cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f7m0cfz2r
title: Data from: Clots reveal anomalous elastic behavior of fiber networks

description: The adaptive mechanical properties of soft and fibrous biological
 materials are relevant to their functionality. The emergence of the
 macroscopic response of these materials to external stress and intrinsic
 cell traction from local deformations of their structural components is
 not well understood. Here, we investigate the nonlinear elastic behavior
 of blood clots by combining microscopy, rheology, and an elastic network
 model that incorporates the stretching, bending, and buckling of
 constituent fibrin fibers. By inhibiting fibrin crosslinking in blood
 clots, we observe an anomalous softening regime in the macroscopic shear
 response as well as a reduction in platelet-induced clot contractility.
 Our model explains these observations from two independent macroscopic
 measurements in a unified manner, through a single mechanical parameter,
 the bending stiffness of individual fibers. Supported by experimental
 evidence, our mechanics-based model provides a framework for predicting
 and comprehending the nonlinear elastic behavior of blood clots and other
 active biopolymer networks in general.
DOI: 10.5061/dryad.s7h44j1cv
title: Data from: Macroecological predictors of evolutionary and plastic potential do not apply at microgeographic scales for a freshwater Cladoceran under climate change

description: Rapid evolutionary adaptation could reduce the negative impacts of climate
 change if sufficient heritability of key traits exists under future
 climate conditions. Plastic responses to climate change could also reduce
 negative impacts. Understanding which populations are likely to respond
 via evolution or plasticity could therefore improve estimates of
 extinction risk. A large body of research suggests that the evolutionary
 and plastic potential of a population can be predicted by the degree of
 spatial and temporal climatic variation it experiences. However, we know
 little about the scale at which these relationships apply. Here, we test
 if spatial and temporal variation in temperature affect genetic variation
 and plasticity of fitness and a key thermal tolerance trait (critical
 thermal maximum; CTmax) at microgeographic scales using a metapopulation
 of Daphnia magna. Specifically, we ask if: (1) there is microgeographic
 adaptation of CTmax and fitness to differences in temperature among the
 pools, (2) pools with greater temporal temperature variation have more
 genetic variation or plasticity in CTmax or fitness, and (3) increases in
 temperature affect the heritability of CTmax and fitness. Although we
 observed genetic variation and plasticity in CTmax and fitness, and
 differences in fitness among pools, we did not find support for the
 predicted relationships between temperature variation and genetic
 variation or plasticity. Furthermore, the genetic variation and plasticity
 we observed in CTmax is unlikely sufficient to reduce the impacts of
 climate change. CTmax plasticity was minimal and heritability was 72%
 lower when D. magna developed at the higher temperatures predicted under
 climate change. In contrast, the heritability of fitness increased by 53%
 under warmer temperatures suggesting an increase in overall evolutionary
 potential unrelated to CTmax under climate change. More research is needed
 to understand evolutionary and plastic potential under climate change and
 how that potential will be altered in future climates.
DOI: 10.5061/dryad.4xgxd25g8
title: Data from: Arriving late and lean at a stopover site is selected against in a declining migratory bird population

description: Loss and/or deterioration of refuelling habitats have caused population
 declines in many migratory bird species, but whether this results from
 unequal mortality among individuals varying in migration traits remains to
 be shown. Based on 13 years of body mass and size data of great knots
 (Calidris tenuirostris) at a stopover site of the Yellow Sea, combined
 with resightings of individuals marked at this stopover site along the
 East Asian-Australasian Flyway, we assessed year to year changes in annual
 apparent survival rates, and how apparent survival differed between
 migration phenotypes (their i.e. migration timing and fuel stores). The
 measurements occurred over a period of habitat loss and/or deterioration
 in this flyway. We found that the annual apparent survival rates of great
 knots rapidly declined from 2006 to 2018, late-arriving individuals with
 small fuel stores exhibiting the lowest apparent survival rate. There was
 an advancement in mean arrival date and an increase in the mean fuel load
 of stopping birds over the study period. Our results suggest that
 late-arriving individuals with small fuel loads were selected against.
 Thus, habitat loss and/or deterioration at staging sites may cause changes
 in the composition of migratory phenotypes at the population-level.
DOI: 10.5061/dryad.rbnzs7hhs
title: Taxonomy and Phylogeny of the Family Suberitidae (Porifera: Demospongiae) in California

description: This study presents a comprehensive taxonomic revision of the family
 Suberitidae (Porifera: Demospongiae) for California, USA. We include the
 three species previously known from the region, document two additional
 species previously known from other regions, and formally describe four
 new species as Pseudosuberites latke sp. nov., Suberites californiana sp.
 nov., Suberites kumeyaay sp. nov., and Suberites agaricus sp. nov.
 Multi-locus DNA sequence data is presented for seven of the nine species,
 and was combined with all publicly available data to produce the most
 comprehensive global phylogeny for the family to date. By integrating
 morphological and genetic data, we show that morphological characters may
 be sufficient for regional species identification but are likely
 inadequate for global classification into genera that reflect the
 evolutionary history of the family. We therefore propose that DNA
 sequencing is a critical component to support future taxonomic revisions.
  
description: Taxonomy and phylogeny of the family Suberitidae (Porifera: Demospongiae)
 in California Supplementary data 5 files: 1.Table_S1_archival.csv Metadata
 for all samples investigated. Newly collected samples are associated with
 a "collection ID", which is a unique identifier used until the
 sample was voucher in a museum and given a voucher number. Samples with a
 museum voucher but no collection ID were loaned by the corresponding
 museum. the collection ID is also referenced in the raw spicule data file
 and in the Genbank flatiles, as these data were produced before the
 samples had museum voucher IDs. Genbank numbers are provided for samples
 with genetic data. 2.Raw_spicule_data.csv Measurement data from all
 spicules. Lengths and widths are provided for each spicule;
 "n/a" indicates a measurement was not taken. 3.S3 occurance
 data.csv Sampling effort and locations. Only species found in recent
 shallow-water surveys are shown. For all subtidal sites, the number of
 sampling dives is listed, and the cumulative dive time is an estimate of
 search effort. 4.S4 cox1 alignment.fasta Alignment of cox1 samples in
 fasta format 5.S4 28S alignment.fasta Alignment of 28S samples in fasta
 format
DOI: 10.15468/dl.4un5w8
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003623-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c58s4k319
title: MassIVE MSV000100621 - 2026_PSU_HFTuber-extracts_NEG-LCMS
title: hydnophytum formicarum tuber extracts 1) methanol 2) Non-Anionic fraction 3)10% anionic fraction 4) 30% Anionic fraction 5) 50% Anionic fraction
DOI: 10.5061/dryad.6q573n644
title: Submesoscale dynamics in the Bay of Bengal: Inversions and instabilities

description: High-resolution observations reveal the complex processes controlling the
 evolution and subduction of a cold and salty, dense filament in the Bay of
 Bengal. The filament, likely formed through coastal upwelling, was
 advected offshore by a mesoscale strain field and brought adjacent to
 fresher water from runoff and rain. The front on an edge of the dense
 filament is observed to undergo restratification and steepening,
 responding to evolving mesoscale and submesoscale convergence and
 divergences. Measurements and analyses indicate the development of both
 small-scale instabilities (such as SI) and slightly larger-scale
 ageostrophic secondary circulation, acting in concert to subduct and stir
 surface heat into the interior. Our results highlight the importance of
 small-scale three-dimensional dynamics in setting upper ocean properties
 in the Bay of Bengal.
description: # Submesoscale Dynamics in the Bay of Bengal: Inversions and Instabilities
 [https://doi.org/10.5061/dryad.6q573n644](https://doi.org/10.5061/dryad.6q573n644) The data included in this set consists of physical properties of the upper ocean from a July 2019 survey of the Bay of Bengal from in-situ and satellite instrumentation. ## Description of the data and file structure **Thermohaline variability** Four .mat files labeled "Section\_X.mat" correspond to four transects from a shipboard profiling system (FastCTD). This data is in-situ and should be plotted on an x-z plane. These datasets include: * temperature [degrees Celsius] * salinity [psu] * density [kg/m<sup>3</sup>] * time * geographical coordinates (latitude and longitude) * depth, P [m] **Velocity data** The velocity data provided is derived from shipboard ADCP systems (sadcp\_tot.mat). The ADCP data used in this paper (300 kHz) can be accessed from the first structure in the cell array of sadcp\_tot.mat and includes: * zonal and meridional velocities, u and v [m/s] * time * geographical coordinates (latitude and longitude) * depth [m] **Meteorological data** Atmospheric and surface ocean data is contained in the files "MET\_190XXX.mat", where XXX refers to the dates July 17-20, 2019. Each file contains a structure detailing: * air temperature [degrees C] * accumulated precipitation [mm] * short wave radiation [W/m<sup>2</sup>] * wind speed [m/s] * wind direction [degrees, direction wind is coming from] * time ## Code/Software The software used to open and analyze these files was MATLAB.
DOI: 10.15468/dl.2agjwe
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((15.31045 37.81451,15.16817 37.90678,15.06909 37.94686,14.95222 37.9689,14.75913 37.95087,14.69561 37.90879,14.66004 37.78842,14.67021 37.64975,14.74134 37.50679,14.79978 37.43621,14.94968 37.42411,15.11482 37.40796,15.2571 37.47252,15.31045 37.81451))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Geotrupidae, Lucanidae, Scarabaeidae, Aphodiidae)"
 ]
}

 The dataset includes 105 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003622-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q5qw8q
title: Occurrence Download

description: A dataset containing 1723 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Plantae [GBIF Backbone Taxonomy])",
 "GadmGid is one of (COL.2.34_2)"
 ]
 }
 ]
}

 The dataset includes 1723 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003621-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2rvmxf
title: Occurrence Download

description: A dataset containing 2977 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ypthima asterope"
 ]
}

 The dataset includes 2977 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003620-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4x5ze8
title: Occurrence Download

description: A dataset containing 12309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-73.08115 3.91355,-73.02655 3.92346,-73.02586 3.92369,-73.02495 3.92426,-73.02438 3.92489,-72.9647 3.99235,-72.96419 3.99302,-72.94742 4.01895,-72.94699 4.01993,-72.93869 4.03925,-72.93819 4.04047,-72.93804 4.04093,-72.91861 4.11957,-72.91858 4.11978,-72.91844 4.1421,-72.91844 4.14298,-72.91912 4.14484,-72.92705 4.16294,-72.92842 4.16471,-72.92923 4.16525,-72.93005 4.16569,-73.00641 4.18501,-73.00819 4.18541,-73.01015 4.18549,-73.07113 4.1861,-73.0721 4.1861,-73.64134 4.1773,-73.64187 4.17729,-73.76208 4.04857,-73.75767 4.04134,-73.75641 4.04056,-73.74341 4.03336,-73.7428 4.03312,-73.74201 4.0328,-73.32028 3.95567,-73.08115 3.91355))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 12309 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003619-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.66t1g1k6v
title: Testing the links between bird diversity, alien species and disturbance within a human-modified landscape

description: Introduced alien species are associated with lower taxonomic, functional
 and phylogenetic diversity of native communities and negative impacts on
 ecosystem functioning. This is particularly evident in habitats where
 human disturbance may favour alien species, posing an additional stressor
 on native communities. Following the community resistance hypothesis
 (higher diversity promotes higher resistance to invasion), we predicted:
 i) higher taxonomic, functional and phylogenetic diversity (TD, FD and PD
 respectively) in non-invaded bird communities (i.e. no alien bird
 species); and, ii) higher diversity and resistance to invasion in less
 human-disturbed areas. We surveyed bird communities in a modified
 Mediterranean landscape subject to varying levels of human disturbance. We
 tested whether TD, FD and PD were significantly different between
 non-invaded and invaded bird communities, and assessed the effect of land
 classes (forest, agriculture, urban), landscape composition and
 heterogeneity on these metrics. We found that non-invaded communities
 retained higher TD and FD, but not PD, than invaded communities. Alien
 birds occupied marginal niches in invaded communities, and did not fully
 compensate for the taxonomic and functional diversity loss caused by the
 absence of native species. These results were consistent across different
 land classes, suggesting weak environmental filtering of communities.
 Generally, less human-modified and more heterogeneous areas supported
 higher TD regardless of the presence of alien species. FD and PD of
 invaded communities decreased with increases in human-modified areas,
 whereas non-invaded communities were not affected. Our results suggest
 that even within a human-modified landscape, invaded community diversity
 is more affected by, and thus has a lower resilience to, disturbance.
 Restoring and protecting natural habitats within human-modified landscapes
 is likely to increase the resilience of native species.
DOI: 10.5061/dryad.d51c5b08g
title: Tapajos K67 tropical forest seasonal flux tower data

description: Seasonal (16-day) eddy covariance measurements that include water, carbon,
 and energy flux, radiation, canopy temperature, humidity, and ancillary
 calculations such as evaporation, transpiration, and leaf area
 index.  Data was collected at the Tapajós National Forest,
 Santarem K67 (BR-Sa1), a tropical primary forest (2.857°S,
 54.959°W).  Measurements correspond to the periods: April 2001 -
 January 2006, July 2008 - July 2012, and January 2015 - July
 2020.  The 16-day fluxes and meteorological data were obtained
 from an average daily cycle based on hourly observations. As a result, we
 refrain from assigning greater significance to specific hours when the
 fluxes tend to be complete, and vice versa (for instance, in cases of
 missing flux values due to afternoon rainfall events). Daytime values were
 selected as above a 5 W m-2 top of the atmosphere radiation (TOA; W m-2)
 and labeled as LEdaytime in the case of latent heat flux (LE), Hdaytime
 for sensible heat flux (H), and so on.
description: Eddy covariance (EC) instrumentation was installed on a 64 m tall
 tower in 2000. Since then, water and energy fluxes have been measured
 using the closed-path method. Hourly turbulent fluxes were subject to
 quality control, by removing rainy periods, outliers due to instrument
 malfunction (e.g. pump failure) or when the calibration system failed
 (e.g. N<sub>2</sub> gas run-out). See Restrepo-Coupe, et al.
 (2013). What drives the seasonality of photosynthesis across the Amazon
 basin? A cross-site analysis of eddy flux tower measurements from the
 Brasil flux network. Agricultural and Forest Meteorology, 182–183,
 128–144
description:  The data is provided in comma-delimited format (*.txt).
DOI: 10.15151/esrf-es-2318152007
title: Structural Biology at EMBL Grenoble, IBS-CIBB, IAB and ILL

description: This proposal clusters macromolecular crystallography (MX) and biological small angle X-ray scattering (bioSAXS) projects at the EMBL Grenoble, IBS-CIBB, IAB and ILL. It combines groups working on different topics with a major focus on cell signaling proteins, ubiquitination pathways, nucleic acid-protein complexes, sarcomere development, host-pathogen interactions and drug discovery. The BAG group has been quite productive this last year/reporting period, as summarized in the report, with many results still being further analysed and follow-up experiments planned. Most notably, the BAG has produced 7 PDB depositions, 1 SASDB deposition and 10 publications in peer reviewed journals. The proposers have long-standing experience in the use, as well as the development of beam lines for MX and bioSAXS, and have participated in successive successful BAG applications over the years, mostly at the ESRF. The BAG responsible is again Andrew McCarthy (EMBL Grenoble) for this application round.
DOI: 10.5061/dryad.9cnp5hqqg
title: Beetle evolution illuminates the geological history of the world’s most diverse tropical archipelago

description: The geologically-complex Indo-Australian-Melanesian archipelago (IAMA)
 hosts extraordinarily high levels of species richness and endemism and has
 long served as a natural laboratory for studying biogeography and
 evolution. Nonetheless, its geological history and the provenance and
 evolution of its biodiversity remain poorly understood. Here, we provide a
 geological scenario for the IAMA informed by a time-calibrated molecular
 phylogeny of 1,006 species of Trigonopterus weevils—an exceptionally
 diverse radiation of regionally-endemic flightless beetles. Moreover, we
 performed a statistical biogeographic analysis and examined timing and
 patterns in the accumulation of lineages residing in a priori-defined
 geographic units comprising the IAMA. We estimate that Trigonopterus
 originated in Australia during the early Paleogene. Subsequent rapid
 diversification in the area of the present-day Papuan Peninsula suggests
 the presence of proto-Papuan islands by the middle Eocene; the New Guinea
 North Coast Ranges were colonized in the late Eocene, followed by the New
 Guinea Highlands and the Bird´s Head Peninsula. We inferred the presence
 of terrestrial habitat in the North Moluccas and Sulawesi in the late
 Oligocene and the subsequent rapid colonization of Sundaland and the
 Lesser Sunda Islands. New Caledonia and Samoa were colonized from the
 Papuan Peninsula, and their faunas also diverged in the late Oligocene.
 These biota-informed time estimates are compatible with geological data
 from the region and shed new light on IAMA paleogeography, even where
 geological evidence has been lost to erosion. Beetle evolution thus
 appears to have closely tracked the geological evolution of the IAMA,
 revealing a uniquely well-resolved view of regional biogeography.
DOI: 10.14469/hpc/15679
title: NMR Data for 37c. tris(2,4,6-trichlorophenyl) borate. 1H

description: Raw spectrometer NMR Data
DOI: 10.5061/dryad.2z34tmps6
title: Meta-model for Patagonian grass steppe dynamics - library of transition matrices for steppe dynamics under sheep grazing

description: One of the central problems in ecology is how to scale from small-scale
 observations and experiments to large-scale patterns and processes. One
 approach to such upscaling is to use dynamic simulation models, but their
 application to large scales relevant for management is limited by
 computational costs, and their outputs are difficult to analyse without a
 systematic strategy. Our general objective is to propose such a strategy.
 The idea is to approximate the dynamics of detailed simulation models
 through a set of states, external drivers, and transition matrices, and
 then use Markov chain and network analysis of the resulting transition
 matrices to gain insights into the dynamics of the underlying detailed
 model. We used the individual-based model COIRON, which simulates the
 dynamics of semiarid grass steppes in Patagonia (Argentina) under
 alternative grazing management, as example. Our specific objectives are to
 identify pathways of degradation and rehabilitation, as well as critical
 grazing thresholds and early-warning vegetation states to guide
 sustainable grazing management in these steppes. Our results indicate
 nonlinear effects of stocking rate and grazing season on steppe dynamics.
 Markov chain analysis suggests benefits of seasonal over continuous
 grazing at intermediate stocking rates, and network analysis of recovery
 and degradation trajectories shows that intermediate stocking rates
 maximize differences between grazing seasons. Finally, our analysis
 identified specific vegetation states as early warning signals that
 indicate a high risk of irreversible vegetation changes. Patagonian grass
 steppes should ideally be managed with multi-paddock grazing at moderate
 stocking rates around 0.5 sheep·ha-1. The transition matrices summarize
 the relevant key features of the detailed model for larger scales, and
 applying Markov and network theory provides a systematic strategy to
 analyse its dynamics to respond to biological questions, both are often
 difficult to obtain by direct analysis of the detailed model.
description: The meta-model was built according to the upscaling procedure for
 agent-based models presented in the publication. In this way, we produced
 a library of state and transition models to represent the community
 dynamics of western grass steppes in Patagonia across different grazing
 seasons and stocking rates.
description: README Meta-model State-and-Transition Models for Patagonian Grass Steppes
 under sheep grazing Each file containes the transition matrices for each
 grazing condition and sheep stocking rates. There are 4 main files to
 represent: ungrazed, continuous grazing, cold-season grazing and
 warm-season grazing. In ungrazed file there is only 1 matrix from ungrazed
 condition, but there are 8 matrices for grazing files by summarizing a
 gradient of sheep stocking rates (i.e. 0.25, 0.5, 0.75, 1, 1.25, 1.5,
 1.75, 2).