length to ask whether seed count is an accurate representation of
 parental fitness in the monocarpic herb Lobelia inflata. Simple seed count
 suggests a paradoxical fitness advantage under constrained season length.
 However, we find that the apparent fitness advantage of a constrained
 season length is overridden by low relative per-seed fitness. Furthermore,
 the fitness deficit in the constrained environment is associated primarily
 with an accelerating decrease in viability and seedling survival in seeds
 derived from fruits produced progressively later in the season. In this
 study, the overall fitness value of a seed under a constrained season is
 0.774 of that observed under a long season.
description: Please see Wen & Simons Read Me file.
DOI: 10.7291/d1467k
title: Heat flux and temperature at depth beneath InSight landing site through time

description: The heat flux and thus temperature gradient of the Martian crust is
 critical for comparison with measurements of crustal properties. This
 allows for constraints upon the inferred thermal history of Mars. Each
 file contains the heat flux and temperature at several depths as a
 function of time after Mars formed, but assuming different crustal
 properties.
description: The data are outputs of a 3D thermal evolution model of Mars
 (Plesa <em>et al.</em> 2018) at the InSight landing site on
 Mars (4°N, 136°E). Details of each selected case are presented in Table S1
 of the Supplementary Material to Plesa <em>et al.</em>
 (2018).
description: The first 5 lines of each datafile detail what each row and
 column display, including their units. Temperature is given at 11 depths,
 denoted as a radial distance from the center of Mars (where the last
 column is the surface). For finer resolution, we linearly interpolate
 temperature between depths in our own work.
DOI: 10.5061/dryad.bg79cnp7v
title: Leave me alone: solitary females attract more mates in a nocturnal insect

description: Spatial distributions of sexual competitors and potential mating partners
 have a large impact on sexual selection and mating systems. Typically,
 such effects are investigated with regard to male aggregations. However,
 females may also need to compete for mating opportunities. Here, we
 investigated consequences of clustering and rival attractiveness on female
 mate attraction success under field conditions in a nocturnal beetle, the
 common glow-worm, Lampyrus noctiluca. We placed dummy females of two glow
 intensity (attractiveness) levels either alone or in clusters of varying
 attractiveness compositions. We found that by displaying alone rather than
 in a cluster, females have a higher probability of mating and greater
 potential to exercise mate choice. Within clusters, females of both
 attractiveness levels had the highest probability of mating when having
 neighbours of only the less attractive type. These results show that both
 the presence and attractiveness of rivals can strongly influence
 females' mate attraction. The findings also suggest that the
 distribution of wild females matches better with female than male
 benefits. Hence, the results highlight the important links between spatial
 distribution of females, male mate searching and sexual selection.
description: Data from an experimental setup run in the field. Individuals
 were counted and measured.
description: The Excel document has 2 data sheets. The first sheet shows male
 occurrence and count data and the second one shows male size data. In
 total, 389 males were caught during the experiment, but the size data
 are available for 380 of them, as per detailed in the paper.
DOI: 10.5061/dryad.tqjq2bvvv
title: HLA Class II specificity assessed by high-density peptide microarray interactions

description: The ability to predict and/or identify MHC binding peptides is an
 essential component of T cell epitope discovery; something that ultimately
 should benefit the development of vaccines and immunotherapies. In
 particular, MHC class I (MHC-I) prediction tools have matured to a point
 where accurate selection of optimal peptide epitopes is possible for
 virtually all MHC-I allotypes; in comparison, current MHC class II
 (MHC-II) predictors are less mature. Since MHC-II restricted CD4+ T cells
 control and orchestrate most immune responses, this shortcoming severely
 hampers the development of effective immunotherapies. The ability to
 generate large panels of peptides and subsequently large bodies of
 peptide-MHC-II interaction data is key to the solution of this problem; a
 solution that also will support the improvement of bioinformatics
 predictors, which critically relies on the availability of large amounts
 of accurate, diverse and representative data. Here, we have used
 recombinant HLA-DRB1*01:01 and HLA-DRB1*03:01 molecules to interrogate
 high-density peptide arrays, in casu containing 70,000
 random peptides in triplicates. We demonstrate that the binding data
 acquired contains systematic and interpretable information reflecting the
 specificity of the HLA-DR molecules investigated. Collectively, with a
 cost per peptide reduced to a few cents combined with the flexibility of
 recombinant HLA technology, this poses an attractive strategy to generate
 vast bodies of MHC-II binding data at an unprecedented speed and for the
 benefit of generating peptide-MHC-II binding data as well as improving
 MHC-II prediction tools.
description: Binding of HLA-DRB1*01:01 and HLA-DRB1*03:01 to high density
 peptide arrays containing 63k random 13-mer peptides in triplicate. The
 binding data was used to train artificial neural networks (ANN) capable of
 predicting HLA-DR binding and specificity. 
 HLA-DRB1*01:01 and HLA-DRB1*03:01 were re-folded with peptides
 synthesized on the peptide array and subsequently stained with mAb clone
 L243 and a anti-mouse-Cy3 before scanning with a laser scanner at one
 micron resolution.  The obtained signals were used to
 train artifcial neural networks (ANNs) where the final network ensamble
 were able to predict the binding of unknown peptides to the respective
 HLAs.
DOI: 10.5061/dryad.66t1g1jzv
title: Data from: The genetic landscape of axonal neuropathies in the middle aged and elderly: focus on MME (supplementary information)

description: OBJECTIVE: To test the hypothesis that monogenic neuropathies such as
 Charcot-Marie-Tooth disease (CMT) contribute to frequent but often
 unexplained neuropathies in the elderly, we performed genetic analysis of
 230 patients with unexplained axonal neuropathies and disease onset
 &gt;35 years. METHODS: We recruited patients, collected clinical data
 and conducted whole-exome sequencing (WES, n=126) and MME single-gene
 sequencing (n=104). We further queried WES repositories for MME variants
 and measured blood levels of the MME-encoded protein neprilysin. RESULTS:
 In the WES cohort, the overall detection rate for assumed disease-causing
 variants in genes for CMT or other conditions associated with neuropathies
 was 18.3% (familial cases 26.4%, apparently sporadic cases 12.3%). MME was
 most frequently involved and accounted for 34.8% of genetically solved
 cases. The relevance of MME for late-onset neuropathies was further
 supported by detection of a comparable proportion of cases in an
 independent patient sample, preponderance of MME variants among patients
 compared to population frequencies, retrieval of additional late-onset
 neuropathy patients with MME variants from WES repositories, and low
 neprilysin levels in patients’ blood samples. Transmission of MME variants
 was often consistent with an incompletely penetrant autosomal dominant
 trait and less frequently with autosomal recessive inheritance.
 CONCLUSIONS: A detectable fraction of unexplained late-onset axonal
 neuropathies is genetically determined, either by variants in CMT genes or
 genes involved in other conditions that affect the peripheral nerves and
 can mimic a CMT phenotype. MME variants can act as completely penetrant
 recessive alleles but also confer dominantly inherited susceptibility to
 axonal neuropathies in an aging population.
DOI: 10.15468/dl.xhck5c
title: Occurrence Download

description: A dataset containing 885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Moxostoma valenciennesi"
 ]
}

 The dataset includes 885 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002323-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sf7m0cg31
title: Data from: Queen succession conflict in the paper wasp Polistes dominula is mitigated by age-based convention

description: Reproduction in cooperative animal groups is often dominated by one or a
 few individuals, with the remaining group members relegated to
 non-reproductive helping roles. This reproductive skew can evolve if
 helpers receive fitness benefits such as potential future inheritance of
 the breeding position, but the mechanisms by which inheritance is
 determined are not well resolved. Polistes paper wasps form highly
 reproductively skewed groups and inheritance of the breeding position is
 likely to play a key role in the maintenance of this social structure,
 making them excellent models for the processes by which simple societies
 are maintained. Reproductive succession is thought to be determined via an
 age-based convention in some Polistes species, but there is also evidence
 for contest-based succession systems in which the replacement queen uses
 physical aggression to overpower and thereby subordinate her nestmates.
 Here we provide evidence that queen succession in colonies of the European
 paper wasp Polistes dominula is determined via convention rather than
 contest, with little disruption to the colony’s social functioning. We use
 queen removal experiments and fine-scale behavioral analyses to confirm
 that age is a strong predictor of succession, and that behavioral
 responses to queen removal are restricted to the oldest individuals rather
 than being experienced equally across the group. We provide the most
 comprehensive and detailed experimental analysis on the dynamics of
 breeder succession in a cooperatively breeding invertebrate to date,
 thereby shedding light on the mechanisms by which animal societies are
 able to maintain cohesion in the face of within-group conflict.
description: Data pertain to behavioral observations of
 early-season <em>Polistes dominula</em> nests, collected near
 Florence, Italy and filmed in laboratory conditions at the University of
 Florence. Footage was annotated by an observer using BORIS software as
 described in Taylor <em>et al</em> and the attached README
 file, and the resulting raw annotation files are provided here, while an
 accompanying Excel sheet provides metadata for each annotation
 file.  Full methodology for the collection and rearing
 of wasps is provided in Taylor <em>et al</em>.
description: A README file is attached, and an excel sheet with metadata for
 each set of observation is included in the uploaded data. This sheet
 includes any videos for which data are missing, indicated by a row of
 blanks where the metadata would otherwise be.
DOI: 10.5061/dryad.95x69p8gk
title: Out in the open: behavior’s effect on predation-risk and thermoregulation by aposematic caterpillars

description: Warning coloration should be under strong stabilizing selection but often
 displays considerable intraspecific variation. Opposing selection on color
 by predators and temperature is one potential explanation for this seeming
 paradox. Despite the importance of behavior for both predator avoidance
 and thermoregulation, its role in mediating selection by predators and
 temperature on warning coloration has received little attention. Wood
 tiger moth caterpillars, Arctia plantaginis, have aposematic coloration,
 an orange patch on the black body. The size of the orange patch varies
 considerably: individuals with larger patches are safer from predators,
 but having a small patch is beneficial in cool environments. We
 investigated microhabitat preference by these caterpillars and how it
 interacted with their coloration. We expected caterpillar behavior to
 reflect a balance between spending time exposed to maximize basking and
 spending time concealed to avoid detection by predators. Instead, we found
 that caterpillars preferred exposed locations regardless of their
 coloration. Whether caterpillars were exposed or concealed had a strong
 effect on both temperature and predation risk, but caterpillars in exposed
 locations were both much warmer and less likely to be attacked by a bird
 predator (great tits, Parus major). This shared optimum may explain why we
 observed so little variation in caterpillar behavior and demonstrates the
 important effects of behavior on multiple functions of coloration.
description: <strong>See Readme files for more information about each
 file. Thermal images and recordings of predation experiments can be made
 available upon request.</strong>
 <strong>HiddenExposedBirdData</strong>
 Bird-level data from the predation experiment.
 <strong>HiddenExposedCatData</strong>
 Caterpillar-level data from the predation experiment
 <strong>longLabBehave</strong>
 Data from the long-term (one day) caterpillar behavior
 experiment
 <strong>outsideCatTemp</strong>
 Data from the experiment testing the effects of color pattern and
 exposure on caterpillar temeprature.
 <strong>repeatTest</strong>
 Remeasurement of the temperature of a subset of caterpillars from
 shortLabBehave to test repeatability of method.
 <strong>shortLabBehave</strong>
 Data from the short-term (20 min) caterpillar behavior
 experiment
DOI: 10.15468/dl.mp72jk
title: Occurrence Download

description: A dataset containing 220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anthyllis polycephala",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 220 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002324-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3xsj3txcj
title: In vivo microbial coevolution favours host protection and plastic downregulation of immunity

description: Microbiota can protect their hosts from infection. The short timescales in
 which microbes can evolve presents the possibility that ‘protective
 microbes’ can take-over from the immune system of longer-lived hosts in
 the coevolutionary race against pathogens. Here, we found that coevolution
 between a protective bacterium (Enterococcus faecalis) and a virulent
 pathogen (Staphylococcus aureus) within an animal population
 (Caenorhabditis elegans) resulted in more disease suppression than when
 the protective bacterium adapted to uninfected hosts. At the same time,
 more protective E. faecalis populations became costlier to harbour and
 altered the expression of 134 host genes. Many of these genes appear to be
 related to the mechanism of protection, reactive oxygen species
 production. Crucially, more protective E. faecalis populations
 downregulated a key immune gene, sodh-1, known to be effective against S.
 aureus infection. These results suggest that a microbial line of defence
 is favoured by microbial coevolution and may cause hosts to plastically
 divest of their own immunity.
description: The evolution experiment consisted of two treatments:
 (i) <em>S. aureus</em> and <em>E.
 faecalis</em> were co- passaged within <em>C.
 elegans </em>(and so allowed to coevolve), and (ii) <em>E.
 faecalis</em> was passaged alone within <em>C.
 elegans</em>. Each treatment consisted of five replicate populations
 with 10 passages.  Protective ability was assessed by
 calculating the proportion of dead worms in the population after 24h
 pathogen exposure, with and without <em>E.
 faecalis</em> co-colonisation. Cost was assessed by calculating the
 proportion of dead worms in the population after 24h exposure
 to <em>E. faecalis</em>. Both cost and protection experiments
 were repeated twice independently and the counts of total and dead worms
 were summed prior to statistical analysis. <em>E.
 faecali</em>s-mediated suppression of <em>S.
 aureus</em> via reactive oxygen species production was assessed in
 vitro. We performed this experiment with either coevolved or evolved
 populations of <em>E. faecalis </em>against the ancestral
 stock of <em>S. aureus.</em> Bacteria were cultured overnight
 in THB shaking (200rpm) at 30°C. THB solution was made with 0.25M
 potassium phosphate buffer containing superoxide dismutase from bovine
 erythrocytes (Sigma-Aldrich) and catalase from bovine liver
 (Sigma-Aldrich), each at a concentration of 0.25mg ml-1. An enzyme-free
 THB solution served as control with only 0.25M potassium phosphate buffer.
 After standardising the bacteria (OD600 of 1.00), 3μl of each species was
 added to 194μl of THB and shaken at 30°C for 24h. Colony-forming units per
 ml (CFU/ml) of <em>S. aureus</em> were counted by plating
 dilutions onto MSA plates. This experiment was repeated two independent
 times and the results were averaged per replicate population.
DOI: 10.5061/dryad.zcrjdfn7p
title: Data from: Reconfiguration of functional brain networks and metabolic cost converge during task performance

description: The ability to solve cognitive tasks depends upon adaptive changes in the
 organization of whole-brain functional networks. However, the link between
 task-induced network reconfigurations and their underlying energy demands
 is poorly understood. We address this by multimodal network analyses
 integrating functional and molecular neuroimaging acquired concurrently
 during a complex cognitive task. Task engagement elicited a marked
 increase in the association between glucose consumption and functional
 brain network reorganization. This convergence between metabolic and
 neural processes was specific to feedforward connections linking the
 visual and dorsal attention networks, in accordance with task requirements
 of visuo-spatial reasoning. Further increases in cognitive load above
 initial task engagement did not affect the relationship between metabolism
 and network reorganization but only modulated existing interactions. Our
 findings show how the upregulation of key computational mechanisms to
 support cognitive performance unveils the complex, interdependent changes
 in neural metabolism and neuro-vascular responses.
description: Data of 22 healthy human participants was collected using
 simultaneous PET/MR imaging at rest and during task performance (easy and
 hard level). Data are processed and include individual
 brain maps in MNI-space of glucose metabolism, cerebral blood flow, BOLD
 task effects and functional connectivity. Individual DCM results from BOLD
 imaging are provided. Group results include separate
 one-sample t-tests for each imaging modality. The conjunction map
 represents the intersection of group task effects (hard level) across
 glucose metabolism, cerebral blood flow and BOLD changes.
 Data are fully anonymized.