cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.crjdfn345
title: Hump-shaped relationship between aggregation tendency and body size within fish populations

description: A distribution with high spatial variability may impair the bet-hedging
 capacity of a population, threatening population sustainability.
 Although the association between aggregation and life history traits of a
 species (e.g. body size) has been documented, the relationship
 between aggregation and size within a population has rarely
 been explored. As selective over-fishing may induce size
 truncation in the targeted stocks,it is critical to understand if such a
 truncation also undermines the distribution patterns of the
 population. In this study, we examined if and how the
 ‘aggregation tendency’ varies among different size classes of a
 population. Aggregation tendency was quantified as the exponent b of
 Taylor’s power law (V = a × Mb), which measures the change in spatial
 variance (V) with the mean abundance (M) of a population. We estimated b
 by size class for each of the nine commercially important fish species in
 the North Sea, using ICES survey data from 1991 to 2015. Our study found
 that the relationship between b and body size within a population is
 hump-shaped, with a peak slightly larger than the 50% mature length of the
 species. This result indicates larger adults in a population tend to
 distribute less heterogeneously when abundance increases, suggesting that
 larger size classes play a critical role in reducing the variability of
 population distribution. Our findings highlight the importance of
 considering the combined effects of fishing-induced size truncation and
 changes in aggregation patterns in fishery management. That is,
 maintaining the size and spatial structure for the target stocks of
 selective fisheries is critical for the sustainability of the populations.
description: The raw cpue data, maturation stage, and fishing mortality data
 were downloaded from the DATRAS (https://datras.ices.dk/Data_products/Download/Download_Data_public.aspx). The temperature data was download from the ICES website (https://ocean.ices.dk/HydChem/HydChem.aspx?plot=yes). The life history traits data was extracted from Thorp et al.'s (2015) study.  Using R code (https://github.com/ruo-yu-Pan/Hump-shaped-relationship_Aggregation-tendency_vs_bodysize), we processed the raw data, calculated the size-based Taylor's exponents, and investigated the effect of body size and temperature on the size-based Taylor's exponents within the population.
description: The data used and the outcome in the estimation of size-based
 Taylor's power law and the relationship between aggregation tendency
 and body size in the North Sea.
 SizeAggregTend_data.zip
DOI: 10.5061/dryad.t76hdr817
title: How do children and adolescents experience healthcare professionals? Scoping review and interpretive synthesis

description: Objective Explore children’s and adolescents’ (CADs’) lived experiences of
 healthcare professionals (HCPs). Eligibility criteria Research articles
 containing direct first-person quotations by CADs (aged 0-18 years
 inclusive) describing how they experienced HCPs. Scoping review
 methodology provided a six-step framework to, first, identify and organise
 existing evidence. Interpretive phenomenology provided methodological
 principles for, second, an interpretive synthesis of the life-worlds of
 CADs receiving healthcare, as represented by verbatim accounts of their
 experiences. Five key databases (Ovid MEDLINE, Embase, Scopus, CINAHL
 Plus, and Web of Science), from inception through to January 2019,
 reference lists, and opportunistically identified publications. Tabulation
 of study characteristics, contextual information, and verbatim extraction
 of all ‘relevant’ (as defined above) direct quotations. Analysis of basic
 scope of the evidence-base. The research team worked reflexively and
 collaboratively to interpret the qualitative data and construct a
 synthesis of children’s experiences. To consolidate and elaborate the
 interpretation, we held two focus groups with CAD inpatients in a
 children’s hospital. 669 quotations from 99 studies described CADs’
 experiences of HCPs. Favourable experiences were of forming trusting
 relationships and being involved in healthcare discussions and decisions;
 less favourable experiences were of not relating to or being unable to
 trust HCPs and/or being excluded from conversations about them. HCPs
 fostered trusting relationships by being personable, wise, sincere, and
 relatable. HCPs made CADs feel involved by including them in
 conversations, explaining medical information, and listening to CADs’
 wider needs and preferences.These findings strengthen the case for making
 CADs partners in healthcare despite their youth. We propose that a
 criterion for high-quality child-centred healthcare should be that HCPs
 communicate in ways that engender trust and involvement.
description: Authors searched five key databases (Ovid MEDLINE, Embase,
 Scopus, CINAHL Plus, and Web of Science), from inception through to 11th
 January 2019, reference lists, and opportunistically identified
 publications. Articles presenting first-person direct quotations from
 children and adolescents aged up to 18 years (inclusive) and describing
 experiences of healthcare professionals were included. All relevant
 quotations were extracted, along with ages and genders, to provide the
 dataset.  Quotations were analysed using interpretive
 phenomenology and Braun and Clarke's thematic analysis. 
description: All source articles are cited and missing values indicated.
DOI: 10.5061/dryad.08kprr52t
title: The use of nanobodies in a sensitive ELISA test for SARS-CoV-2 Spike 1 protein

description: A rapid detection method for SARS-CoV-2 spike protein is essential for
 control of COVID19. We investigated various combinations of engineered
 nanobodies in a sandwich ELISA to detect the Spike protein of SARS-CoV-2.
 We have identified an optimal combination of nanobodies. These were
 selectively functionalised to further improve antigen capture. This
 dataset contains data from ELISA experiments described in the
 manuscript.                                                                                                                                           Plate coating of nanobodies for ELISA by passive adsorption vs biotinylation was compared. A series of nanobody pairings (two cluster 2 ACE2-binding epitope and two cluster 1 CR3022 epitope) were screened for optimum sensitivity. The optimal pair were then tested against a series of SARS-COV-2 antigens: recombinant spike 1 protein; recombinant receceptor binding domain (RBD); pseudotyped HIV-1 and heat-empigen inactivated SARS-CoV-2 virus. X-ray irradiated SARS-CoV-2 was also tested. Sensitivity to these antigens was compared with nanobodies biotinylated a) site-selectively and b) in a non-specific stochastic manner. Batch-to-batch viral variation and effects of inactivating agents were investigated. Limit of detection was compared against delta and beta viral mutants. Combining optimal nanobody pairing and site-selective biotinylation, we observed a limit of detection of 147 pg/mL for Spike protein; 33 pg/mL for RBD; 16 TCID50/mL of pseudovirus and 15 ffu/mL of heat-Empigen inactivated SARS-CoV-2. The pairing also showed sensitivity towards delta variant. We have demonstrated the use and sensitivity of nanobodies in ELISA by detection of recombinant and viral SARS-CoV-2 antigens.
description: The data supplied is raw absorbance data for ELISA. The data was
 collected on a Spectramax M3 microplate reader (Molecular
 Devices).<br> The data was processed using Prism software. Variable
 slopes were modelled using Prism's sigmoidal 4-parameter logistic
 curve. To determine slope gradient, values in linear range were modelled
 using simple linear regression. Standard deviation was calculated using
 the built-in prism analysis.
description: All ELISA data is supplied in one Prism file, each dataset is
 given in the order displayed in the main manuscript, followed by ELISA
 data from supporting information.<br> A word document describing
 which figure relates to which prism dataset is also supplied for
 clarity. Some anomalous replicates were omitted for the
 final analyses; these are included in the supplied datasets and
 highlighted in blue, and are: Figure 3, for Biotinx-C5-Fc/C1-Fc-HRP: all
 third replicates. Figure 4b (same data also in SOI Figure 2) -
 one replicate value is removed.
DOI: 10.5061/dryad.6hdr7sr17
title: Far-field effects of impulsive noise on coastal bottlenose dolphins

description: Increasing levels of anthropogenic underwater noise have caused concern
 over their potential impacts on marine life. Offshore renewable energy
 developments and seismic exploration can produce impulsive noise which is
 especially hazardous for marine mammals because it can induce auditory
 damage at shorter distances and behavioural disturbance at longer
 distances. However, far-field effects of impulsive noise remain poorly
 understood, causing a high level of uncertainty when predicting the
 impacts of offshore energy developments on marine mammal populations. Here
 we used a 10-year dataset on the occurrence of coastal bottlenose dolphins
 over the period 2009-2019 to investigate far-field effects of impulsive
 noise from offshore activities undertaken in three different years.
 Activities included a 2D seismic survey and the pile installation at two
 offshore wind farms, 20-75 km from coastal waters known to be frequented
 by dolphins. We collected passive acoustic data in key coastal areas and
 used a Before-After Control-Impact design to investigate variation in
 dolphin detections in areas exposed to different levels of impulsive noise
 from these offshore activities. We compared dolphin detections at two
 temporal scales, comparing years and days with and without impulsive
 noise. Passive acoustic data confirmed that dolphins continued to use the
 impact area throughout each offshore activity period, but also provided
 evidence of short-term behavioural responses in this area. Unexpectedly,
 and only at the smallest temporal scale, a consistent increase in dolphin
 detections was observed at the impact sites during activities generating
 impulsive noise. We suggest that this increase in dolphin detections could
 be explained by changes in vocalization behaviour. Marine mammal
 protection policies focus on the near-field effects of impulsive noise;
 however, our results emphasize the importance of investigating the
 far-field effects of anthropogenic disturbances to better understand the
 impacts of human activities on marine mammal populations.
description: Echolocation detectors
 (CPODs; Chelonia Ltd) were deployed between 2009 and 2019 to investigate
 the variation in dolphin detections in relation to the impulsive noise
 from three energy developments: a seismic survey for oil and gas
 exploration and the installation of foundation piles for two offshore wind
 farms (Beatrice Offshore Wind Farm and Moray East Offshore Wind
 Farm). Data on
 the timing of the seismic survey and piling operations were provided by
 the developers (Oil and Gas UK Ltd., COWRIE, Beatrice Offshore Wind Ltd.
 and Moray Offshore Wind Farm East).
description: Data consist of 7 files and
 include the datasets and R code required to repeat all the analyses. A
 full description of the files provided in the Readme.txt file:
 OFB_FarField_DPH.csv OFB_FarField_BOWL.csv OFB_FarField_MEOW.csv OFB_FarField_BACI_Obtain_DPH_Dataset.R OFB_FarField_DPH_for_BACI.csv OFB_FarField_BACI_DPH_Models.R OFB_FarField_Readme.txt
DOI: 10.5061/dryad.9zw3r22f9
title: Lepidoptera caterpillars barcodes in FASTA format

description: The dataset contains COI barcodes of Lepidoptera caterpillars collected
 from a subtropical forest in Jiangxi, China.
description: Lepidopteran larvae were collected six times in 2017 and 2018
 (April, June and September in each year). We collected all caterpillars by
 beating individual trees and knocking down resident insects. Lepidopteran
 caterpillars are much more restricted in their mobility than adult and
 flying insects and have a high probability of being collected from the
 trees they actually feed on (see also Wardhaugh et al., 2012). We beat the
 trees with a padded stick over a white sheet (1.5 m × 1.5 m) and collected
 all caterpillars knocked down from the trees (Schuldt et al., 2014). We
 sampled all trees in the first rows of each plot for a total 80 living
 trees in each plot. We used DNA-barcoding to identify herbivore-host plant
 associations along declining levels of tree diversity in a large-scale,
 subtropical biodiversity experiment. We tested for effects of tree species
 richness, host functional and phylogenetic diversity, and host functional
 (leaf trait) and phylogenetic composition and composition, and leaf trait
 composition on taxonomic species, phylogenetic, and network composition of
 herbivore communities. Our data from six sampling periods represent 6821
 mitochondrial cytochrome c oxidase subunit I (COI) sequences of
 lepidopteran larvae, clustered into 447 molecular operational taxonomic
 units.
DOI: 10.5061/dryad.c59zw3r7f
title: Relationships between plant-soil feedbacks and functional traits

description: Plant-soil feedbacks (PSF) and functional traits are two active but not
 well theoretically integrated areas of research. However, PSF and traits
 are both affected by life history evolution, so the two should
 theoretically be related. We provide a conceptual framework to link plant
 functional traits to two types of PSF metrics, and hypothesize that
 individual PSF (plant performance in conspecific versus heterospecific
 soil) should be related to the fast-slow trait spectrum, while pairwise
 PSF (the sum of the individual feedbacks for two species growing in each
 other’s soils) should be related to trait dissimilarity. We performed
 meta-analyses to test these hypotheses by compiling two datasets, one
 dataset consisting of individual PSF values and plant trait values
 (specific leaf area, SLA; leaf N concentration, LNC; specific root length,
 SRL; fine root diameter, FRD; plant height; seed mass), and the second
 consisting of pairwise PSF values and trait dissimilarity. Our
 meta-analyses showed that individual PSF values were more negative in
 faster-growing species with greater SLA, LNC and SRL, supporting the
 growth-defence trade-off hypothesis. Plant height was positively
 correlated with individual PSF, perhaps because large, long-lived plants
 defend against pathogens better than smaller, shorter-lived plants. We
 also found that larger-seeded species had more positive or less negative
 PSF, likely reflecting greater tolerance of soil pathogens. The direction
 of relationships between trait dissimilarity and pairwise PSF varied with
 trait identity. Dissimilarities in SRL and FRD were negatively correlated
 with pairwise PSF, while height dissimilarity was positively correlated
 with pairwise PSF. The contrasting relationships may reflect distinct
 links between trait dissimilarity and niche and fitness differences.
 Synthesis. Our results demonstrate how an integration of PSF and
 trait-based approaches can advance plant community ecology.
DOI: 10.5061/dryad.5mkkwh765
title: Data from: Dinosaurian survivorship schedules revisited: new insights from an age-structured population model

description: Little is known on dinosaur population biology due to insufficient
 information on age-dependent fecundities and mortalities. So far,
 survivorship curves (hereafter SC) of only six dinosaurs (four
 tyrannosaurs, one ceratopsian, one hadrosaur) were erected from bone
 assemblages of aged specimens. They indicate high survival throughout most
 of their life with presumable higher mortalities after hatching and
 increasing mortalities towards its end. However, all studies ignored that
 assemblages must preserve stationary age distributions (i.e., the
 population’s age distribution is stable and its size is constant over time
 as overall population fecundities match mortalities, hereafter SAD
 population) to infer a reliable SC for a taxon. To assess SCs of these
 dinosaurs, I built a simple population model with age-dependent
 fecundities and survival rates. Its few input parameters are maximum
 longevity, age at sexual maturation and maximum annual offspring number,
 on which information exists in these dinosaurs. As bone histological
 studies and scaling relationships provide estimates on its three
 parameters, my model is also applicable to other extinct taxa.
             Modelling suggests that bone assemblages did not preserve SAD populations. SCs determined for SAD populations of Albertosaurus sarcophagus, Gorgosaurus libratus, Dasplatosaurus torosus and Tyrannosaurus rex indicated that low mortalities follow high mortalities early in their life or that mortalities were rather constant throughout their life. In Psittacosaurus lujiatuensis modelling suggests low mortalities throughout most of its life that increase towards its end. The SC of Maiasaura peeblesorum was not questioned by my model as it is unable to capture sigmoidal or other composite SCs.
description: Analysed samples of age structures of dinosaurs and extant
 species were compiled from literature. The paper
 related to this record presents an age-structured population model that is
 used to re-analyse samples regrading the survivorship curve's
 shape. R-scripts used for analyses done in this paper
 are found here as well as supplementary information on results
 obtained. 
description: Please read the README file for instructions on how to run the
 R-scripts and adapt them for own analysis.
DOI: 10.5061/dryad.n02v6wwxb
title: Supporting data for the article ‘Three-years monitoring of roadkills trends in a road adjacent to a national park in Panama’

description: Roadkill monitoring can provide important information about spatial and
 temporal trends, including influential factors on the probability of
 wildlife – collisions. Such data are important for applying mitigation
 measures that reduce the mortality of species of conservation concern.
 Unfortunately, road ecology is not a mainstream discipline in some regions
 of the world and Central America represents one of those cases. I aimed to
 monitor roadkills in a road next to a national Park in Panama for three
 years. I examined whether there was variation in the number of roadkills
 across taxa (birds, mammals and reptiles), year (2017 – 2020), season (dry
 vs rainy) and whether monthly average precipitation and temperature
 influenced the probability of roadkill occurrence. Additionally, I
 performed a spatial analysis to identify roadkill hotspots. Mammals and
 reptiles were the most common roadkills. Roadkills tended to decrease with
 increases in temperature and precipitation. A separate analysis of the two
 most commons roadkills (iguanas and tamanduas) provided similar trends.
 The spatial analysis helped to identify a hotspot located in a curved
 section of the road and surrounded by water. This is the first study to
 examine for any road in Panama - through statistical modeling –
 factors that may influence the occurrence of roadkill events. The
 results suggest that vehicle collisions exert a similar pressure
 on all taxa and the geometry of the road or distance to the water are also
 influential.  These data sets include monthly roadkill
 counts with average monthly precipitation and temperature during
 the dry and rainy season, over a period of three
 years (ALL.DATA). Two separate data sets (IGUANAS and
 TAMANDUAS) contain data as described for the tab ALL.DATA but
 only with data for green iguanas (Iguana iguana) and Northern Tamandua
 (Tamandua mexicana), respectively. For the spatial analysis, the data set
 COORDINATES show the location of each roadkill event, identified
 by latitude and longitude, date, taxa, IUCN status, scientific
 name and common name.
DOI: 10.5061/dryad.zs7h44j8x
title: Estimation of species divergence times in presence of cross-species gene flow

description: Cross-species introgression can have significant impacts on phylogenomic
 reconstruction of species divergence events. Here, we used simulations to
 show how the presence of even a small amount of introgression can bias
 divergence time estimates when gene flow is ignored in the analysis. Using
 advances in analytical methods under the multispecies coalescent (MSC)
 model, we demonstrate that by accounting for incomplete lineage sorting
 and introgression using large phylogenomic data sets this problem can be
 avoided. The multispecies-coalescent with-introgression (MSci) model is
 capable of accurately estimating both divergence times and ancestral
 effective population sizes, even when only a single diploid individual per
 species is sampled. We characterize some general expectations for biases
 in divergence time estimation under three different scenarios: 1)
 introgression between sister species, 2) introgression between non-sister
 species, and 3) introgression from an unsampled (i.e., ghost) outgroup
 lineage. We also conducted simulations under the isolation-with-migration
 (IM) model, and found that the MSci model assuming episodic gene flow was
 able to accurately estimate species divergence times despite high levels
 of continuous gene flow. We estimated divergence times under the MSC and
 MSci models from two published empirical datasets with previous evidence
 of introgression, one of 372 target enrichment loci from baobabs
 (Adansonia), and another of 1,000 transcriptome loci from fourteen species
 of the tomato relative, Jaltomata. The empirical analyses not only confirm
 our findings from simulations, demonstrating that the MSci model can
 reliably estimate divergence times, but also show that divergence time
 estimation under the MSC can be robust to the presence of small amounts of
 introgression in empirical datasets with extensive taxon sampling.