cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n02v6wwxj
title: Digital holographic microscope recordings of passive motion of small particles

description: Digital holographic microscopy provides the ability to observe throughout
 a volume that is large compared to its resolution without the need to
 actively refocus to capture the entire volume. This enables simultaneous
 observations of large numbers of small objects within such a volume. We
 have constructed a microscope that can observe a volume of 0.4 x 0.4 x 1.0
 µm with submicrometer resolution (in xy) and 2 µm resolution (in z) for
 observation of microorganisms and minerals in liquid environments on Earth
 and on potential planetary missions. Because environmental samples are
 likely to contain mixtures of inorganics and microorganisms of comparable
 sizes near the resolution limit of the instrument, discrimination between
 living and non-living objects may be difficult. The active motion of
 motile organisms can be used to readily distinguish them from non-motile
 objects (live or inorganic), but additional methods are required to
 distinguish non-motile organisms and inorganic objects that are of
 comparable size but different composition and structure. We demonstrate
 the use of passive motion to make this discrimination by evaluating
 diffusion and buoyancy characteristics of cells, styrene beads, alumina
 particles, and gas-filled vesicles of micron scale in the field of view.
description: Holographic microscopy was performed using a custom off-axis
 common path instrument as described previously [24]. Briefly, the paired
 objective lenses had a numerical aperture (NA) of 0.3, yielding an
 effective magnification of 19.6x. The wavelength used was 405 nm, supplied
 by a diode laser (Thorlabs S1FC405); at this wavelength, the microscope’s
 lateral spatial resolution as measured with an Air Force test target was
 0.8 µm. Samples for recording were diluted into a 1.0 mm deep chamber
 having both a reference channel (filled with medium or
 H<sub>2</sub>O) and a sample channel. The chamber was bounded
 by a microscope slide and coverslip. Data acquisition
 was performed using a custom open-source software package, DHMx [29]. All
 recordings were performed at a frame rate of 15 fps for a total of 20-60 s
 per recording. Reconstruction in amplitude and/or phase was performed
 using the angular spectrum method [30] using custom Fiji plug-ins as
 previously described [31]. Phase reconstructions made use a reference
 hologram to remove noise [32]; this reference hologram was the median of
 all holograms in the recording. The lateral field of view was 356 x 365 µm
 for 2048 x 2048 pixels, and the axial z-spacing was chosen to be 1-2 µm
 based upon the particle size and nominal axial resolution of the system of
 2 µm.
DOI: 10.15468/dl.tsk3q2
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Aerial surveys of cetaceans in the Zeehan, Apollo and Beagle Australian Marine Parks, Australia (2021-2024)"
 ]
}

 The dataset includes 104 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002877-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sbcc2fr6s
title: Data from: Urban street lighting differentially affects community attributes of airborne and ground-dwelling invertebrate assemblages

description: The introduction of artificial light at night (ALAN) into natural and
 urbanised landscapes is a known and highly pervasive disruptor of
 invertebrate communities. However, the effect of variation in intensity
 and spectra of ALAN on invertebrate communities inhabiting different
 spatial niches is little understood. Further, the remarkable ability of
 ALAN to continue to disrupt biodiversity even in chronically-illuminated
 urban landscapes is not often acknowledged. Here, we simultaneously
 sampled airborne and ground-dwelling invertebrate assemblages under and
 between urban streetlights to explore the effects on community composition
 and abundance of a) proximity to decadal (i.e long-illuminated) nocturnal
 street lighting and b) variation in the spectral output of light. The two
 assemblages responded differently. For airborne invertebrates, night-time
 abundance doubled, and night-time assemblage composition was significantly
 different for traps under, compared with between, streetlights. These
 differences in abundance were not affected by streetlight intensity, and
 were absent in day samples, suggesting that even weak ALAN may be causing
 short-term redistribution of nocturnal invertebrates. Further, the
 abundance (but not composition) effects of ALAN on airborne invertebrates
 increased when the streetlights emitted a higher proportion of
 short-wavelength light. In contrast, for ground-dwelling invertebrates, we
 found only marginal effects of proximity and spectrum of lighting on
 abundance and no effect on assemblage composition. However, more intense
 streetlighting reduced abundance and altered composition at traps both
 under and between lights. Synthesis and Applications: Public lighting
 managers must consider ALAN impacts on invertebrate communities not only
 when introducing ALAN to naïve environments, but also when changing
 lighting in areas that are highly urbanised and exposed to decades of
 artificial light at night. Further, lighting proposals and environmental
 monitoring of invertebrate communities must take into account effects on
 both ground-dwelling and airborne assemblages, as these may respond very
 differently to the presence, intensity and spectrum of ALAN.
description: See: <em>Readme file for Lockett et al
 2021.xlsx</em>
description: See: <em>Readme file for Lockett et al
 2021.xlsx</em>
DOI: 10.5061/dryad.bk3j9kdcg
title: Non-protected areas demanding equitable conservation strategies as of protected areas in Central Himalayan region

description: The present study aims to explore the mammalian diversity of Darjeeling
 district using camera traps along with questionnaire survey in protected
 area (PA) and non- protected area (Non-PA). We also attempted to
 understand the influence of habitat variables on mammalian species
 richness using the generalized linear mixed models (GLMM). A total of 30
 mammal species were recorded of which 21 species were detected through
 camera trapping with the most abundant records of barking deer (Muntiacus
 muntjak) and  least of the elusive Chinese pangolin (Manis
 pentadactyla) and red panda (Ailurus fulgens). Additionally, melanistic
 forms of four mammals were also recorded. The mammalian species richness,
 their capture rate and naïve occupancy did not differ significantly among
 the PA and Non-PA. The GLMM revealed that the proportions of oak and
 bamboo in the forest, percentage canopy cover and camera trap operational
 days (wAICc = 0.145, wBIC = 0.603) were significant predictors of species
 richness in the study. We suggest Non-PA forest of Darjeeling should be
 given equal conservation importance as to the PA. Landscape based
 conservation planning will be imperative for achieving long term
 conservation goals in the study area.
DOI: 10.5061/dryad.xsj3tx9fs
title: Data from: Quantifying adaptive divergence of the snowfinches in a common landscape

description: Aim: Species living in a shared environment face similar selective
 pressures and often evolve adaptive divergence to avoid competition.
 Quantifying phenotypic divergence and its genetic parallelism among
 sympatric species is important for understanding of ecologically moderated
 biodiversity. Here we integrate ecologic, phenotypic and genomic datasets
 to study to what extent three sympatrically snowfinches (Montifringilla
 adamsi, Pyrgilauda ruficollis and Onychostruthus taczanowskii) differ in
 their adaptations in order to co-exist in a shared environment. Location:
 Qinghai-Tibetan Plateau Methods: We used principal component analysis to
 summarize and compare environmental and phenotypic divergence. We compared
 phenotypes relevant to body and beak sizes (n=68) because they are
 indicators of niche and food segregation, thus critical for establishing
 co-existence of sympatric birds. We used comparative genomics (n=33) to
 identify genetic loci that are highly divergent between species as well as
 loci unique for each of species. Using vector analyses, we integrated
 correlation and permutation to quantify parallelism between phenotypic and
 genetic divergences. Results: We found that body and beak sizes are
 significantly different among three snowfinches. The phenotypic
 differentiations are greater in species that share similar ecological
 conditions than in those that do not. We showed that genes related to
 developmental process are over-represented within highly divergent genomic
 regions and unique genetic loci of each species. We found that the extent
 of phenotypic divergence between snowfinch pairs is more strongly
 correlated with the magnitude of divergence in developmental genes than in
 the whole-genome. Main Conclusions: Adaptive divergence of sympatric
 snowfinches is highly constrained on developmental genes. As this genetic
 divergence is strongly correlated with divergence of the traits related to
 segregation in niche and food resources, this correlation reflects either
 causal effects or indirect consequences of ecological mediated changes.
 Our study provides novel insights into the mechanisms underlying
 evolutionary versatility and ecological success among sympatric species.
DOI: 10.5061/dryad.xwdbrv1dn
title: Legacy effects of seed dispersal mechanisms shape the spatial interaction network of plant species in Mediterranean forests

description: 1. Seed dispersal by frugivores plays a key role in structuring and
 maintaining tree diversity in forests. However, little is known about how
 the spatial legacy of seed dispersal and early recruitment shapes spatial
 patterns and the spatial interaction network of plant species in mature
 forest communities. 2. We analysed two fully mapped mixed Pine-Oak forest
 communities using spatial point pattern analysis to determine (i) the
 detailed structure of the intraspecific spatial patterns of saplings and
 adults, (ii) the intra- and interspecific spatial interaction of saplings,
 adults, and saplings relative to adults, (iii) the spatial patterns of
 species richness at the community level, and (iv) whether seed dispersal
 mechanisms affect the plant-plant interaction networks and the ratio of
 adult to sapling neighbourhood densities used as surrogate for spatial
 self-thinning. 3. The intraspecific spatial patterns of saplings and
 adults showed in general complex nested cluster structures that were
 similar for sapling and adult stages, despite of substantial self-thinning
 in some dry-fruited species. The spatial network of saplings was
 characterized by positive spatial interactions. Adults of several tree
 species facilitated saplings in their proximity; however, adults of
 dry-fruited species, but not those of fleshy-fruited ones, lost almost all
 positive interactions that occurred at the sapling stage. Besides,
 interaction strength between adults was positive and often significantly
 stronger if both species were fleshy-fruited. At the community level, the
 forests were structured into multispecies clumps across all life stages.
 4. Synthesis. Our analyses highlight the importance of the spatial legacy
 of seed dispersal and early recruitment in the assembly of plant
 communities. Particularly, animal seed dispersal can lead to multispecies
 clusters and positive spatial associations across life stages in
 Mediterranean forests, with surprisingly little signatures of negative
 interactions. Our analysis suggests that changes of the spatial structure
 across plant life stages are driven by seed dispersal mechanisms and
 subsequent spatial self-thinning, generating a spatial footprint at the
 sapling stage that conditions the long-term interactions between adult
 plants. Combining spatial point pattern analysis with network analysis and
 species traits is a promising way to disentangle the processes underlying
 observed patterns of local diversity.
DOI: 10.5061/dryad.j0zpc86fc
title: Discoid decorations function to shield juvenile Argiope spiders from avian predator attacks

description: Decorating behavior is common in various animal taxa and serves a variety
 of functions from camouflage to communication. One predominant function
 cited for decoration is to avoid predators. Conspicuous, disc-like
 (discoid) silk decorations spun by orb-web Argiope juvenile spiders are
 hypothesized, among others, to defend spiders against visual predators by
 concealing spider outlines on the web, deflecting attacks, shielding them
 from view or masquerading as bird-droppings. However, the direct evidence
 is limited for a specific mechanism by which discoid decorations may deter
 predators. Here we evaluate the mechanisms by which discoid decorations
 may defend Argiope juveniles against naïve chicks. Using visual modelling,
 we show that avian predators are able to distinguish spiders from discoid
 decorations. Using chick predation experiments, we found that the naïve
 chicks readily pecked any objects, ruling out the possibility of their
 neophobia. Significantly more chicks attacked spiders when they were
 exposed to chicks, regardless of whether their webs had discoid
 decorations, but few chicks attacked spiders when they were behind the
 decorations. We also found that significantly few chicks attacked
 decorations when spiders were absent or behind the decorations. We thus
 conclude that discoid decorations function to deter avian predators by
 shielding the spider from view or distracting, not by deflecting attacks,
 concealing the spider’s outline or masquerading as bird-droppings. This
 study sheds light on the study of other similar anti-predator strategies,
 in a wide range of spider species and other animals that use decorating
 strategies. --
DOI: 10.5061/dryad.z612jm6cb
title: REMI-seq analysis of D. discoideum cells treated with Lithium or Valproic acid

description: A critical aspect of toxicity evaluation is developmental and reproductive
 toxicity (DART) testing. Traditionally, DART testing has been conducted in
 vivo in mammalian model systems. New legislation aimed at reducing animal
 use and the prohibitive costs associated with DART testing, together with
 a need to understand the genetic pathways underlying developmental
 toxicity means there is a growing demand for alternative model systems for
 toxicity evaluation. Here we explore the potential of the eukaryotic
 social amoeba Dictyostelium discoideum, which is already widely used as a
 simple model system for cell and developmental biology, as a potential
 non-animal model for DART testing. We developed assays for high-throughput
 screening of toxicity during D. discoideum growth and development. This
 allowed the toxicity of a broad range of test compounds to be
 characterized, which revealed that D. discoideum can broadly predict
 mammalian toxicity. In addition, we show that this system can be used to
 perform functional genomic screens to compare the molecular modes of
 action of different compounds. For example, genome wide screens for
 mutations that affect lithium and valproic acid toxicity allowed common
 and unique biological targets and molecular processes mediating their
 toxicity to be identified. These studies illustrate that D. discoideum
 could represent a predictive non-animal model for DART testing due to its
 amenability to high throughput approaches and molecular genetic
 tractability.
description: See ReadMe file
DOI: 10.5061/dryad.zcrjdfncc
title: Performances (survival and growth) and functional traits of tree seedlings along light and water gradients

description: A foundational assumption of trait-based ecology is that individual
 performances should be predicted by its functional traits. However, the
 trait-performance relationships reported in literature were typically
 weak, probably due to the ignorance of interactions between
 traits and environments, intraspecific trait variability and hard traits
 (directly linked to physiological processes of interest). We
 conducted an experiment of planting 900 seedlings of six tree species
 separately (one seedling per pot) along experimentally manipulated light
 and water gradients, monitored their survival and growth, and measured
 their morphological, photosynthetic and hydraulic traits. Most
 trait-performance relationships depended on the environments, either
 marginally changing (weak trait × environment interaction) or even
 reversing (strong trait × environment interaction) along light or water
 gradients in our experiment. Such trait × environment
 interactions were more likely to be detected in growth models
 using individual-level traits than models using species mean
 traits, but seedling growth was not better modelled with
 individual-level traits than species mean traits. Additionally, none of
 the hard traits (photosynthetic and hydraulic traits) were better
 predictors than soft traits (morphological traits) modeling seedling
 growth and survival along light and water gradients. Our study highlights
 the necessities of considering trait × environment
 interactions when predicting response of plants to changing
 environments. The benefits of using individual-level traits or hard traits
 to predict plant performance might be reduced or even cancelled if their
 measurement errors are not well controlled.
DOI: 10.7272/q6kk9927
title: Data from: Coupling between motor cortex and striatum increases during sleep over long-term skill learning

description: The strength of cortical connectivity to the striatum influences the
 balance between behavioral variability and stability. Learning to
 consistently produce a skilled action requires plasticity in
 corticostriatal connectivity associated with repeated training of the
 action. However, it remains unknown whether such corticostriatal
 plasticity occurs during training itself or “offline” during time away
 from training, such as sleep. Here, we monitor the corticostriatal network
 throughout long-term skill learning in rats and find that non-REM (NREM)
 sleep is a relevant period for corticostriatal plasticity. We first show
 that the offline activation of striatal NMDA receptors is required for
 skill learning. We then show that corticostriatal functional connectivity
 increases offline, coupled to emerging consistent skilled movements and
 coupled cross-area neural dynamics. We then identify NREM sleep spindles
 as uniquely poised to mediate corticostriatal plasticity, through
 interactions with slow oscillations. Our results provide evidence that
 sleep shapes cross-area coupling required for skill learning.
description: This dataset contains behavioral and electrophysiology data
 collected from Long-Evans rats during long-term reach-to-grasp skill
 learning. 
description: This dataset accompanies the paper entitled
 "<em>Coupling between motor cortex and striatum increases
 during sleep over long-term skill learning</em>".
DOI: 10.5061/dryad.79cnp5hvz
title: The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

description: Species often experience spatial environmental heterogeneity across their
 range, and populations may exhibit signatures of adaptation to local
 environmental characteristics. Other population genetic processes, such as
 migration and genetic drift, can impede the effects of local adaptation.
 Genetic drift in particular can have a pronounced effect on population
 genetic structure during large-scale geographic expansions, where a series
 of founder effects leads to decreases in genetic variation in the
 direction of the expansion. Here we explore the genetic diversity of a
 desert lizard that occupies a wide range of environmental conditions and
 that has experienced post-glacial expansion northwards along two
 colonization routes. Based on our analyses of a large SNP dataset, we find
 evidence that both climate and demographic history have shaped the genetic
 structure of populations. Pronounced genetic differentiation was evident
 between populations occupying cold versus hot deserts, and we detected
 numerous loci with significant associations with climate. The genetic
 signal of founder effects, however, is still present in the genomes of the
 recently expanded populations, which comprise subsets of genetic variation
 found in the southern populations, and we found substantial evidence that
 genetic diversity of lizards differs along the two colonization routes.
description: We acquired tissue samples (toe or tail tissues) from 72
 individuals of <em>P. platyrhinos</em> from 32 localities (1-5
 samples/locality) across the species range spanning the Mojave, Sonoran,
 and Great Basin deserts. We then generated double-digest RADseq libraries
 for all samples using the protocol of Peterson et al. and processed
 sequence data with dDocent.
description: A README file that provides details on each script and data file
 is provided in the compressed directory.
DOI: 10.5061/dryad.8gtht76pv
title: Ge-Row data of deformation localization of raw coal and briquette coal

description: To compare and analyze the difference in deformation and damage law of
 soft and hard porous media materials, the digital image correlation is
 used to evaluate the heterogeneous development of strain fields of hard
 and brittle raw coal and soft plastic briquette coal materials under
 uniaxial compression. Through the defined statistical indexes, the
 quantitative characterization of deformation localization is realized, and
 the material damage constitutive model based on the statistical indexes of
 strain field is established. The results show that the yield stage of raw
 coal is not obvious, showing the characteristics of strain hardening and
 X-shaped macroscopic shear failure. The yield stage of briquette coal is
 more obvious, showing the characteristics of strain softening and a
 tensile failure mode. The progress of strain localization can well reflect
 the damage and destruction process of materials. The progress of strain
 localization of briquette coal can be divided into uniform deformation
 stage, localization stage and failure stage, while the stage
 characteristics of localized evolution of raw coal is not obvious. The
 theoretical results of the damage constitutive model defined by
 statistical indexes are in good agreement with the experimental data,
 which well reflect the stress and strain characteristics of the two
 materials.