cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.z6ppnj
title: Occurrence Download

description: A dataset containing 661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphausia vallentini",
 "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 2015"
 ]
}

 The dataset includes 661 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002360-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hdr7sqvf9
title: Spectral-power associations reflect amplitude modulation and within-frequency interactions on the sub-second timescale and cross-frequency interactions on the seconds timescale

description: We investigated the global structure of intrinsic cross-frequency dynamics
 by systematically examining power-based temporal associations among a
 broad range of oscillation frequencies both within and across EEG-based
 current sources (sites). We focused on power-based associations that could
 reveal unique timescale dependence independently of interacting
 frequencies. Large spectral-power fluctuations across all sites occurred
 at two characteristic timescales, sub-second and seconds, yielding
 distinct patterns of cross-frequency associations. On the fast sub-second
 timescale, within-site (local) associations were consistently between
 pairs of beta-gamma frequencies differing by a
 constant Delta-f (particularly Delta-f ~ 10 Hz at posterior sites and Delta-f ~ 16 Hz at lateral sites) suggesting that higher-frequency oscillations are organized into Delta-f amplitude-modulated packets, whereas cross-site (long-distance) associations were all within-frequency (particularly in the &gt;30 Hz and 6-12 Hz ranges, suggestive of feedforward and feedback interactions). On the slower seconds timescale, within-site (local) associations were characterized by a broad range of frequencies selectively associated with ~10 Hz at posterior sites and associations among higher (&gt;20 Hz) frequencies at lateral sites, whereas cross-site (long-distance) associations were characterized by a broad range of frequencies at posterior sites selectively associated with ~10 Hz at other sites, associations among higher (&gt;20 Hz) frequencies among lateral and anterior sites, and prevalent associations at ~10 Hz. Regardless of timescale, within-site (local) cross-frequency associations were weak at anterior sites indicative of frequency-specific operations. Overall, these results suggest that the fast sub-second-timescale coordination of spectral power is limited to local amplitude modulation and insulated within-frequency long-distance interactions (likely feedforward and feedback interactions), while characteristic patterns of cross-frequency interactions emerge on the slower seconds timescale. The results also suggest that the occipital alpha oscillations play a role in organizing higher-frequency oscillations into ~10 Hz amplitude-modulated packets to communicate with other regions. Functional implications of these timescale-dependent cross-frequency associations await future investigations.
description: EEG was recorded while participants (N=24) rested with their eyes
 closed (for about 5 minutes) with 64 scalp electrodes using a BioSemi
 ActiveTwo system (www.biosemi.com). The EEG data have been pre-processed
 as described in the Materials and Methods section of the associated
 article. The file named "rest_eyes_closed.mat" contains the data
 prior to applying a surface-Laplacian transform. The file named
 "rest_eyes_closed_SL.mat" contains the surface-Laplacian
 transformed data. The data are formated for MATLAB.
DOI: 10.5061/dryad.xwdbrv1b5
title: Defining species when there is gene flow

description: Whatever one’s definition of species, it is generally expected that
 individuals of the same species should be genetically more similar to each
 other than they are to individuals of another species. Here we show that
 in the presence of cross-species gene flow, this expectation may be
 incorrect. We use the multispecies coalescent model with migration or
 introgression to study the impact of gene flow on genetic differences
 within and between species and highlight a surprising but plausible
 scenario in which different population sizes and asymmetrical migration
 rates cause a genetic sequence to be on average more closely related to a
 sequence from another species than to a sequence from the same species.
 Our results highlight the extraordinary impact that even a small amount of
 gene flow may have on the genetic history of the species. We suggest that
 contrasting long-term migration rate and short-term hybridization rate,
 both of which can be estimated using genetic data, may be a powerful
 approach to detecting the presence of reproductive isolation mechanisms
 and to define species boundaries.
description: Computer generated.
description: Supplementary figures S1 and S2.
DOI: 10.5281/zenodo.18348686
title: Data for James et al. 'Swimming mode determines shielding of odor traces in turbulenc'

description: Data and plot scripts to generate the figures presented in the following manuscript:Martin James, Francesco Viola and Agnese Seminara, 'Swimming mode determines shielding of odor traces in turbulence'
DOI: 10.5281/zenodo.18348685
title: Data for James et al. 'Swimming mode determines shielding of odor traces in turbulenc'

description: Data and plot scripts to generate the figures presented in the following manuscript:Martin James, Francesco Viola and Agnese Seminara, 'Swimming mode determines shielding of odor traces in turbulence'
DOI: 10.7291/d1tq1p
title: Data from: Global hotspots for coastal ecosystem-based adaptation

description: Helping the world’s coastal communities adapt to climate change impacts
 requires evaluating the vulnerability of coastal communities and assessing
 adaptation options. This includes understanding the potential for
 ‘natural’ infrastructure (ecosystems and the biodiversity that underpins
 them) to reduce communities’ vulnerability, alongside more traditional
 ‘hard’ infrastructure approaches. Here we present a spatially explicit
 global evaluation of the vulnerability of coastal-dwelling human
 populations to key climate change exposures and explore the potential for
 coastal ecosystems to help people adapt to climate change (ecosystem-based
 adaptation (EbA)). We find that mangroves and coral reefs are particularly
 well situated to help people cope with current weather extremes, a
 function that will only increase in importance as people adapt to climate
 change now and in coming decades. We find that around 30.9 million people
 living within 2km of the coast are highly vulnerable to tropical storms
 and sea-level rise (SLR). Mangroves and coral reefs overlap these threats
 to at least 5.3 and 3.4 million people, respectively, with substantial
 potential to dissipate storm surges and improve resilience against SLR
 effects. Significant co-benefits from mangroves also accrue, with 896
 million metric tons of carbon stored in their soils and above- and
 below-ground biomass. Our framework offers a tool for prioritizing
 ‘hotspots’ of coastal EbA potential for further, national and local
 analyses to quantify risk reduction and, thereby, guide investment in
 coastal ecosystems to help people adapt to climate change. In doing so, it
 underscores the global role that conserving and restoring ecosystems can
 play in protecting human lives and livelihoods, as well as biodiversity,
 in the face of climate change.
description: Details of how these data were processed can be found in the
 Methods and Supplementary Materials of Jones et al. Global hotspots for
 coastal ecosystem-based adaptation 2020 (PLOS ONE).
description: A brief summary of the dataset(s) follows:
 data_grid_10min.shp (vector shapefile; Geograpihc Coordinate
 System, WGS 1984 ): global grid (10 minute resolution) constrained to the
 cells within the low elevation coastal zone as defined in  Jones et al.
 Global hotspots for coastal ecosystem-based adaptation 2020 (PLOS ONE). 
 Attribute fields include<br> ID=unique cell identifier;<br>
 country=country name;<br> country_iso=country code (ISO alpha
 3);<br> man_ha=mangrove extent in cell (hectares);<br>
 coral_ha=coral reef extent in cell (hectares);<br> pop=total
 population in cell (within 25 km of coast);<br> pop_2km=total
 population in cell (within 2 km of coast);<br> ac=adaptive capacity
 of cell;<br> sensit=sensitivity of cell;<br> expos=exposure of
 cell;<br> vulner=vulnerability of cell;<br> bm_high=carbon
 biomass estimate (upper bound) in cell;<br> bm_low=carbon biomass
 estimate (lower bound) in cell;.
DOI: 10.5061/dryad.x0k6djhg7
title: Digital image correlation (DIC) measurement of contact stiffness

description: Measurements with digital image correlation of normal and tangential
 contact stiffness for ground Ti-6Al-4V interfaces suggest a linear
 relationship between normal contact stiffness and normal load and a linear
 relationship between tangential contact stiffness and tangential load. The
 normal contact stiffness for these surfaces is observed approximately to
 be inversely proportional to an equivalent surface roughness parameter,
 defined for two surfaces in contact. The ratio of the tangential contact
 stiffness to the normal contact stiffness at beginning of a load step is
 seen to be given approximately by the Mindlin ratio. A simple empirical
 model is proposed to estimate both normal and tangential contact stiffness
 at different loads for ground Ti-6Al-4V surfaces of known surface
 roughness and coefficient of friction.
description: Experimental images and load data were analysed with Digital
 Image Correlation using DaVis StrainMaster software. This was
 post-processed with MATLAB.
description: <b>Summary</b> Raw image and load
 data are provided for all the tests. Each test consists of normal loading,
 tangential loading, and normal unloading sections. The measured pixel
 length for each test is provided. The data from digital image correlation
 (DIC) obtained from the raw images are provided. These are processed with
 MATLAB scripts. Further information can be obtained from the
 manuscript.  <b>Details</b>
 <b>‘RawImageAndLoad’ folder:
 </b> The raw experimental images and
 load data corresponding to each test section is provided in respective
 folders. The measured pixel length for each test is provided
 also. 
 <b>'DIC_Data' folder:
 </b> Raw images were processed by DIC
 software (DaVis StrainMaster) for each test section. The output files from
 StrainMaster alongside a load data file and DIC settings information file
 are provided in respective folders for each test section.  
 
 <b>'Matlab_FinalProcessing'
 folder:</b> The MATLAB codes used to process
 the DIC Data for each test section are provided, in respective
 folders  3.1      
 For processing normal loading and unloading test sections run scripts with
 prefixes A,B,C,D,E and F (in this order), within the respective
 folder. The first
 script 'A_LoopFiles' will ask for a name for the test and the
 location of the DIC data for that test section. Provide the relevant
 folder found in 'DIC_Data' folder. 3.2       For processing tangential
 loading test sections. Run scripts with prefixes A,B1,B2,B3, C1,C2, and C3
 (in this order), in the respective folder. The first script
 'A_LoopFiles' will ask for a name for the test and the folder
 location of the DIC data for that test section. Provide the relevant
 folder found in 'DIC_Data' folder.
DOI: 10.5061/dryad.4qrfj6q79
title: Viruses harness YxxØ motif to interact with host AP2M1 for replication: A vulnerable broad-spectrum antiviral target

description: Targeting a universal host protein exploited by most viruses would be a
 game-changing strategy that offers broad-spectrum solution and rapid
 pandemic control including the current COVID-19. Here, we found a common
 YxxØ-motif of multiple viruses that exploits host AP2M1 for intracellular
 trafficking. A library chemical, N-(p-amylcinnamoyl)anthranilic
 acid (ACA), was identified to interrupt AP2M1-virus interaction and
 exhibit potent antiviral efficacy against a number of viruses in vitro and
 in vivo, including the influenza A viruses (IAVs), Zika virus (ZIKV),
 human immunodeficiency virus, and coronaviruses including MERS-CoV and
 SARS-CoV-2. YxxØ mutation, AP2M1 depletion, or disruption by ACA causes
 incorrect localization of viral proteins, which is exemplified by the
 failure of nuclear import of IAV nucleoprotein and diminished endoplasmic
 reticulum localization of ZIKV-NS3 and enterovirus-A71-2C proteins,
 thereby suppressing viral replication. Our study reveals an evolutionarily
 conserved mechanism of protein-protein interaction between host and virus
 that can serve as a broad-spectrum antiviral target.
DOI: 10.5061/dryad.z612jm68p
title: Reactivation of latent infections with migration shapes population-level disease dynamics

description: Annual migration is common across animal taxa and can dramatically shape
 the spatial and temporal patterns of infectious disease. Although
 migration can decrease infection prevalence in some contexts, these
 energetically costly long-distance movements can also have
 immunosuppressive effects that may interact with transmission processes in
 complex ways. Here we develop a mechanistic model for the reactivation of
 latent infections driven by physiological changes or energetic costs
 associated with migration (i.e., “migratory relapse”) and its effects on
 disease dynamics. We determine conditions under which migratory relapse
 can amplify or reduce infection prevalence across pathogen and host traits
 (e.g., infectious periods, virulence, overwinter survival, timing of
 relapse) and transmission phenologies. We show that relapse at either the
 start or end of migration can dramatically increase prevalence across the
 annual cycle and may be crucial for maintaining pathogens with low
 transmissibility and short infectious periods in migratory populations.
 Conversely, relapse at the start of migration can reduce the prevalence of
 highly virulent pathogens by amplifying culling of infected hosts during
 costly migration, especially for highly transmissible pathogens and those
 transmitted during migration or the breeding season. Our study provides a
 mechanistic foundation for understanding the spatiotemporal patterns of
 relapsing infections in migratory hosts, with implications for zoonotic
 surveillance and understanding how infection patterns will respond to
 shifts in migratory propensity associated with environmental change.
 Further, our work suggests incorporating within-host processes into
 population-level models of pathogen transmission may be crucial for
 reconciling the range of migration–infection relationships observed across
 migratory species.
DOI: 10.15468/dl.hs93px
title: Occurrence Download

description: A dataset containing 1463 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Archidendron clypearia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1463 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002361-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8cz8w9gm7
title: Effects of herbivore assemblage on the spatial heterogeneity of soil nitrogen in eastern Eurasian steppe

description: 1. The spatial heterogeneity of soil limiting resources is one of the most
 important factors maintaining biodiversity and ecosystem functions. There
 is a general concern that herbivore grazing plays a central role in
 modifying soil resources heterogeneity.  However, most studies
 have examined how large herbivores as a group affect soil heterogeneity.
 There is limited knowledge about how assemblages of different herbivore
 species may influence soil heterogeneity, and whether the herbivore
 assemblage effects might vary with grassland types. 2. Here we conducted a
 four-year grazing experiment to examine the effects of different herbivore
 assemblages (no grazing; cattle grazing; sheep grazing and mixed grazing
 of cattle and sheep) on the spatial heterogeneity of soil N availability
 across three types of grasslands (meadow steppe, typical steppe, desert
 steppe) in eastern Eurasian steppe. 3. The results showed that all the
 herbivore grazing increased the heterogeneity of soil N availability in
 the three grasslands with different precipitation (only cattle grazing and
 mixed grazing of cattle and sheep in meadow steppe did not reach a
 statistically significant level). The consistently increased heterogeneity
 of soil N availability was primarily due to the effect of animal excreta
 addition, which weakened in drier grasslands, likely because of the slower
 excreta decomposition. Moreover, sheep excreta contributed more to soil N
 heterogeneity than that of other herbivore assemblages, and the effect was
 statistically significant in meadow steppe and typical steppe with
 relative high precipitation. 4. Synthesis and applications. Our study
 indicates that sheep could have larger potential to maintain and enhance
 grassland heterogeneity than cattle especially in grassland ecosystems
 with high precipitation. We therefore suggest that managing above-ground
 herbivore species is important for conserving and promoting grassland soil
 heterogeneity, and that the management should also take into account local
 environmental conditions such as
 precipitation.
DOI: 10.5281/zenodo.18395292
title: pH-dependent structural dynamics of the neuropeptide Y in aqueous solution

description: All input and parameter files for Molecular Dynamics simulations, Constant pH Molecular Dynamics simulations and all python codes used for analysis can be found here.
DOI: 10.5061/dryad.f1vhhmgtd
title: Warming acts through earlier snowmelt to advance but not extend alpine community flowering

description: Large-scale warming will alter multiple local climate factors in alpine
 tundra, yet very few experimental studies examine the combined yet
 distinct influences of earlier snowmelt, higher temperatures and altered
 soil moisture on alpine ecosystems. This limits our ability to predict
 responses to climate change by plant species and communities. To address
 this gap, we used infrared heaters and manual watering in a fully
 factorial experiment to determine the relative importance of these climate
 factors on plant flowering phenology, and response differences among plant
 functional groups. Heating advanced snowmelt and flower initiation, but
 exposed plants to colder early-spring conditions in the period prior to
 first flower, indicating that snowmelt timing, not temperature, advances
 flowering initiation in the alpine community. Flowering duration was
 largely conserved; heating did not extend average species flowering into
 the latter part of the growing season but instead flowering was completed
 earlier in heated plots. Although passive warming experiments have
 resulted in warming-induced soil drying suggested to advance flower
 senescence, supplemental water did not counteract the average species
 advance in flowering senescence caused by heating or extend flowering in
 unheated plots, and variation in soil moisture had inconsistent effects on
 flowering periods. Functional groups differed in sensitivity to earlier
 snowmelt, with flower initiation most advanced for early-season species
 and flowering duration lengthened only for graminoids and forbs. We
 conclude that earlier snowmelt, driven by increased radiative heating, is
 the most important factor altering alpine flowering phenology. Studies
 that only manipulate summer temperature will err in estimating the
 sensitivity of alpine flowering phenology to large-scale warming. The
 wholesale advance in flowering phenology with earlier snowmelt suggests
 that alpine communities will track warming, but only alpine forbs and
 graminoids appear able to take advantage of an extended snow-free
 season. 
description: This dataset was collected during field surveys from 2009-2013 at
 the Alpine Treeline Warming experiment on Niwot Ridge at the Mountian
 Research Station, CO.
description: Please see the accompanying README which describes all data and
 code.
DOI: 10.5061/dryad.dbrv15dz0
title: Cellular plasticity in response to suppression of storage proteins in the Brassica napus embryo

description: The trade-off between protein and oil storage in oilseed crops has been
 tested here in oilseed rape (Brassica napus) by analyzing the effect of
 suppressing key genes encoding protein storage products (napin,
 cruciferin). The phenotypic outcomes were assessed using nuclear magnetic
 resonance and mass spectrometry imaging, microscopy, transcriptomics,
 proteomics, metabolomics, lipidomics, immunological assays as well as by
 flux balance analysis. Surprisingly, the profile of storage products was
 only moderately changed in RNAi transgenics. However, embryonic cells had
 undergone remarkable architectural rearrangements. The suppression of
 storage proteins led to the elaboration of membrane stacks enriched with
 oleosin (6-fold higher protein abundance) and novel ER morphology. Protein
 rebalancing, and amino acid metabolism were focal points of the metabolic
 adjustments to maintain embryonic carbon/nitrogen homeostasis. Flux
 balance analysis indicated a rather minor additional demand for cofactors
 (ATP, NADPH). The conclusion was that cellular plasticity in seeds
 protects against perturbations to its storage capabilities, and hence
 contributes materially to homeostasis. The study provides novel
 mechanistic insights into the intriguing link between lipid and protein
 storage, which have implications for biotechnological strategies directed
 at the improvement of oilseed crops.
description: Proteomics, metabolomics, RNA-sequencing, Magnetic resonance
 imaging, MALDI
DOI: 10.5061/dryad.ksn02v71d
title: Metabolic rate, context-dependent selection, and the competition-colonization trade-off

description: Metabolism is linked with the pace‐of‐life, co‐varying with survival,
 growth, and reproduction. Metabolic rates should therefore be under strong
 selection and, if heritable, become less variable over time. Yet
 intraspecific variation in metabolic rates is ubiquitous, even after
 accounting for body mass and temperature. Theory predicts variable
 selection maintains trait variation, but field estimates of how selection
 on metabolism varies are rare. We use a model marine invertebrate to
 estimate selection on metabolic rates in the wild under different
 competitive environments. Fitness landscapes varied among environments
 separated by a few centimeters: interspecific competition selected for
 higher metabolism, and a faster pace‐of‐life, relative to competition‐free
 environments. Populations experience a mosaic of competitive regimes; we
 find metabolism mediates a competition‐colonization trade‐off across these
 regimes. Although high metabolic phenotypes possess greater competitive
 ability, in the absence of competitors, low metabolic phenotypes are
 better colonizers. Spatial heterogeneity and the variable selection on
 metabolic rates that it generates is likely to maintain variation in
 metabolic rate, despite strong selection in any single environment.