cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8sf7m0cj8
title: Raking the ocean surface : new patterns of coordinated motion in seabirds

description: Coordinated movements of seabirds exploiting a prey patch are known to
 increase prey encounter and capture rates of individuals. These
 behaviours, based on effective cooperation between seabirds, have only
 been reported at small scale, i.e. the scale of the prey patch. However,
 the efficient prey exploitation by seabirds in vast oceans require larger
 scale processes such as information transfers between individuals. Indeed,
 information transfers between foraging seabirds (e.g. changes in
 behaviour) reduce their search cost while increasing their prey encounter
 rate. Whether or not these information transfer processes imply active
 cooperation is unknown. Using images from fishing boat radars in the
 eastern tropical Atlantic, we show the existence of frequent medium-scale
 patterns of coordinated flights of seabird groups, consisting in seabird
 fronts (“rake” patterns) of 0.3 to 4.4 km width, displacing cohesively
 over 1.2 to 10.6 km and lasting between 2 and 19 min. For these rakes to
 be maintained, seabird groups have to adjust their flight speeds and
 directions, while they are on average distant of 500 m from each other,
 what cannot occur by chance. These findings suggest the existence of
 collective and coordinated movements in seabirds during prey searching at
 several kilometres' scale. This potential cooperation between
 foraging seabird groups brings new insight in the evolutionary
 trajectories of seabirds life-style.
description: This dataset contains two types of files : -
 in .zip files : anonymized radar images (all recorded during year 2016)
 that were used in this study. Time of recording is included in the file
 name, and images are classified in monthly repertories. FORMAT :
 .png ex : <em>Image_April_151649.png
 </em>corresponds to an image recorded in April 2016 at 15:16:49
 . - wind components, wind directions, wind speed, sun
 azimut and elevation, relative to the time and location (latitude and
 longitude, centered on [0 , 0]) of radar image recordings. FORMAT :
 .mat ex : <em>DataFile_2016_April.mat
 </em>corresponds to metadata (wind and sun complementary data,
 anonymized location) relative to each radar image recorded in April
 2016.
DOI: 10.5061/dryad.zs7h44j5m
title: Ancient tropical extinctions at high latitudes contributed to the latitudinal diversity gradient

description: Global biodiversity currently peaks at the equator and decreases toward
 the poles. Growing fossil evidence suggest this hump-shaped latitudinal
 diversity gradient (LDG) has not been persistent through time, with
 similar diversity across latitudes flattening out the LDG during past
 greenhouse periods. However, when and how diversity declined at high
 latitudes to generate the modern LDG remains an open question. Although
 diversity-loss scenarios have been proposed, they remain mostly
 undemonstrated. We outline the ‘asymmetric gradient of extinction and
 dispersal’ framework that contextualizes previous ideas behind the LDG
 under a time-variable scenario. Using phylogenies and fossils of
 Testudines, Crocodilia and Lepidosauria, we find that the hump-shaped LDG
 could be explained by (1) disproportionate extinctions of high-latitude
 tropical-adapted clades when climate transitioned from greenhouse to
 icehouse, and (2) equator-ward biotic dispersals tracking their climatic
 preferences when tropical biomes became restricted to the equator.
 Conversely, equivalent diversification rates across latitudes can account
 for the formation of an ancient flat LDG. The inclusion of fossils in
 macroevolutionary studies allows revealing time-dependent extinction rates
 hardly detectable from phylogenies only. This study underscores that the
 prevailing evolutionary processes generating the LDG during greenhouses
 differed from those operating during icehouses.
description: This folder includes the datasets and commands supporting the
 biogeographic (DEC analysis) and diversification (PyRate and BiSSE
 analyses) results It also includes the Appendix 1 with
 the results of biogeographic analyses.
DOI: 10.5066/p9pdx9x3
title: U.S. Geological Survey Inland Bathymetric and Topobathymetric Survey Inventory, version 4

description: The U.S. Geological Survey (USGS) Inland Bathymetric and Topobathymetric Survey Inventory, v. 4 includes a survey records inventory and dataset footprints (when available) for inland bathymetric and topobathymetric surveys published by the USGS for the conterminous US, Alaska, and Puerto Rico. Survey records include water feature, state, publication title, data vintage, mission, online linkage to reports and datasets, collection methods, survey and survey product resolution, datums, geoid, and accuracy information if known. This database, identified as the USGS Inland Bathymetric and Topobathymetric Survey Inventory, v.4, has been approved for release by the U.S. Geological Survey (USGS). Although this database has been subjected to rigorous review and is substantially complete, the USGS reserves the right to revise the data pursuant to further analysis and review. Furthermore, the database is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use.
DOI: 10.5061/dryad.70rxwdbtq
title: Data from: Noradrenergic projections from the locus coeruleus to the amygdala constrain fear memory reconsolidation

description: Memory reconsolidation is a fundamental plasticity process in the brain
 that allows established memories to be changed or erased. However, certain
 boundary conditions limit the parameters under which memories can be made
 plastic.  Strong memories do not destabilize, for instance,
 although why they are resilient is mostly unknown. Here, we extend the
 understanding of the mechanisms implicated in reconsolidation-resistant
 memories by investigating the hypothesis that specific modulatory signals
 shape memory formation into a state that lacks lability. We find that the
 activation of the noradrenaline-locus coeruleus system (NOR-LC) during
 strong fear memory encoding increases molecular mechanisms of stability at
 the expense of lability in the amygdala. Preventing the NOR-LC from
 modulating strong fear encoding results in the formation of memories that
 can undergo reconsolidation within the amygdala and thus are vulnerable to
 post-reactivation interference. Thus, the memory strength boundary
 condition on reconsolidation is set at the time of encoding by the action
 of the NOR-LC.
DOI: 10.17909/q0dp-x410
title: Data from TESS observations

description: It includes the LightCurve files and the full frame images for the blazar PKS 0735+178 observed in sectors 44, 45, and 46.
DOI: 10.5061/dryad.s7h44j13t
title: The impacts of body mass on immune cell concentrations in birds

description: Body mass affects many biological traits, but its impacts on immune
 defenses are fairly unknown. Recent research on mammals found that
 neutrophil concentrations disproportionately increased (scaled
 hypermetrically) with body mass, a result not predicted by any existing
 theory. Although the scaling relationship for mammals might predict how
 leukocyte concentrations scale with body mass in other vertebrates,
 vertebrate classes are distinct in many ways that might affect their
 current and historic interactions with parasites and hence the evolution
 of their immune systems. Subsequently, here, we asked which existing
 scaling hypothesis best-predicts relationships between body mass and
 lymphocyte, eosinophil, and heterophil concentrations—the avian functional
 equivalent of neutrophils—among &gt;100 species of birds. We then
 examined the predictive power of body mass relative to life-history
 variation, as an extensive literature indicates that the timing of key
 life events has influenced immune system variation among species. Finally,
 we ask whether avian scaling patterns differ from the patterns we observed
 in mammals. We found that an intercept-only model best-explained
 lymphocyte and eosinophil concentrations among birds, indicating that the
 concentrations of these cell types were both independent of body mass. For
 heterophils, however, body mass explained 31% of the variation in
 concentrations among species, much more than life-history variation (4%).
 As with mammalian neutrophils, avian heterophils scaled hypermetrically
 (b=0.19 +/- 0.05), but more steeply than mammals (~1.5x;
 0.11+/- 0.03). As such, we discuss why birds might require more
 broadly-protective cells compared to mammals of the same body size.
 Overall, body mass appears to have strong influences on the architecture
 of immune systems.
DOI: 10.5061/dryad.5x69p8d0t
title: Dynamic expression of MMP28 during cranial morphogenesis

description: Matrix metalloproteinases (MMP) are a large family of proteases comprising
 24 members in vertebrates. They are well known for their extracellular
 matrix remodelling activity. MMP28 is the last member of the family to be
 discovered. It is a secreted MMP involved in wound healing, immune system
 maturation, cell survival and migration. MMP28 is also expressed during
 embryogenesis in human and mouse. Here we describe the detailed expression
 profile of MMP28 in Xenopus laevis embryos. We show that MMP28 is
 expressed maternally and accumulates at neurula and tailbud stages
 specifically in the cranial placode territories adjacent to migrating
 neural crest cells. As a secreted MMP, MMP28 may be required in normal
 neural crest-placode interactions.
DOI: 10.5061/dryad.xd2547ddg
title: Data from: Development of a sustainability assessment algorithm and its validation using case studies on cryogenic machining

description: This work presents a comprehensive structure for evaluating the
 sustainability of machining processes. Industries can contribute towards
 developing a sustainable future by using algorithms that evaluate the
 sustainability of their processes. Inspired by the literature, the
 proposed model involves a set of metrics that are critical in evaluating
 the impact of a process on society, environment, and economy. The
 flexibility of this model allows decision-makers to use the available
 responses to identify the most favorable process. The entropy weight
 method was suggested for objectively calculating the weights of each
 indicator. A multi-criteria decision-making method i.e., Technique for
 Order Preference based on Similarity to Ideal Solution (TOPSIS), was used
 to rank processes in the decreasing order of their sustainability. The
 proposed algorithm was successfully validated with case studies from the
 published literature. A MATLAB code was also created so that industries
 may expeditiously apply this method to evaluate the sustainability of
 machining processes.
DOI: 10.5061/dryad.qbzkh18dr
title: Data from: Macro-detritivores assist resolving the dryland decomposition conundrum by engineering an underworld heaven for decomposers

description: Litter decomposition in most terrestrial ecosystems is regulated by
 moisture-dependent microorganism activity, among other things.
 Decomposition models typically underestimate rates of plant litter
 decomposition in drylands, suggesting the existence of additional drivers
 of decomposition. Attempts to reveal these drivers have predominantly
 focused on abiotic degradation agents, alternative moisture sources, and
 soil-litter mixing. The role of burrowing animals in promoting
 decomposition has received less attention despite greatly contributing to
 plant litter transfer from the harsh desert surface to the moister and
 nutrient-rich environment belowground. Our goal was to explore how
 macro-detritivore burrows affect plant litter mineralization dynamics. We
 introduced 13C-labeled litter belowground into (1) desert isopod
 (Hemilepistus reaumuri) burrows and (2) artificial burrows, and
 aboveground on top of (3) isopod fecal pellet mounds and (4) bare soil
 crust. We compared the litter mass loss between the four treatments and
 used cavity ring-down spectroscopy to reveal the in situ mineralization
 dynamics. No litter mineralization was evident during the dry summer
 months both above- and belowground. Following rain events, mineralization
 rates spiked in all four micro-environments, quickly diminishing
 aboveground while slowly waning belowground. Total litter mass loss was
 twofold higher below- than aboveground and was significantly higher in
 isopod burrows compared to artificial burrows. Our findings demonstrate
 that burrowing macro-detritivores promote litter decomposition in deserts
 by transferring organic matter to their burrows where favorable climatic
 conditions and a nutrient-enriched environment foster microbial activity.
 Thus, attempts to resolve the dryland decomposition conundrum should not
 be limited to exploring factors that allow decomposition under harsh
 desert surface climatic conditions, but focus on the role that animals
 play in facilitating decomposer-friendly environments to which they
 translocate plant litter.
description: To explore the <i>in situ</i> plant litter
 mineralization dynamics while discounting other sources of carbon
 emission, we utilized a <sup>13</sup>C stable isotope labeling
 approach. Based on soil CO<sub>2</sub> flux and
 δ<sup>13</sup>C measurements, we calculated C mineralization
 from the labeled litter. We performed these measurements at monthly
 intervals during a 10-month period, with increased sampling frequency
 following rain events. We complemented the <i>in situ</i>
 mineralization exploration with quantification of litter mass loss over
 the course of the whole experimental period.
DOI: 10.25338/b8xw4b
title: zigzag: A Hierarchical Bayesian Mixture Model for Inferring the Expression State of Genes in Transcriptomes

description: Transcriptomes are key to understanding the relationship between genotype
 and phenotype. The ability to infer the expression state (active or
 inactive) of genes in the transcriptome offers unique benefits for
 addressing this issue. For example, qualitative changes in gene expression
 may underly the origin of novel phenotypes, and expression states are
 readily comparable between tissues and species. However, inferring the
 expression state of genes is a surprisingly difficult problem, owing to
 the complex biological and technical processes that give rise to observed
 transcriptomic datasets. Here, we develop a hierarchical Bayesian mixture
 model that describes this complex process, and allows us to infer
 expression state of genes from replicate transcriptomic libraries. We
 explore the statistical behavior of this method with analyses of simulated
 datasets--where we demonstrate its ability to correctly infer true (known)
 expression states--and empirical-benchmark datasets, where we demonstrate
 that the expression states inferred from RNA-seq datasets using our method
 are consistent with those based on independent evidence. The power of our
 method to correctly infer expression states is generally high and,
 remarkably, approaches the maximum possible power for this inference
 problem. We present an empirical analysis of primate-brain transcriptomes,
 which identifies genes that have a unique expression state in humans. Our
 method is implemented in the freely-available R package zigzag.
description: Simulated data sets. MCMC log files and
 posterior probabilites of active gene expression generated by
 zigzag. Public data used to benchmark method (described
 in manuscript)
DOI: 10.5061/dryad.pk0p2ngjx
title: Custom MALDI-TOF Mass Spectrometric Database for identification of environmental Burkholderia and related genera

description: Success of microbial natural products discovery programs is dependent on
 quick and concise discrimination between isolates from diverse
 environments. However, laboratory isolation and identification of priority
 genera using current 16S rRNA PCR-based methods is both challenging and
 time-consuming. In clinical settings, MALDI-TOF MS is used to rapidly
 identify unknown bacterial pathogens, yet this has not been widely adapted
 for isolation of environmental bacteria. To expedite isolation of
 Gram-negative proteobacterial order Burkholderiales, we have created a
 main spectral (MSP) library for the Bruker Biotyper MALDI mass
 spectrometer that includes 95 entries of Burkholderia, Caballeronia,
 Paraburkholderia, and other environmentally related genera. We tested the
 effectiveness of the reference library by analyzing 49 unknown
 environmental isolate strains before comparing to results of traditional
 16S sequencing. The MALDI Biotyper correctly identified all strains to the
 genus level when sufficient reference spectra were available. This dataset
 is freely available to the scientific research community for use in
 taxonomic assignments of environmentally-derived bacteria from the order
 Burkholderiales.
description: The Linington MSP Library (Burkholderia).btmsp dataset was
 acquired on the MALDI Biotyper microflex LT system (Bruker Daltonics).
 Over 2,250 individual mass spectrometry spectra were acquired in the range
 of 3,000 to 15,000 m/z to complete the 95 main spectra (MSP) entries. The
 acquired spectra were processed using associated manufacturer software
 (see publication for details). Library was exported and packaged in a
 *.btmsp format for use with MALDI Biotyper systems.
description: To load this dataset for use in discriminating environmental
 bacteria from environmental sampling campaigns, load into MALDI Biotyper
 systems as a supplemental library. Use MALDI Biotyper Automation Control
 software program to select “Linington MSP Library (Burkholderia)” in the
 wizard.
DOI: 10.5061/dryad.fj6q573r2
title: Diet composition and social environment determine food consumption, phenotype and fitness in an omnivorous insect

description: Nutrition is the single most important factor for individual’s growth and
 reproduction. Consequently, the inability to reach the nutritional optimum
 imposes severe consequences for animal fitness. Yet, under natural
 conditions organisms may face a mixture of stressors that can modulate the
 effects of nutritional asymmetry. For instance, stressful environments
 caused by intense interaction with conspecifics. Here, we subjected the
 house-cricket Acheta domesticus to i) either of two types of diet that
 have proven to affect cricket performance and ii) simultaneously
 manipulated their social environment throughout their complete lifecycle.
 We aimed to track sex-specific consequences for multiple traits during
 insect development throughout all life stages. Both factors affected
 critical life-history traits with potential population-level consequences:
 Diet composition induced strong effects on insect development time,
 lifespan and fitness, whilst the social environment affected the number of
 nymphs that completed development, food consumption and whole-body lipid
 content. Additionally, both factors interactively determined female body
 mass. Our results highlight that insects may acquire and invest resources
 in a different manner when subjected to an intense interaction with
 conspecifics or when isolated. Furthermore, while only diet composition
 affected individual reproductive output, the social environment would
 determine the number of reproductive females, thus indirectly influencing
 population performance.
DOI: 10.15468/dl.wkj8uv
title: Occurrence Download

description: A dataset containing 4375581 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 Pieridae",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 4375581 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002277-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b8t31b
title: Data from: Comparisons of Late Ordovician ecosystem dynamics before and after the Richmondian Invasion reveal consequences of invasive species in benthic marine paleocommunities

description: A thorough understanding of how communities respond to extreme changes,
 such as biotic invasions, is essential to manage ecosystems today. Here we
 constructed fossil food webs to identify changes in Late Ordovician
 (Katian) shallow marine paleocommunity structure and functioning before
 and after the Richmondian Invasion, a well-documented ancient invasion.
 Food webs were compared using descriptive metrics and Cascading Extinction
 on Graphs models. Richness at intermediate trophic levels was
 underrepresented when using only data from the Paleobiology Database
 relative to museum collections, resulting in a spurious decrease in
 modeled paleocommunity stability. Therefore, museum collections and field
 sampling may provide more reliable sources of data for the reconstruction
 of trophic organization in comparison to online data repositories. The
 invasion resulted in several changes in ecosystem dynamics. Despite
 topological similarities between pre- and post-invasion food webs, species
 loss occurred corresponding to a minor decrease in functional groups.
 Invaders occupied all of the pre-invasion functional guilds, with the
 exception of four incumbent guilds that were lost and one new guild,
 corroborating the notion that invaders replace incumbents and fill
 pre-existing niche space. Overall, models exhibited strong resistance to
 secondary extinction, although the post-invasion community had a lower
 threshold of collapse and more variable response to perturbation. We
 interpret these changes in dynamics as a decrease in stability, despite
 similarities in overall structure. Changes in food web structure and
 functioning resulting from the invasion suggest that conservation efforts
 may need to focus on preserving functional diversity if more diverse
 ecosystems are not inherently more stable.