cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70rxwdbtr
title: Anonymized source data files for figures in: Recurrent processes support a cascade of hierarchical decisions

description: Perception depends on a complex interplay between feedforward and
 recurrent processing. Yet, while the former has been extensively
 characterized, the computational organization of the latter remains
 largely unknown. Here, we use magneto-encephalography to localize, track
 and decode the feedforward and recurrent processes of reading, as elicited
 by letters and digits whose level of ambiguity was parametrically
 manipulated. We first confirm that a feedforward response propagates
 through the ventral and dorsal pathways within the first 200 ms. The
 subsequent activity is distributed across temporal, parietal and
 prefrontal cortices, which sequentially generate five levels of
 representations culminating in action-specific motor signals. Our decoding
 analyses reveal that both the content and the timing of these brain
 responses are best explained by a hierarchy of recurrent neural
 assemblies, which both maintain and broadcast increasingly rich
 representations. Together, these results show how recurrent processes
 generate, over extended time periods, a cascade of decisions that
 ultimately accounts for subjects' perceptual reports and reaction
 times.
description: The data were collected at NeuroSpin, Paris, France, with a CTF
 magneto-encraphalogram. Please see the manuscript for details on the
 experimental task. Fig1: The grand average neural
 response to the visual stimuli, averaged over trials and
 subjects. Fig2: Decoding performance across time (.npy
 files) and space (.stc files). Fig4: Temporal
 generalisation decoding performance for each feature.
 Fig 5: Re-aligned temporal generalisation matriced for each
 feature, and corresponding by-trial reaction times. Fig
 6: Probabalistic output of the classifier over time, for the perceived
 letter/digit category (perceptual decision) and the motor action (motor
 decision).
description: The files are of two formats: .npy and .stc.
   .npy files can be read using the Numpy
 module in python, e.g.: import numpy as np
 data = np.load('file_name.npy')
 https://numpy.org/doc/stable/reference/generated/numpy.load.html     .stc files can be read using the MNE module in python, e.g.: from mne import read_source_estimate stc = read_source_estimate('stc_name-lh.stc') note that reading in the data from just one hemisphere file will automatically read the data for the other one too. https://mne.tools/stable/generated/mne.read_source_estimate.html
DOI: 10.5061/dryad.547d7wm59
title: Data from: Direct and indirect effect of cannibalism and intraguild predation in the two sibling Harmonia ladybird beetles

description: In this study, we focused on the direct (i.e. predation) and indirect
 (i.e. potential threat from coexisting with a larger individual) effects
 of cannibalism and intraguild predation (IGP) during larval stages of two
 sibling ladybird beetles. These effects play an important role in the
 coexistence of the generalist–common Harmonia axyridis and specialist–rare
 H. yedoensis (Coleoptera: Coccinellidae). Direct predation effect of
 cannibalism and IGP were asymmetric in the two sibling ladybird beetles;
 the fourth instar larvae of H. axyridis were better intraguild predators
 than cannibals, while the reverse was true in the larvae of H. yedoensis.
 Neither cannibalism nor IGP significantly affected female body weight in
 either species. Larval H. axyridis surviving exposure to cannibalism or
 IGP had a reduced number of ovarioles as adults, whereas adult H.
 yedoensis ovarioles were not affected. For the indirect effects, longer
 developmental times in males and females and a lower total number of
 ovarioles in females were detected in H. axyridis. In H. yedoensis,
 shorter developmental time of males, lighter adult weight and fewer total
 ovarioles in females were observed. Olfactometer choice experiments
 clarified that the fourth instar larvae of H. axyridis avoided the first
 instar conspecific larvae, while those of H. yedoensis were attracted to
 the odours from H. axyridis and conspecifics. Thus, H. axyridis has an
 avoidance mechanism only for cannibalism but not for IGP, whereas H.
 yedoensis does not have any avoidance mechanism. These different
 behaviours in the direct and indirect effects of cannibalism and IGP
 observed in the laboratory may play important roles in the coexistence of
 generalist–common H. axyridis and specialist–rare H. yedoensis in natural
 conditions, compensating for the large handicap of H. yedoensis at
 reproductive interference from H. axyridis.
description: We focused on the direct and indirect effects of cannibalism and
 intraguild predation (IGP) during larval stages of two sibling ladybird
 beetles <em>Harmonia axyridis</em> and <em>H.
 yedoensi</em>s.
DOI: 10.15468/dl.fwgg6q
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Androcalymma glabrifolium",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002308-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ht76hdrc7
title: Data from: Habitat loss in the restricted range of the endemic Ghanaian cichlid Limbochromis robertsi

description: Remote sensing has become an integral and invaluable tool to inform
 biodiversity conservation and monitoring of habitat degradation and
 restoration over time. Despite the disproportionately high levels of
 biodiversity loss in freshwater ecosystems worldwide, ichthyofauna are
 commonly overlooked in favor of other keystone species. Freshwater fish,
 as indicators of overall aquatic ecosystem health can also be indicators
 of larger scale problems within an ecosystem. As a case study with
 multi-temporal, multi-resolution satellite imagery, we examined
 deforestation and forest fragmentation around the Atewa Forest Reserve,
 Ghana. Within small creeks, Limbochromis robertsi, a unique freshwater
 cichlid with an extremely limited distribution range can be found.
 Historically, the land cover in the area has undergone substantial
 deforestation for agriculture and artisanal small-scale mining. In the
 1389 km2 study area we found deforestation accelerated along with
 increased forest fragmentation in the 2014 – 2017 period (167.4 km2 of
 deforestation) with the majority of the forest loss along the river and
 creek banks due to small-scale mining operations and increased
 agriculture. Field visits indicated a decrease in the total L. robertsi
 population by approximately 90% from the early 1990s to 2018. Its
 distribution has been reduced to higher elevations by anthropogenic
 habitat barriers at low elevations and the presence of predatory species.
 Loss of Riparian forest through land use and cover change to mining and
 agriculture contributes to the habitat degradation for these endemic
 species. The fine spatial and temporal scale studies required to assess
 habitat characteristics is not captured by global or continental scale
 datasets.
DOI: 10.5061/dryad.wdbrv15k8
title: Data from: Mechanical and structural adaptations to migration in the flight feathers of a Palaearctic passerine

description: Current avian migration patterns in temperate regions have been developed
 during the glacial retreat and subsequent colonization of the ice-free
 areas during the Holocene. This process resulted in a geographic gradient
 of greater seasonality as latitude increased that favoured
 migration-related morphological and physiological (co)adaptations. Most
 evidence of avian morphological adaptations to migration comes from the
 analysis of variation in the length and shape of the wings, but the
 existence of intra-feather structural adjustments has been greatly
 overlooked despite their potential to be under natural selection. To shed
 some light on this question, we used data from European robins Erithacus
 rubecula overwintering in Campo de Gibraltar (Southern Iberia), where
 sedentary robins coexist during winter with conspecifics showing a broad
 range of breeding origins and, hence, migration distances. We explicitly
 explored how wing length and shape, as well as several functional (bending
 stiffness), developmental (feather growth rate) and structural (size and
 complexity of feather components) characteristics of flight feathers
 varied in relation to migration distance, which was estimated from the
 hydrogen stable isotope ratios of the summer-produced tail feathers. Our
 results revealed that migration distance not only favoured longer and more
 concave wings, but also promoted primaries with a thicker dorsoventral
 rachis and shorter barb lengths, which in turn conferred more bending
 stiffness to these feathers. We suggest that these intra-feather
 structural adjustments could be an additional, largely unnoticed,
 adaptation within the avian migratory syndrome that might have the
 potential to evolve relatively quickly to facilitate the occupation of
 seasonal environments.
description: Variable definitions included in 2nd tab of spreadsheet
DOI: 10.15468/dl.5hxxrm
title: Occurrence Download

description: A dataset containing 61516 records in GBIF matching the query:
SELECT
 '429' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= -107.00476756053553
 AND decimalLongitude &lt;= -95.90519603780048
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 61516 records were derived from 171 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002294-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7280/d1pq3w
title: Data from: Assessing uncertainties and approximations in solar heating of the climate system

description: Plain language summary of the manuscript "Assessing Uncertainties and
 Approximations in Solar Heating of the Climate System" to be
 published in Journal of Advances in Modeling Earth Systems:
 "Solar heating of the climate system-- the atmosphere, land surface,
 and ocean--drives the climate. Accurate numerical calculation of solar
 heating is a core component of the models we use to project and prepare
 for climate change. The community has identified many potential sources of
 error and published studies showing how to improve the solar heating codes
 used in climate models. Here we assemble a wide range of these errors,
 either numerical approximations or uncertainties in defining atmospheric
 conditions, and put them through the same test: calculating the
 atmospheric and surface heating over a month of simulated climate
 conditions. Combining the new calculations here with previous work, we
 discuss more than a dozen specific areas where improvements could be made
 and identify high-priority actions."
description: Solar-J code is developed at UC Irvine, an 8-stream radiative
 transfer module to be implemented in climate models such as E3SM supported
 by the Department of Energy. In developing Solar-J, we conducted a suite
 of numerical experiments addressing about a dozen common errors due to
 approximations or simplifications in radiative transfer process. We either
 built these approximations as alternatives into Solar-J code or compared
 them directly to the current 2-stream radiative transfer code (RRTMG-SW),
 a widely used package in  the current climate simulation models. We have
 analyzed 22 paired numerical experiments. The Fotran source code of the
 Solar-J, the numerical output and the scripts in producing the figures and
 tables in the manuscript are archived here.
DOI: 10.5061/dryad.mgqnk98wq
title: Dendritic integration in olfactory bulb granule cells upon simultaneous multi-spine activation: Low thresholds for non-local spiking activity

description: The inhibitory axonless olfactory bulb granule cells form reciprocal
 dendrodendritic synapses with mitral and tufted cells via large spines,
 mediating recurrent and lateral inhibition. As a case in point for
 dendritic transmitter release, rat granule cell dendrites are highly
 excitable, featuring local Na+ spine spikes and global Ca2+- and
 Na+-spikes. To investigate the transition from local to global signaling
 we performed holographic, simultaneous two-photon uncaging of glutamate at
 up to twelve granule cell spines, along with whole-cell recording and
 dendritic two-photon Ca2+ imaging in acute juvenile rat brain slices.
 Coactivation of less than ten reciprocal spines was sufficient to generate
 diverse regenerative signals that included regional dendritic Ca2+-spikes
 and dendritic Na+-spikes (D-spikes). Global Na+-spikes could be triggered
 in one third of granule cells. Individual spines and dendritic segments
 sensed the respective signal transitions as increments in Ca2+ entry.
 Dendritic integration as monitored by the somatic membrane potential was
 mostly linear until a threshold number of spines was activated, where
 often D-spikes along with supralinear summation set in. As to the
 mechanisms supporting active integration, NMDA receptors strongly
 contributed to all aspects of supralinearity, followed by dendritic
 voltage-gated Na+- and Ca2+-channels, whereas local Na+ spine spikes as
 well as morphological parameters barely mattered. Because of the low
 numbers of coactive spines required to trigger dendritic Ca2+ signals and
 thus possibly lateral release of GABA onto mitral and tufted cells, we
 predict that thresholds for granule cell-mediated bulbar lateral
 inhibition are low. Moreover, D-spikes could provide a plausible substrate
 for granule cell-mediated gamma oscillations.
description: Electrophysiology, 2P Ca<sup>2+</sup> imaging, 2P
 holographic multi-site glutamate uncaging. Data was recorded in MES
 (Femtonics) and analyzed in Igor (Wavemetrics) and Excel.
DOI: 10.15468/dl.n93g52
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Robsonella campbelli",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002309-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m905qftxs
title: Climate and mating systems as drivers of global diversity of parental care in frogs

description: Aim Amphibians exhibit unusually diverse reproductive modes, including a
 wide array of parental care strategies. The evolutionary drivers of this
 diversity, however, remain unclear. Here we investigate three major
 factors which may predict interspecific variation in parental care
 strategies: climate, intrasexual selection and social environment. We
 hypothesise that some care forms evolved to cope with harsh conditions
 such as dry or unpredictable habitats. We contrast this prediction with
 the hypothesis that parental roles have coevolved with the social
 environment and mating systems.  Location Global. Major taxa
 studied Frogs and toads (Anura, Amphibia). Time period Extant taxa that
 represent approximately 220 million years of evolutionary history Methods
 Using geographic and behavioural data for 971 species of frogs and toads
 that represent 45 anuran families, we quantify the global distribution of
 four forms of parenting separately for males and females: nest building,
 nest and/or tadpole attendance, carrying and nourishment. We use
 phylogenetic comparative analyses to investigate whether climate, social
 environment and mating systems predict interspecific variation in parental
 care. Results Our results show that climatic effects contribute to
 parental care diversity: under cool and humid climates males provide
 offspring attendance, while endotrophy, whereby the female provides all
 nutrients for the offspring until metamorphosis, occurs under predictable
 temperatures. In addition, we found other associations between mating
 systems and parental care forms: uniparental clutch attendance by males is
 present in species with territorial defence, while cooperative nest
 building co-occurs with sperm competition. The type of parental care is
 not associated with adult sex ratios. Main conclusions No specific form of
 care is associated with hostile environments; actually, some care forms
 occur under beneficial conditions, while others are used independently
 from the climate. Instead, parenting diversity has closely coevolved with
 mating systems in frogs.
DOI: 10.5061/dryad.b2rbnzsbc
title: Data from: Colour pattern variation forms local background matching camouflage in a leaf-mimicking toad

description: Optimal camouflage can, in principle, be relatively easily achieved in
 simple, homogeneous, environments where backgrounds always have the same
 color, brightness, and patterning. Natural environments are, however,
 rarely homogenous and species often find themselves viewed against varied
 backgrounds where the task of concealment is more challenging. One result
 of variable backgrounds is the evolution of intraspecific phenotypic
 variation which may either be generalized, with multiple
 similarly cryptic patterns, or specialized, with each discrete
 color form maximizing concealment against a single component of the
 background. We investigated the role of phenotypic variation in a highly
 variable population of the Neotropical toad Rhinella
 margaritifera using visual modeling and a computer-based
 detection task. We found that phenotypic variation was not divided into
 discrete color morphs and all toads were well camouflaged against the
 forest floor. However, although the whole population may appear to consist
 of random samples from the background, the toads were a particularly close
 match to the leaf litter, suggesting that they masquerade as dead leaves,
 which are themselves variable. Furthermore, rather than each color form
 being equally effective against a single background, each toad was
 specialized towards its own particular local surroundings, as suggested by
 a specialist strategy. Taken together, these data highlight the importance
 of background matching to a nominally masquerading species, as well as how
 habitat heterogeneity at multiple spatial scales may affect the evolution
 of camouflage and phenotypic variation.
DOI: 10.5061/dryad.dncjsxkwd
title: Data from: How self-stigma affects patient activation in persons with type 2 diabetes

description: Objectives Self-stigma is associated with lower patient activation levels
 for self-care in persons with type 2 diabetes mellitus (T2DM). However,
 the causal pathway linking self-stigma with patient activation for
 self-care has not been shown. In order to determine how self-stigma
 affects patient activation for self-care, we tested a two-path
 hypothetical model both directly and as mediated by self-esteem and
 self-efficacy. Design A cross-sectional study Setting 2 university
 hospitals, 1 general hospital, and 1 clinic in Japan Participants T2DM
 outpatients receiving treatment (n = 209) completed a self-administered
 questionnaire comprising the Self-Stigma Scale, Patient Activation
 Measure, Rosenberg Self-Esteem Scale, General Self-Efficacy Scale, Patient
 Health Questionnaire, hemoglobin A1c test, age, sex, and BMI. Primary and
 Secondary Outcome Measures Self-stigma levels were measured by using the
 Self-Stigma Scale. Patient activation levels were measured by the Patient
 Activation Measure. Results Path analysis showed a strong relationship
 between self-stigma and patient activation (χ2 = 27.55, p = 0.120; GFI =
 0.97; AGFI = 0.94; CFI = 0.98; RMSEA = 0.04). Self-stigma had a direct
 effect on patient activation (β = −0.20; p = 0.002). Indirectly,
 self-stigma affected patient activation along two paths (β = 0.31; p
 &lt; 0.001) by reducing self-esteem (β = −0.22; p &lt; 0.001) and
 self-efficacy (β = −0.36; p &lt; 0.001). Conclusions Due to the
 cross-sectional design of the study, longitudinal changes between all the
 variables cannot be established. However, the findings indicate that
 self-stigma affected patient activation for self-care, both directly and
 as mediated by self-esteem and self-efficacy. Interventions that increase
 self-esteem and self-efficacy may decrease self-stigma in T2DM patients,
 thus increasing patient activation for self-care.
description: Please see the README file for more information on the
 dataset.
DOI: 10.5061/dryad.rn8pk0p6m
title: DNA barcoding and morphometric data for Truncilla donaciformis and Truncilla truncata (Bivalvia: Unionidae)

description: Closely-related unionid species often overlap in shell shape and can be
 difficult to accurately identify in the field. Ambiguity in identification
 can have serious impacts on conservation efforts and population surveys of
 endangered species. Truncilla donaciformis and T. truncata are sister
 species that overlap in their distributions and frequently co-occur in
 central North America. Because T. donaciformis is endangered in Canada and
 imperiled in some U.S. jurisdictions, co-occurrence with the
 morphologically-similar T. truncata means that misidentification could
 have serious impacts on status assessments and recovery efforts. The
 objectives of this study were: (1) to employ morphometric analyses in
 combination with DNA barcoding to quantify morphological differences
 between T. donaciformis and T. truncata and (2) to use these methods to
 confirm field identifications and identify problematic specimens.
 Truncilla specimens were photographed and visceral mass swabs taken from
 four rivers in southern Ontario. Positive identifications of all specimens
 were obtained through sequencing a fragment of COI mtDNA. Generated
 sequences were compared to published data from NCBI Genbank using BLAST.
 Traditional and geometric morphometric approaches were used to assign
 specimens to species. Assignments generated were compared to
 identifications based on mtDNA barcodes, with traditional and geometric
 morphometric analyses found to be 90.3% and 99.0% accurate in species
 identifications, respectively. This study confirmed the presence of T.
 donaciformis in Ontario’s Thames River, and revealed that all mussels
 collected for this study from the other three rivers were T. truncata.
 This study reinforces the utility of combining geometric morphometric
 analyses and DNA barcoding for identifying problematic unionid specimens.
DOI: 10.15468/dl.ar2etg
title: Occurrence Download

description: A dataset containing 1845129 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Butterfly distribution records for the UK from Butterfly Conservation, up to 2019",
 "TaxonKey is Lycaenidae",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 1845129 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002301-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.