cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.44ttts
title: Occurrence Download

description: A dataset containing 217 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thladiantha villosula",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 217 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002090-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vt4b8gtng
title: Data from: The smallest known Devonian tetrapod shows unexpectedly derived features, Part 2 of 2

description: A new genus and species
 of Devonian tetrapod, Brittagnathus
 minutus gen. et sp. nov., is described from a single complete
 right lower jaw ramus recovered
 from the Acanthostega mass-death deposit
 in the upper part of the Britta Dal
 Formation (upper Famennian) of Stensiö Bjerg, Gauss Peninsula, East
 Greenland. Visualisation by propagation phase contrast synchrotron
 microtomography (PPC-SRμCT) allows a complete digital dissection
 of the specimen. With a total jaw ramus length of 44.8
 mm, Brittagnathus is by
 far the smallest Devonian tetrapod described to date. It differs from all previously knownDevonian tetrapods in having only a fang pair without a tooth row on the anterior coronoid, and a large posterior process on the posterior coronoid. The presence of an incipient surangular crest and a concave prearticular margin to the adductor fossa together cause the fossa to face somewhat mesially, reminiscent of the condition in Carboniferous tetrapods. A phylogenetic analysis places Brittagnathus crownward to other Devonian tetrapods, adjacent to the Tournaisian genus Pederpes. Together with other recent discoveries, it suggests that diversification of ‘Carboniferous-grade’ tetrapods had already begun before the end of the Devonian and that the group was not greatly affected by the end-Devonian mass extinction.
description: Synchrotron microtomography data set of Devonian tetrapod jaw
 NHMD 116368, holotype and only specimen of Brittagnathus minutus. Part
 2 The specimen, NHMD 116368, (field number MGUH f.n.
 1373) was collected in July 1987 from the Acanthostega-yielding horizon on
 Stensiö Bjerg, Gauss Peninsula, East Greenland. It was initially prepared
 mechanically, which revealed the posterior end of the lateral surface and
 the lower margin and prearticular on the medial surface. In September 2016
 the specimen was imaged using propagation phase contrast synchrotron
 microtomography (PPC-SRmCT) at the European Synchrotron Radiation Facility
 (ESRF) in Grenoble, France. The scan was part of Experiment ES-505 and was
 made courtesy of Valéria Vaskaninova to whom the beamtime had been
 awarded. The voxel size of the scan was 13.49 mm, made with single
 distance phase retrieval and a propagation distance of 5m. The
 reconstructed volume was converted into a stack of 16 bit TIFF
 images. Because each of the 1708 images is a separate
 file, and Dryad imposes a 1000-file limit on data sets, the stack has been
 split in two: this is Part 2, containing the last 735 images. Part 1 is
 available at https://doi.org/10.5061/dryad.sqv9s4n0k
DOI: 10.5061/dryad.jsxksn05k
title: Plant responses to diversity-driven selection and associated rhizosphere microbial communities

description: 1. Plant diversity loss can alter plant interactions and rhizosphere
 microbial communities. These altered interactions in turn exert
 diversity-driven selection pressures to which plants may respond with
 phenotypic changes. Diverse plant communities may favour the survival and
 fitness of individuals with traits that avoid competition. Conversely
 monocultures may accumulate species-specific pests favouring greater
 investment in defence traits. Yet it is unknown how altered plant
 rhizosphere interactions influence the plant diversity-driven selection
 for altered plant phenotypes. 2. We tested for plant diversity-driven
 selection on plant aboveground traits and how these traits are modified by
 their rhizosphere microbial communities after 11 years in experimental
 plant monocultures and mixtures. Plants propagated from monocultures or
 mixtures were grown in combination with their ‘home’ vs. ‘away’ arbuscular
 mycorrhizal fungi (AMF) or non-AMF microbes in two separate experiments
 using five and eight plant species respectively. We hypothesized plants in
 monocultures may be selected for better defence and better performance in
 association with rhizosphere microbial communities compared with plants in
 mixtures. 3. Monoculture and mixture plants significantly differed in
 their aboveground phenotypes. As predicted, plant traits related to
 defence (greater leaf mass per area and leaf dry matter content, reduced
 leaf damage) were more pronounced in monoculture plants in both
 experiments. Effects of the rhizosphere microbial communities, which
 generally enhanced plant growth, tended to be species-specific.
 Significant three-way interactions between diversity-driven selection, AMF
 treatment and plant species showed that home vs. away effects could be
 positive or negative, depending on plant species. 4. We conclude that
 long-term differences in plant diversity lead to selection for altered
 plant phenotypes. Such differences may be further modified in association
 with the AMF microbial communities derived from the different plant
 diversity treatments, but often outcomes are species-specific. This
 suggests that plant species differ in their capacity to respond to
 diversity loss and associated changes in rhizosphere microbial
 communities, making it complicated to predict community-level responses to
 such loss.
DOI: 10.5061/dryad.2fqz612kf
title: Return to work following diagnosis of low-grade glioma: A nationwide matched cohort study

description: Objective: Return-to-work (RTW) following diagnosis of infiltrative
 low-grade gliomas (LGG) is unknown.   Methods: Swedish patients
 with histopathological verified WHO grade II diffuse glioma diagnosed
 between 2005-2015 were included. Data were acquired from several Swedish
 registries. A total of 381 patients aged 18-60 were eligible. A matched
 control population (n=1900) was acquired. Individual data on sick leave,
 compensations, comorbidity, and treatments assigned were assessed.
 Predictors were explored using multivariable logistic
 regression.  Results: One year before surgery/index date, 88 % of
 cases were working compared to 91 % of controls. The proportion of
 controls working remained constant, while patients had a rapid increase in
 sick leave approximately six months prior to surgery. After one and two
 years respectively, 52 % and 63 % of the patients were working. Predictors
 for no-RTW after one year were previous sick leave (OR 0.92, 95 % CI
 0.88-0.96, p &lt;0.001), older age (OR 0.96, 95 % CI 0.94-0.99,
 p=0.005) and lower functional level (OR 0.64 95% CI, 0.45-0.91 p=0.01).
 Patients receiving adjuvant treatment were less likely to RTW within the
 first year. At two years, biopsy (as opposed to resection), female sex and
 co-morbidity were also unfavorable, while age and adjuvant treatment were
 no longer significant.  Conclusions: Approximately half of the
 patients RTW within the first year. Lower functional status, previous sick
 leave, older age, and adjuvant treatment were risk factors for no-RTW at
 one year after surgery. Female sex, co-morbidity, and biopsy only were
 also unfavorable for RTW at two years.
DOI: 10.5061/dryad.rr4xgxd5b
title: Data from: Describing complex structure-function relationships in biomolecules at equilibrium

description: One of the great ambitions of structural biology is to describe
 structure-function relationships quantitatively.  Statistical
 thermodynamics is a powerful, general tool for computing the behavior of
 biological macromolecules at equilibrium, because it establishes a direct
 link between structure and function.  Complex behavior emerges as
 equilibria of multiple reactions are coupled.  Analytical
 treatment of linked equilibria scales poorly with increasing numbers of
 reactions and states as the algebraic constructs rapidly become
 unwieldy.  We therefore developed a generalizable, but
 straightforward computational method to handle arbitrarily complex
 systems.  To demonstrate this approach, we collected a
 multi-dimensional fluorescence landscape of an engineered fluorescent
 glucose biosensor and showed that its features could be modeled with ten
 intricately linked ligand-binding and conformational-exchange reactions.
  This protein represents a minimalist model of sufficient
 complexity to encompass fundamental biomolecular structure-function
 relationships: two- and multi-state conformational ensembles,
 conformational hierarchies, osmolytes, coupling between different binding
 sites and coupling between ligand binding and conformational change.
   The successful fit of this complex, multifaceted
 system demonstrates generality of the method.
DOI: 10.5061/dryad.3xsj3txbh
title: Predation risk and mountain goat reproduction: Evidence for stress-induced breeding suppression in a wild ungulate

description: Abstract 1. Non-consumptive effects of predation can strongly impact
 reproduction and demography of prey species. Still, the underlying
 mechanisms that drive non-consumptive effects are not fully understood,
 and the circumstances under which chronic physiological stress may mediate
 these effects remain unclear. 2. Benefiting from over 23 years of
 environmental, physiological and demographic data, we tested the
 hypothesis that predation risk may impair reproduction of mountain goats
 through chronic elevation of physiological stress. We conducted path
 analyses to assess the relationships between predation risk, faecal
 glucocorticoid metabolites and hair cortisol concentration, and
 reproduction, while taking into account the potential effects of age
 class, sex, body mass, season, and within individual variation in
 glucocorticoid concentration. 3. Predation risk had a direct positive
 effect on the average annual faecal glucocorticoid concentration in the
 population, which in turn negatively affected the proportion of
 reproductive females. The same pattern was observed with hair cortisol
 concentration, but these results were inconclusive potentially due to
 methodological challenges in estimating annual average of hair cortisol at
 the population level. 4. Our study presents one of the first robust
 evidence that stress-mediated breeding suppression can occur in a wild
 ungulate following increased predation risk, thereby providing a major
 insight on the mechanisms underlying non-consumptive effects of predation
 in wild mammals.
description: The data set contains four
 sheets of data collected on marked mountain goats at Caw Ridge, Alberta,
 Canada between 1994-2016. The first and second sheets
 include individual data on glucocorticoid concentration (respectively FGM
 and HCC), age, sex and age-specific mass as well as annual data on
 reproduction, predation risk, population size, and faecal crude protein
 peak date. This data was used in all the analyses presented in the main
 manuscript and to produce Figure 3, Figure 4, Figure 5, Figure S4.1,
 Figure S5.1, and Figure S5.2. The third and fourth sheets is
 restricted to females and include individual data on glucocorticoid
 concentration (respectively FGM and HCC), reproduction, age, and
 age-specific mass as well as annual data on predation risk, population
 size, and faecal crude protein peak date. This data was used for the
 individual level analysis presented in supplementary material S6 and to
 produce Figure S6.1.
DOI: 10.5061/dryad.n02v6wwsx
title: Computerized analysis of brain MRI parameters dynamics in young patients with Cushing Syndrome – a case-control study

description: Background – Young patients with Cushing Syndrome (CS) may develop
 cognitive and behavioral alterations during disease course. Methods - To
 define the implications of CS on the brain, we analyzed consecutive MRI
 scans of patients with (n=29) vs. without CS (n=8). Multiple brain
 compartments were processed for total and gray/white matter (GM/WM)
 volumes and intensities; and cortical volume, thickness and surface-area.
 Dynamics (last/baseline scans ratio per parameter) were analyzed vs.
 cortisol levels and CS status (persistent, resolved and non-CS). Results -
 24-hour urinary free cortisol (24hUFC) measurements had inverse
 correlation with the intensity of subcortical GM structures and of the
 corpus callosum, and with the cerebral WM intensity. 24hUFC dynamics had
 negative correlation with volume dynamics of multiple cerebral and
 cerebellar structures. Patients with persistent CS had less increase in
 cortical thickness and WM intensity, and less decrease in WM volume
 compared with patients with resolution of CS. Patients with resolution of
 their CS had less increase in subcortical GM and cerebral WM volumes, but
 more increase in cortical thickness of frontal lobe vs. controls.
 Conclusion - Changes in WM/GM consistency, intensity and homogeneity in
 patients with CS, may correlate with CS clinical consequences better than
 volume dynamics alone.
description: <b>Supplementary table
 1</b> Comparison of brain MRI parameters, between patients with CS
 achieving vs. not achieving remission <b>Supplementary table
 2</b> Comparison of brain MRI parameter dynamics between patients
 with CS achieving remission vs. controls
DOI: 10.25349/d9zk50
title: PiVR: an affordable and versatile closed-loop platform to study unrestrained sensorimotor behavior

description: Tools enabling closed-loop experiments are crucial to delineate causal
 relationships between the activity of genetically-labeled neurons and
 specific behaviors. We developed the Raspberry Pi Virtual Reality system
 (PiVR) to conduct closed-loop optogenetic stimulation of neural functions
 in unrestrained animals. PiVR is an experimental platform that operates at
 high-temporal resolution (70 Hz) with low latencies (&lt;30 ms), while
 being affordable (&lt;$500) and easy to build (&lt;6 hours).
 Through extensive documentation, this tool was designed to be accessible
 to a wide public, from high-school students to professional researchers
 studying systems neuroscience. We illustrate the functionality of PiVR by
 focusing on sensory navigation in response to gradients of chemicals
 (chemotaxis) and light (phototaxis). We show how Drosophila flies perform
 negative chemotaxis by modulating their locomotor speed to avoid locations
 associated with optogenetically-evoked bitter taste. In Drosophila larvae,
 we use innate positive chemotaxis to compare behavior elicited by real-
 and virtual-odor gradients. Finally, we examine how positive phototaxis
 emerges in zebrafish larvae from the modulation of turning maneuvers to
 orient in virtual white-light gradients. Besides its application to study
 chemotaxis and phototaxis, PiVR is a versatile tool designed to bolster
 efforts to map and to functionally characterize neural circuits.
    
description: For a description of the PiVR tool you may find all technical
 information at www.PiVR.org For a description of the
 behavioral experiments involving Drosophila and Zebrafish, see publication
 with title "PiVR: an affordable and versatile losed-loop platform to
 study unrestrained sensorimotor behavior"
 (https://doi.org/10.1371/journal.pbio.3000712)
description: To recreate figures and movies shown in the the publication with
 the title "<em>PiVR: an affordable and versatile closed-loop
 platform to study unrestrained sensorimotor behavior</em>"
 please: 1. Download the two files:
 "pivr_publication.zip" and "README_ZIP.MD".
 2. Follow instructions in "README_ZIP.MD".
 3. Use the list in "Guide.MD" to find individual
 scripts used to create plots in the publication. Please
 note: The scripts (without the data) used to create the plots can also be
 found on the following gitlab repository:
 https://gitlab.com/LouisLab/pivr_publication
DOI: 10.5061/dryad.tb2rbnzwr
title: Color lures in orb-weaving spiders: a meta-analysis

description: Lures are deceptive strategies that exploit sensory biases in prey,
 usually mimicking a prey’s mate or food item. Several predators exploit
 plant-pollinator systems, where visual signals are an essential part of
 interspecific interactions. Many diurnal, and even nocturnal, orb-web
 spiders present conspicuous body coloration or bright color patches. These
 bright colors are regarded as color-based lures that exploit biases
 present in insect visual systems, possibly mimicking flower colors. The
 prey attraction hypothesis was proposed more than 20 years ago to explain
 orb-web spider coloration. Although most data gathered so far has
 corroborated the predictions of the prey attraction hypothesis, there are
 several studies that refute these predictions. We conducted a multi-level
 phylogenetic meta-analysis to assess the magnitude of the effect of
 conspicuous orb-web spider body coloration on prey attraction. We found a
 positive effect of in favor of the prey attraction hypothesis, however,
 there was substantial heterogeneity between studies. Experimental designs
 comparing conspicuous spiders to painted spiders or empty webs did not
 explain between-studies heterogeneity. The lack of theoretical explanation
 behind the prey attraction hypothesis makes it challenging to address
 which components influence prey attraction. Future studies could evaluate
 whether color is part of a multi-component signal and test alternative
 hypotheses for the evolution of spider colors, such as predator avoidance
 and thermoregulation.
DOI: 10.15468/dl.mdyn9q
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is c2ecae57-6701-485e-9ebd-5f87b2945cb2",
 "TaxonKey is Melanoplus billyharrisi",
 "Year 1900-2026"
 ]
}

 The dataset includes 13 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002091-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jh9w0vt73
title: Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as threats in a hotspot plant genus

description: Comparative models used to predict species threat status can help to
 identify diagnostic features of species at risk. Such models often combine
 variables measured at the species level with spatial variables, causing
 multiple statistical challenges, including phylogenetic and spatial
 non-independence. We present a novel Bayesian approach for modelling
 threat status that simultaneously deals with both forms of
 non-independence and estimates their relative contribution, and we apply
 the approach to modelling threat status in the Australian plant genus
 Hakea. We find that after phylogenetic and spatial effects are accounted
 for, species with greater evolutionary distinctiveness and a shorter
 annual flowering period are more likely to be threatened. The model allows
 us to combine information on evolutionary history, species biology, and
 spatial data, to calculate latent extinction risk (potential for
 non-threatened species to become threatened), estimate the most important
 drivers of risk for individual species, and map spatial patterns in the
 effects of different predictors on extinction risk. This could be of value
 for proactive conservation decision-making based on the early
 identification of species and regions of potential conservation concern.
description: Details on data collection methods can be found in the
 accompanying article.
description: Metadata on the dataset can be found in metadata.html, produced
 using the R package dataspice (https://github.com/ropenscilabs/dataspice). Dinnage_Skeels_Cardillo_tutorial_and_sims.zip contains data necessary to run the tutorial code included in the paper's supplement, as well as simulations designed to test some aspects of the method presented in the paper. It also includes the .Rmd source file used to generate the supplementary tutorial.
DOI: 10.15468/dl.t3y8mw
title: Occurrence Download

description: A dataset containing 844 records in GBIF matching the query:
SELECT
 '420' 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;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 97.85900704989292
 AND decimalLongitude &lt;= 107.89334554252557
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 844 records were derived from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002069-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j6q573n8t
title: Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity

description: Scientific understanding of biodiversity dynamics, resulting from past
 climate oscillations and projections of future changes in biodiversity,
 has advanced over the past decade. Little is known about how these
 responses, past or future, are spatially connected. Analyzing the spatial
 variability in biodiversity provides insight into how climate change
 affects the accumulation of diversity across space. Here, we evaluate the
 spatial variation of phylogenetic diversity of European seed plants among
 neighboring sites and assess the effects of past rapid climate changes
 during the Quaternary on these patterns. Our work shows a marked
 homogenization in phylogenetic diversity across Central and Northern
 Europe linked to high climate change velocity and large distances to
 refugia. Our results suggest that the future projected loss in
 evolutionary heritage may be even more dramatic, as homogenization in
 response to rapid climate change has occurred among sites across large
 landscapes, leaving a legacy that has lasted for millennia.
description: See attached README_for_DataPackage_Saladin_etal.txt for
 additional information