cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fttdz08t6
title: Seagrass and tiger shark data

description: Seagrass conservation is critical for mitigating climate change due to the
 large stocks of carbon they sequester in the seafloor. However, effective
 conservation and its potential to provide nature-based solutions to
 climate change is hindered by major uncertainties regarding seagrass
 extent and distribution. Here, we describe the characterization of the
 world’s largest seagrass ecosystem, located in The Bahamas. We integrate
 existing spatial estimates with an updated empirical remote sensing
 product and perform extensive groundtruthing of the seafloor with 2,542
 diver surveys across remote sensing tiles. We also leverage seafloor
 assessments and movement data obtained from instrument-equipped tiger
 sharks, which have strong fidelity to seagrass ecosystems, to augment and
 further validate predictions. We report a consensus area of at least
 66,000 km2 and up to 92,000 km2 of seagrass habitat across The Bahamas
 Banks. Sediment core analysis of stored organic carbon further confirmed
 the global relevance of the blue carbon stock in this ecosystem. Data from
 tiger sharks proved important in supporting mapping and groundtruthing
 remote sensing estimates. This work provides evidence of major knowledge
 gaps in the ocean ecosystem, the benefits in partnering with marine
 animals to address these gaps, and underscores support for rapid
 protection of oceanic carbon sinks.
DOI: 10.5061/dryad.c59zw3r7j
title: Do early-successional weeds facilitate or compete with seedlings in forest restoration? Disentangling abiotic vs. biotic factors

description: Census data for seedlings part of a weed exclusion experiment at Sal del
 Rey, Texas within a larger field where ~100,000 seedlings were planted in
 October-November 2018. Records seedling height, vigor (0 - dead, &gt;
 0 - alive), branching, and animal damage for 158 individuals of eight
 species classified by growth habit (fast/slow) and distributed in control
 and exclusion (mowed) plots across seven censuses.
description: See methods of linked manuscript.
description: Two of the censuses are pre-treatment (census 0 and census 1),
 and the remainder are after mowing commenced. A small
 number of observations (4) were missing data for one of animal damage,
 branching, or height; these data points are excluded from analyses
 involving these variables. Any remaining missing values
 for animal damage, branching, or height are on dead (vigor = 0)
 individuals.
DOI: 10.5061/dryad.k0p2ngf8n
title: Negotiations Over Parental Care: A Test of Alternative Hypotheses in the Clown Anemonefish

description: In species with biparental care, conflict arises over how much each parent
 provides to their offspring because both parents benefit from shifting the
 burden of care to the other. Here, we tested alternative hypotheses for
 how parents will negotiate offspring care using a wild population of
 clownfish (Amphiprion percula). We experimentally handicapped parents by
 fin-clipping the female in 23 groups, the male in 23 groups, and neither
 parent in 23 groups and measured changes in indicators of female, male,
 and pair effort in response to handicapping. First, we found that
 handicapping resulted in a decrease in the number of eggs laid by
 fin-clipped females and a decrease in the amount of parental care by
 fin-clipped males. Second, contrary to predictions, female effort did not
 change in response to the male being handicapped, or vice versa. Finally,
 the number of embryos that matured to hatching, an indicator of pair
 effort, was not influenced by the manipulation, suggesting that although
 the handicap was effective, clownfish do not face the predicted “cost to
 conflict” when one parent is handicapped. Together, these results test the
 generality of theoretical predictions and uncover novel questions about
 whether and how negotiations operate in systems where interests are
 aligned.
DOI: 10.5061/dryad.z8w9ghxcq
title: Burrow webs: Clawing the surface of interactions with burrows excavated by American badgers

description: Ecosystem engineers are organisms that influence their environment, which
 includes alteration leading to habitat provisioning for other species.
 Perhaps the most well examined guild of species provisioning habitat for
 other species is tree cavity excavators, or woodpeckers (Picidae). Many
 studies have examined the suite of secondary cavity users that rely on
 woodpeckers, and how the ecological network of secondary users,
 collectively referred to as the nest web, changes across communities.
 Despite similar habitat provisioning processes, fewer studies have
 assessed the suite of species associated with burrowers providing access
 to subterranean habitat. Here, we begin to characterize the burrow web
 provisioned by American badgers (Taxidea taxus) and evaluate the diversity
 and frequency of species interactions we detected at abandoned badger
 burrows in Wyoming, USA. We deployed camera-traps at 23 badger burrows and
 identified interactions with the burrow by birds, mammals, and reptiles.
 Overall, we identified 31 other species utilizing badger burrows,
 consisting of 12 mammals, 18 birds, and 1 reptile. Mammals, other than
 American badgers themselves and other fossorial species such as ground
 squirrels (Urocitellus sp.), frequently using burrows included mice
 (Peromyscus sp.), long-tailed weasel (Mustela frenata), pygmy rabbit
 (Brachylagus idahoensis), and desert cottontail (Sylvilagus audubonii). Of
 the 18 bird species detected, most accounted for less than 5% of overall
 detections, besides chipping sparrows (Spizella passerina) at 7.2 – 11.5%
 of detections. The most common category of detection by bird species was
 foraging, contrary to mammals, which used the burrow frequently and were
 commonly observed entering and existing the burrow. This work provides
 additional context on the ecological role American badgers provide within
 their environment. More broadly, this work scratches the surface of many
 remaining questions to explore with the aim of advancing our
 understandings about burrow webs across the diversity of burrowing species
 and the communities in which they occur.
DOI: 10.5061/dryad.kwh70rz43
title: Green quantitative spectrofluorimetric analysis of rupatadine and montelukast at nanogram scale using direct and synchronous techniques

description: Two green sensitive spectrofluorimetric methods at nanogram scale were
 investigated for the determination of rupatadine fumarate (RUP) [method I]
 and its binary mixture with montelukast (MKT) [method II]. Method I is
 concerned with measuring the native fluorescence of RUP in presence of
 0.10 M H2SO4 and 0.10 % w/v sodium dodecyl sulfate at 455 nm after
 excitation at 277 nm. The linearity range of the first method was
 0.20-2.00 µg/mL with detection and quantitation limits of 11.00 ng/mL and
 36.00 ng/mL, respectively. The second method includes the concurrent
 estimation of RUP and MKT in their co-formulated tablet preparation by
 applying first derivative synchronous spectrofluorimetric technique. The
 derivative intensities were measured for the two drugs in aqueous solution
 containing Mcllvaine’s buffer pH 2.60 at fixed wavelength difference (Δλ)
 of 140 nm. Each drug was estimated at the zero contribution of the other.
 For RUP, the intensity was measured at 261 nm while MKT was quantitated at
 371 nm. The method was linear over the range of 0.10-4.00 µg/mL and
 0.20-1.60 µg/mL with limits of detection 4.00 and 5.00 ng/mL and limits of
 quantitation 13.38 and 15.00 ng/mL for RUP and MKT, respectively. The
 method was extended to determine the two analytes in laboratory-prepared
 mixtures and combined tablets. Validation of the two methods was performed
 according the official recommendations of the International Council of
 Harmonization (ICH). Statistical interpretation of data revealed that our
 results were in good agreement with the comparison method. Moreover, the
 greenness of the methods has been assessed and confirmed by applying three
 different reported assessment tools.
DOI: 10.5061/dryad.2ngf1vhnv
title: 3D images of a turtle embryo

description: Turtle eggs containing embryos are exceedingly rare in the fossil record.
 Here, we provide the first description and taxonomic identification, to
 our knowledge, of a fossilized embryonic turtle preserved in an egg, a
 fossil recovered from the Upper Cretaceous Xiaguan Formation of Henan
 Province, China. Through Computed Tomography and Three-Dimensional
 reconstruction, many bones can be clearly displayed, including the
 maxillae, mandibles, ribs, plastral plates, scapula, forelimbs, and hind
 limbs. The specimen is attributed to the Nanhsiungchelyidae
 (Pan-Trionychia), an extinct group of large terrestrial turtles (possibly
 the species Yuchelys nanyangensis). The egg is rigid, spherical, and is
 one of the largest and thickest shelled Mesozoic turtle eggs known.
 Importantly, this specimen allowed identification of other
 nanhsiungchelyid egg clutches and comparison to those of Adocidae, as
 Nanhsiungchelyidae and Adocidae form the basal extinct clade Adocusia of
 the Pan-Trionychia (includes living soft-shelled turtles). Despite the
 differences in habitat adaptations, nanhsiungchelyids (terrestrial) and
 adocids (aquatic) shared several reproductive traits, including relatively
 thick eggshells, medium size clutches and relatively large eggs, which may
 be primitive for trionychoids (including Adocusia and Carrettochelyidae).
 The unusually thick calcareous eggshell of nanhsiungchelyids compared to
 those of all other turtles (including adocids) may be related to a nesting
 style adaptation to an extremely harsh environment.
description: The egg (with embryonic bones) was scanned using a 225 kV
 micro-CT scanner at 170 KV and 0.12 mA, with a resolution ratio of 37.64
 μm, which was designed by IHEP. The 3D models of the embryonic remains
 were reconstructed through the use of Mimics 17 software.
DOI: 10.15468/dl.pxtp6v
title: Occurrence Download

description: A dataset containing 384 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Selenaspidus articulatus)"
 ]
}

 The dataset includes 384 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002895-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nk98sf7tq
title: In the eye of the beholder: Is color classification consistent amongst human observers?

description: Colorful displays have evolved in multiple plant and animal species as
 signals to mutualists, antagonists, competitors, mates, and other
 potential receivers. Studies of color have long relied on subjective
 classifications of color by human observers. However, humans have a
 limited ability to perceive color compared to other animals, and human
 biological, cultural, and environmental variables can influence color
 perception. Here, we test the consistency of human color classification
 using fruit color as a model system. We used reflectance data of 67
 tropical fruits and surveyed 786 participants to assess the degree to
 which (i) participants of different cultural and linguistic backgrounds
 agree on color classification of fruits; and (ii) human classification to
 a discrete set of commonly used colors (e.g. red, blue, green) corresponds
 to natural clusters based on light reflectance measures processed through
 visual systems of other animals. We find that individual humans tend to
 agree on the colors they attribute to fruits across language groups.
 However, these colors do not correspond to clearly discernible clusters in
 di- or tetrachromatic visual systems. These results indicate that
 subjective color categorizations tend to be consistent amongst observers
 and can be used for large synthetic studies, but also that they do not
 reflect natural categories that are relevant to animal observers.
DOI: 10.5281/zenodo.13777359
title: Research data for "Intermediates of Forming Transition Metal Dichalcogenide Heterostructures Revealed by Machine Learning Simulations"

description: This dataset supports the paper "Intermediates of Forming Transition Metal Dichalcogenide Heterostructures Revealed by Machine Learning Simulations". 

Included Files:



ocp_active.zip: Modified version of ocp (https://github.com/Open-Catalyst-Project/ocp) tailored for active learning applications.

deployed.pth: MLP model.

chemiscopy_run.py: Script integrating the chemiscopy and nequip modules, designed for dataset visualization.

new_energy.py: Modified version of the nequip module, featuring a repulsive potential function.

SI-data.extxyz: The datasets in extxyz format.


How to use the modified version of the nequip module:

To train this version of the potential function, it is recommended to use nequip<=0.5.6 (on Linux). The NequIP training files need to be updated as follows:

model_builders:
 - new_energy.EnergyModel                
 - StressForceOutput               
min_bond_len: 1.8

Then run:

export PYTHONPATH=${PYTHONPATH}:$PWDnequip-train config.yml # Train the potential functionnequip-deploy build --train-dir nequipresultsdir build.pth # Deploy the trained model
DOI: 10.5281/zenodo.18397127
title: Research data for "Intermediates of Forming Transition Metal Dichalcogenide Heterostructures Revealed by Machine Learning Simulations"

description: This dataset supports the paper "Intermediates of Forming Transition Metal Dichalcogenide Heterostructures Revealed by Machine Learning Simulations". 

Included Files:



ocp_active.zip: Modified version of ocp (https://github.com/Open-Catalyst-Project/ocp) tailored for active learning applications.

deployed.pth: MLP model.

chemiscopy_run.py: Script integrating the chemiscopy and nequip modules, designed for dataset visualization.

new_energy.py: Modified version of the nequip module, featuring a repulsive potential function.

SI-data.extxyz: The datasets in extxyz format.


How to use the modified version of the nequip module:

To train this version of the potential function, it is recommended to use nequip<=0.5.6 (on Linux). The NequIP training files need to be updated as follows:

model_builders:
 - new_energy.EnergyModel                
 - StressForceOutput               
min_bond_len: 1.8

Then run:

export PYTHONPATH=${PYTHONPATH}:$PWDnequip-train config.yml # Train the potential functionnequip-deploy build --train-dir nequipresultsdir build.pth # Deploy the trained model
DOI: 10.5061/dryad.dfn2z3528
title: Data from: Intra-specific differences in cognition: Bumblebee queens learn better than workers

description: Species’ cognitive traits are shaped by their ecology, and even within a
 species, cognition can reflect the behavioural requirements of individuals
 with diffferent roles. Social insects have a number of discrete roles
 (castes) within a colony, and thus offer a useful system to determine how
 ecological requirements shape cognition. Bumblebee queens are a critical
 point in the lifecycle of their colony, since its future success is
 reliant on a single individual’s ability to learn about floral stimuli
 while finding a suitable nest site; thus, one might expect particularly
 adept learning capabilities at this stage. I compared wild Bombus
 vosnesenskii queens and workers on their ability to learn a colour
 association and found that queens performed better than workers. In
 addition, queens of another species, B. insularis, a cuckoo species with a
 different lifecycle but similar requirements at this stage, performed
 equally well as the non-parasitic queens. To control for differences in
 foraging experience, I then repeated this comparison with lab-based B.
 impatiens, and found that unmated queens performed better than workers.
 These results add to the body of work on how ecology shapes cognition and
 opens the door to further research in comparative cognition using wild
 bees.
DOI: 10.5061/dryad.j6q573nf6
title: FGF-2-dependent signaling activated in aged human skeletal muscle promotes intramuscular adipogenesis

description: Aged skeletal muscle is markedly affected by fatty muscle infiltration and
 strategies to reduce the occurrence of intramuscular adipocytes are
 urgently needed. Here, we show that fibroblast growth factor-2 (FGF-2) not
 only stimulates muscle growth, but also promotes intramuscular
 adipogenesis. Using multiple screening assays upstream and downstream of
 microRNA (miR)-29a signaling, we located the secreted protein and
 adipogenic inhibitor SPARC to an FGF-2 signaling pathway that is conserved
 between skeletal muscle cells from mice and humans and that is activated
 in skeletal muscle of aged mice and humans. FGF-2 induces the
 miR-29a/SPARC axis through transcriptional activation of FRA-1, which
 binds and activates an evolutionary conserved AP-1 site element proximal
 in the miR-29a promoter. Genetic deletions in muscle cells and
 AAV-mediated overexpression of FGF-2 or SPARC in mouse skeletal muscle
 revealed that this axis regulates differentiation of fibro/adipogenic
 progenitors in vitro and intramuscular adipose tissue
 (IMAT) formation in vivo. Skeletal muscle from human donors aged
 &gt; 75 years versus &lt; 55 years showed activation of
 FGF-2-dependent signaling and increased IMAT. Thus, our data highlights a
 disparate role of FGF-2 in adult skeletal muscle and reveals a novel
 pathway to combat fat accumulation in aged human skeletal muscle.
description: Please see: Mathes S, Fahrner A, Ghoshdastider U, Rüdiger HA,
 Leunig M, Wolfrum C, Krützfeldt J. FGF-2-dependent signaling activated in
 aged human skeletal muscle promotes intramuscular adipogenesis. Proc Natl
 Acad Sci U S A. 2021.
description: See README.txt for an explanation of the data.
DOI: 10.5061/dryad.9kd51c5hf
title: Identification of infectious agents in early marine Chinook and Coho salmon associated with cohort survival

description: Recent decades have seen an increased appreciation for the role infectious
 diseases can play in mass mortality events across a diversity of marine
 taxa. At the same time many Pacific salmon populations have declined in
 abundance as a result of reduced marine survival. However, few studies
 have explicitly considered the potential role pathogens could play in
 these declines. Using a multi-year dataset spanning 59 pathogen taxa in
 Chinook and Coho salmon sampled along the British Columbia coast, we
 carried out an exploratory analysis to quantify evidence for associations
 between pathogen prevalence and cohort survival, and between pathogen load
 and body condition. While a variety of pathogens had moderate to strong
 negative correlations with body condition or survival for one host species
 in one season, we found that Tenacibaculum maritimum and Piscine
 orthoreovirus had consistently negative associations with body condition
 in both host species and seasons, and were negatively associated with
 survival for Chinook salmon collected in the fall and winter. Our
 analyses, which offer the most comprehensive examination of associations
 between pathogen prevalence and Pacific salmon survival to date, suggest
 that pathogens in Pacific salmon warrant further attention, especially
 those whose distribution and abundance may be influenced by anthropogenic
 stressors.
description: The collection and creation of these data will be described in a
 forthcoming manuscript.
description: See attached read me file.
DOI: 10.5061/dryad.xwdbrv1dq
title: Sea snake approaches to divers

description: Scuba-divers on tropical coral-reefs often report unprovoked “attacks” by
 highly venomous Olive sea snakes (Aipysurus laevis). Snakes swim directly
 towards divers, sometimes wrapping coils around the diver’s limbs and
 biting. Based on a focal animal observation study of free-ranging Olive
 sea snakes in the southern Great Barrier Reef, we suggest that these
 “attacks” are misdirected courtship responses. Approaches to divers were
 most common during the breeding season (winter) and were by males rather
 than by female snakes. Males also made repeated approaches, spent more
 time with the diver, and exhibited behaviours (such as coiling around a
 limb) also seen during courtship. Agitated rapid approaches by males,
 easily interpreted as “attacks”, often occurred after a courting male lost
 contact with a female he was pursuing, after interactions between rival
 males, or when a diver tried to flee from a male. These patterns suggest
 that “attacks” by sea snakes on humans result from mistaken identity
 during sexual interactions. Rapid approaches by females occurred when they
 were being chased by males. Divers that flee from snakes may inadvertently
 mimic the responses of female snakes to courtship, encouraging males to
 give chase. To prevent escalation of encounters, divers should keep still
 and avoid retaliation.
description: A diver recorded interactions with free-ranging snakes.
DOI: 10.5061/dryad.wstqjq2mt
title: Associations among cotyledon developmental stability, canalization and phenotypic plasticity in response to shading and burial depth in five herbaceous species at early seedling stage

description: Premise of research. Cotyledons have important functions in early seedling
 stage and have important effects on later stages, but we know little about
 the relationships among developmental stability, canalization and
 phenotypic plasticity in cotyledons. Methodology. We conducted a
 field experiment with five herbaceous species, by subjecting them
 to contrasting light conditions and burial depths and measuring their
 cotyledon size and fluctuating asymmetry (random deviation from perfect
 bilateral symmetry, indicating developmental stability or instability),
 coefficient of variation and plasticity of cotyledon size, to
 investigate the relationships among cotyledon developmental
 stability, canalization and plasticity in response to shading and deep
 burial. Pivotal results.   Pharbitis purpurea, Convolvulus
 arvensis and Carpesium abrotanoides had
 increased cotyledon size in response to shading at both burial
 depths; Abutilon theophrasti showed reduced cotyledon
 size in response to shading vs. full light at shallow depth, but greater
 cotyledon size in response to both shading and deep burial. Shading
 increased cotyledon fluctuating asymmetry
 of P. purpurea and C. abrotanoides,
 while deep burial decreased it. Cotyledon fluctuating asymmetry had
 positive correlations with coefficient of variation and plasticity in
 response to shade in shading, with little correlation between coefficient
 of variation and plasticity. Conclusions.   Results
 suggested A. theophrasti may have greater
 tolerance for multiple stresses than the other species, and deep
 burial may improve shade tolerance of cotyledons through moderate level of
 stress selection. Both developmental instability and decreased
 canalization may indicate the state of faster growth.
 Developmental instability can facilitate more-active response to shading
 in cotyledon, while the relationship between canalization and plasticity
 should be more complex.