cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.djh9w0w15
title: Data from: Laminar microcircuitry of visual cortex producing attention-associated electric fields

description: Cognitive operations are widely studied by measuring electric fields
 through EEG and ECoG. However, despite their widespread use, the neural
 circuitry giving rise to these signals remains unknown because the
 functional architecture of cortical columns producing attention-associated
 electric fields has not been explored. Here, we detail the laminar
 cortical circuitry underlying an attention-associated electric field
 measured over posterior regions of the brain in humans and monkeys. First,
 we identified visual cortical area V4 as one plausible contributor to this
 attention-associated electric field through inverse modeling of cranial
 EEG in macaque monkeys performing a visual attention task. Next, we
 performed laminar neurophysiological recordings on the prelunate gyrus and
 identified the electric-field-producing dipoles as synaptic activity in
 distinct cortical layers of area V4. Specifically, activation in the
 extragranular layers of cortex resulted in the generation of the
 attention-associated dipole. Feature selectivity of a given cortical
 column determined the overall contribution to this electric field. Columns
 selective for the attended feature contributed more to the electric field
 than columns selective for a different feature. Last, the laminar profile
 of synaptic activity generated by V4 was sufficient to produce an
 attention-associated signal measurable outside of the column. These
 findings suggest that the top-down recipient cortical layers produce an
 attention-associated electric field that can be measured extracortically
 with the relative contribution of each column depending upon the
 underlying functional architecture.
description: Data were collected using linear multielectrode arrays positioned
 orthogonal to area V4 in the prelunate gyrus of two macaque monkeys
 performing a visual search task.
description: Data are formatted for use in MATLAB. ReadMe contains information
 pertinent to the dataset variables.
DOI: 10.5061/dryad.zs7h44j99
title: Individual and species variation in mixed-species aggregations of harvestmen

description: This dataset is associated with the published paper Escalante, I,
 M Domínguez, D Gómez-Ruiz, and G Machado. Benefits and costs of
 multi-specific aggregations in harvestmen (Arachnida: Opiliones).
 Frontiers in Ecology and Evolution (DOI 10.3389/fevo.2021.766323). Please
 refer to the paper for the extensive explanations on the collection,
 analysis, presentation, and analyses of the data.  We provide the
 first description of mixed-species roosting aggregations of seven species
 of the genus Prionostemma from Costa Rica. We surveyed
 several plants (trees and palms) for the presence of harvestmen of seven
 different species across time (14 days). These harvestmen are frequently
 found in aggregations. Hence, we also counted the number of individuals in
 each aggregation. Additionally, we counted the number of legs in each
 harvestmen, as well as the number of parasitic mite larvae found in the
 harvestmen's bodies. With all of this information, we were able to
 explore the effects of the roosting status (solitary/aggregated), the
 aggregation size, and the species composition of the aggregations (single-
 or multi-species aggregations) with potential benefits (less damage, i.e.,
 individuals with all of their legs) and costs (a higher parasitic
 infection).
description: We surveyed trees during the daytime looking for harvestmen
 roosting in solitary, in pairs, or in aggregations. We noted the number
 and species of all individuals in the group, and we noted the number of
 legs present, as well as the number of ectoparasitic mites.
DOI: 10.5061/dryad.r2280gbdg
title: What feeds on Quercus ilex L.? A biogeographical approach to studying trophic interactions in a Mediterranean keystone species

description: Holm oak (Quercus ilex L.) is regarded as a keystone plant species.
 Although trophic interactions may affect the phytophagous species
 distribution and abundance, the number of arthropod species using holm oak
 as a food resource and their levels of host specificity is not yet known.
 Here we aim to quantify these species, their feeding strategies and
 conservation status, investigate the taxonomic relatedness in each trophic
 guild and assess their degree of host specificity with the holm oak.We
 reviewed the existing literature and compiled information about all
 arthropod species that feed on Q. ilex, as well as their feeding
 strategies and conservation status. We also investigated the relationships
 between trophic guilds and the taxonomic relatedness of species and
 assessed the degree of climatic niche overlap with holm oak. We found that
 605 species feed on seven different parts of the holm oak plant (i.e.,
 feeding strategies). More than 90% of these species lack a conservation
 status assessment and eight are threatened by human activities, either as
 vulnerable, endangered, or critically endangered. A significant
 phylogenetic relationship was found between taxonomic relatedness and
 groups of arthropods that feed on the same part of the plant (i.e.,
 trophic guilds). Twenty percent of the species had similar niches, thereby
 indicating the potentially high host dependence of these species. This
 study highlights the significance of a keystone tree species for arthropod
 conservation and the need for further research into the distribution and
 conservation status of arthropod species in Mediterranean holm oak
 woodlands.
DOI: 10.5061/dryad.0vt4b8h0f
title: Exceptional variation in the appearance of Common Murre eggs reveals their potential as identity signals

description: We studied the ground colors and maculations of 161 Common Murre (Uria
 aalge) eggs laid by 43 females in 3 small breeding groups on the cliffs of
 Skomer Island, Wales, in 2016–2018. Both the colors and maculations varied
 much more among than within females, providing quantitative evidence for
 the egg traits that might facilitate the parents’ ability to identify
 their own eggs on the crowded breeding ledges where the density is
 typically ~20 eggs m–2. Ground colors had a trimodal distribution of hue
 values (whitish to pale brown, pale blue, or vivid blue-green) and
 maculations ranged from none to complex squiggles and blotches. The eggs
 laid by each female in different years were similar to one another, and
 replacement eggs laid by females within years were also more similar to
 their first egg than to other eggs in the same breeding group. Egg
 appearance did not differ among the 3 breeding groups that we studied. Our
 findings thus support anecdotal observations that, within and between
 years, female Common Murres lay eggs that have similar ground colors and
 maculations. We do not, however, find evidence that there is much
 difference among the eggs laid in different parts of a colony.
description: Photographs of eggs under
 standardized conditions in the field. Analyzed colors and some simple
 maculation metrics from digital photographs.
description: See README file.
DOI: 10.5061/dryad.tqjq2bw0d
title: Lianas and trees exhibit divergent intrinsic water-use efficiency along elevational gradients in South American and African tropical forests

description: Elevational gradients provide excellent opportunities to explore long-term
 morphological and physiological responses of plants to environmental
 change. We determined the difference in the elevational pattern of foliar
 carbon isotope composition (δ13C) between lianas and trees, and assessed
 whether this difference arises from changes in photosynthesis or stomatal
 conductance. We also explored the pattern of nutrient limitations with the
 elevation of these two growth forms. We conducted inventories of lianas
 and trees using standardized techniques along elevational gradients in
 Ecuador and Rwanda. We determined the values of several foliar traits
 including δ13C and chemical traits in dominant liana and tree species. We
 set up Bayesian linear mixed-effect models to quantify the effects of
 elevation and these two growth forms, and the difference of the effect of
 elevation between the two growth forms on each of the foliar traits. We
 found consistent growth form specific divergences in foliar δ13C and
 carbon to nitrogen ratio (C:N) responses to elevation. While we noted a
 meaningful increase in foliar δ13C and C:N with elevation for trees,
 lianas did not exhibit such a trend. Foliar δ13C and C:N remained
 relatively constant for lianas along the transects. The physiological
 processes at the basis of foliar carbon isotope fractionation shift
 differently in lianas and trees along elevation. Lianas operate at
 relatively constant intrinsic water- and nitrogen- use efficiencies with
 elevation as opposed to trees. Altogether, the study suggests the
 existence of a functional divergence of water and nutrient use strategies
 between lianas and trees along tropical elevational transects.
DOI: 10.5061/dryad.cjsxksn67
title: Codes for simulation and data for: The relationship between local and regional extinction rates depends on species distribution patterns

description: The rapid loss of biodiversity poses a great threat to ecosystem functions
 and services. Credible estimation of species extinction rates is essential
 for understanding the magnitude of biodiversity loss and for informing
 conservation, but this has been a challenge because estimated extinctions
 are unverifiable due to the lack of data. In this study, we investigated
 the relationship between local and regional extinctions and assessed the
 effects of range size, spatial segregation, and patchiness of species
 distribution on this local-regional extinction relationship. We found that
 regional extinction rates had a convex relationship with local extinction
 rates, that is, the regional extinction rate was most likely to be lower
 than the average local rate. The regional rates deviated from local rates
 as the sampling area decreased. The difference between local and regional
 extinction rates (local-regional extinction difference) became larger if a
 higher number of species had larger range sizes and patchiness. We also
 detected that there were interactive effects among these factors. Species
 segregation had a weak positive relationship with the local-regional
 extinction difference if more species had relatively large range sizes. As
 the sampling areas increased, the range size showed smaller positive
 effects on local-regional differences, but patchiness showed larger
 positive effects. The local-regional extinction relationship of this study
 provides insights into the spatial scaling of biodiversity loss and offers
 some important cues for estimating regional extinctions from local data in
 future studies.
description: This dataset includes three files: (1) the R code file for
 simulation of local-regional extinction relationships; (2) The simulation
 results; (3) the data for figure 4.
DOI: 10.5061/dryad.pc866t1p9
title: Comparing full-field data from structural components with complicated geometries

description: A new decomposition algorithm based on QR factorisation is introduced for
 processing and comparing irregularly shaped stress and deformation
 datasets found in structural analysis. The algorithm improves the
 comparison of two-dimensional data fields from the surface of components
 where data is missing from the field of view due to obstructed measurement
 systems or component geometry that results in areas where no data is
 present. The technique enables the comparison of these irregularly shaped
 datasets without the need for interpolation or warping of the data. This
 ensures comparisons are only made between the available data in each
 dataset and thus similarity metrics are not biased by missing data. The
 decomposition and comparison technique has been applied during an impact
 experiment, a modal analysis, and a fatigue study, with the stress and
 displacement data obtained from finite element analysis, digital image
 correlation and thermoelastic stress analysis. The results demonstrate
 that the technique can be used to process data from a range of sources and
 suggests the technique has the potential for use in a wide variety of
 applications.
DOI: 10.5061/dryad.n8pk0p2w0
title: Both real-time and long-term environmental data perform well in predicting shorebird distributions in managed habitat

description: Highly mobile species, such as migratory birds, respond to seasonal and
 inter-annual variability in resource availability by moving to better
 habitats. Despite the recognized importance of resource thresholds,
 species distribution models typically rely on long-term average habitat
 conditions, mostly because large-extent, temporally-resolved,
 environmental data are difficult to obtain. Recent advances in remote
 sensing make it possible to incorporate more frequent measurements of
 changing landscapes; however, there is often a cost in terms of model
 building and processing and the added value of such efforts is unknown.
 Our study tests whether incorporating real-time environmental data
 increases the predictive ability of distribution models, relative to using
 long-term average data. We developed and compared distribution models for
 shorebirds in California’s Central Valley based on high temporal
 resolution (every 16-days), and 17-year long-term average, surface water
 data. Using abundance-weighted boosted regression trees, we modeled
 monthly shorebird occurrence as a function of surface water availability,
 crop type, wetland type, road density, temperature, and bird data source.
 While modeling with both real-time and long-term average data provided
 good fit to withheld validation data (0.79 &lt; AUC &lt; 0.89
 across taxa), there were small differences in model performance. The best
 models incorporated long-term average conditions and spatial pattern
 information for real-time flooding (e.g. perimeter-area ratio of real-time
 water bodies). There was not a substantial difference in the performance
 of real-time and long-term average data models within time periods when
 real-time surface water differed substantially from the long-term average
 (specifically during drought years 2013-2016) and in intermittently
 flooded months or locations. Spatial predictions resulting from the models
 differed most in the southern region of the study area where there is
 lower water availability, fewer birds, and lower sampling density.
 Prediction uncertainty in the southern region of the study area highlights
 the need for increased sampling in this area. Because both sets of data
 performed similarly, the choice of which data to use may depend on the
 management context. Real-time data may ultimately be best for guiding
 dynamic, adaptive conservation actions whereas models based on long-term
 averages may be more helpful for guiding permanent wetland protection and
 restoration. --
description: Please see manuscript and supplement.
DOI: 10.5061/dryad.9w0vt4bgg
title: Data for PNASnexus article Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell phenotype

description: Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to
 self-renew in order to maintain tissue architecture and homeostasis. Adult
 salivary glands have been documented to harbor SSPC, which have been shown
 to play a vital role in the regeneration of the glandular structures post
 radiation damage. We have previously demonstrated that activation of
 aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde
 accumulation in SSPC, leading to less apoptosis and improved salivary
 function. We subsequently found that sustained pharmacological ALDH3A1
 activation is critical to enhance regeneration of murine submandibular
 gland after radiation damage. Further investigation shows that ALDH3A1
 function is crucial for SSPC self-renewal and survival even in the absence
 of radiation stress. Salivary glands from Aldh3a1-null mice have fewer
 acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological
 inhibition in SSPC leads to a decrease in mitochondrial DNA copy number,
 lower expression of mitochondrial specific genes and proteins, structural
 abnormalities, lower membrane potential, and reduced cellular respiration.
 Loss or inhibition of ALDH3A1 also elevates ROS levels and accumulation of
 ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product),
 leading to decreased survival of murine SSPC that can be rescued by
 treatment with 4-HNE specific carbonyl scavengers. Our data indicate that
 ALDH3A1 activity protects mitochondrial function and is important for the
 regeneration activity of SSPC. This knowledge will help to guide our
 translational strategy of applying ALDH3A1 activators in the clinic to
 prevent radiation-related hyposalivation in head and neck cancer patients.
description: Flow cytometry experiments:
 The data file was exported and analysed using Flowjo software.
 All the data was normalized to the control of the experiment.
 Immmunostaining experiments:
 The immunostaining images were uploaded and quantified using
 ImageJ software. The color threshold was set for each antibody stain and
 was kept consistent across all groups. The intensity was measured,
 quantified and represented as mean fluoresence intensity for
 immunofluoresence or Mean Arbitary units for Immunohistochemistry
 experiment. PCR based
 experiments: The protocol for PCR is
 described in the manuscript. The expression was normalized to the WT
 group. All other data
 sets: The experiment and analyses is well
 described in the manuscript.
DOI: 10.5061/dryad.j9kd51ccz
title: Mimosa catherinensis SNP data sets

description: To inform management strategies for conservation of Mimosa catharinensis –
 a narrow endemic, critically endangered plant species – we identified
 1,497 unlinked SNP markers derived from a reduced representation
 sequencing method (i.e., ddRADseq). This set of molecular markers was
 employed to assess intrapopulation genetic parameters and the demographic
 history of one extremely small population of M. catharinensis located in
 the Brazilian Atlantic Forest. We observed a moderate level of genetic
 diversity for M. catharinensis. Interestingly, M. catharinensis, which is
 a lianescent shrub with no indication of seed production for at least two
 decades, presented high levels of outcrossing and no evidence of
 inbreeding. However, the reconstruction of demographic history of M.
 catharinensis indicate that the population should be suffered a recent
 bottleneck.
description: DNA was extracted from leaf samples of all collected individuals
 employing the NucleoSpin® kit (Machereney-Nagel GmbH & Co. KG)
 following manufacturer’s guidelines. After extraction, the quality of each
 sample was verified using Thermo Scientific NanoDrop 2000
 Spectrophotometer (Thermo Fisher Scientific Inc.) and the concentration of
 double-strand DNA (dsDNA) was obtained by using Qubit dsDNA Assay Kit
 (Invitrogen). The genomic library was prepared using a double-digest
 restriction site-associated DNA sequencing (i.e., ddRADseq) protocol with
 modifications proposed by Nazareno et al. (2017). Data
 quality was checked using the program FastQC version: 0.11.8. The file
 containing raw sequence reads was analyzed in Stacks 2.41 (Catchen et al.
 2011; Catchen et al. 2013; Rochette et al. 2019) using de novo<i>
 </i>assembly.
description: There are seven csv files that contain the genotypes for all the
 33 samples (column A, rows 4 to 36) for each locus. Each csv file contains
 data with different percentage of missing data, varying from 0% to 30%. At
 each csv file, the locus name always starts in column B.
DOI: 10.5061/dryad.18931zcxx
title: The awareness, visibility and support for young carers across Europe: a Delphi study

description: Across Europe, young carers (YCs) and their need for support receive
 limited attention in the media, policy and empirical research, even
 though, similar to adult carers, they also provide care to ill family
 members. The Delphi study, a qualitative research methodology, which
 provides the focus for this article, had the overall aim of exploring
 existing successful strategies to support YCs. Compared to YCs, even less
 is known about adolescent young carers (AYCs), a group that is in a
 critical life transition phase. The study forms part of an EU Horizon 2020
 funded research project on AYCs aged 15–17 years old. A two-round Delphi
 study was conducted with 66 experts on YCs from 10 European countries.
 Topics included: (i) visibility and awareness-raising of YCs at local,
 regional, and national levels, (ii) current interventions to support YCs,
 and (iii) future strategies to support YCs. Experts reported a lack of
 visibility and awareness about YCs in general, and AYCs in particular.
 Although awareness is slowly increasing in most countries, with the UK
 ranked highest, experts acknowledged that it remains challenging to
 identify YCs in many countries. Furthermore, the level and type of support
 available for YCs differs, with most countries mainly offering support on
 a local level. Diverse views were expressed regarding future strategies to
 support YCs. Experts highlighted the importance of specific legislation to
 formalise the rights of YCs, and the issue of whether young people should
 be safeguarded from caregiving or if this should be considered part of
 regular family life. They also emphasised the relevance of available
 integrated support services for YCs, including schools, family, health and
 social care. In most European countries, there is a lack of awareness and
 visibility on YCs. Identification of YCs is a crucial first step and there
 is need for a common definition of YCs, together with greater
 opportunities for young adults to identify themselves as YCs.
description: Via telephone, online or physical interviews. Data was
 transcribed and summarized using a thematic analysis.
description: The dataset includes the
 ME-WE interview guide of round 1 in English, The interview guide that was
 used during the first round of the Delphi study. The dataset also includes the
 ME-WE interview guide of round 2 used in the UK, The summary of the
 results from the first round; 1. General results first round (per topic),
 2. Country specific results, and 3. In-depth results from the country
 where the interview took place (this case UK). After every section,
 questions where added for the experts.
DOI: 10.5061/dryad.k6djh9w6w
title: Regridded subset of MODIS chlorophyll, OC-CCI chlorophyll, MODIS sea surface temperature; basin bathymetric depth

description: The North Atlantic phytoplankton bloom depends on a confluence of
 environmental factors that drive transient periods of exponential
 phytoplankton growth and interannual variability in bloom magnitude. I
 analyze interannual bloom variability in the North Atlantic via extreme
 value theory where the Generalized Extreme Value Distribution (GEVD) is
 fitted spatially to annual maxima of satellite-measured surface
 chlorophyll. I find excellent agreement between the observed distribution
 of interannual bloom maxima and those predicted from the GEVD. The spatial
 distribution of fitted GEVD parameters closely follows basin bathymetry
 where the largest extremes and heaviest distribution tails are found on
 the continental shelves and slopes. Trend analyses suggest weak evidence
 for changes in GEVD parameters, despite regional trends in mean
 chlorophyll levels and sea surface temperature. These results provide a
 framework to quantify interannual bloom variability and call for further
 work examining how extreme blooms propagate through food webs and
 contribute to carbon export.
description: Data are a regridded subset of publicly available MODIS
 chlorophyll a, OC-CCI chlorophyll a.