cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17991350
title: Conceptual Framework for Onco-Physics: Innovative Modulation of Tumor Physical Properties through Osmotic Pressure and Surface Tension Engineering

description: This conceptual manuscript delineates a pioneering paradigm in onco-physics, conceptualizing solid tumors as physical materials endowed with quantifiable osmotic pressure, surface tension, and fluid-mechanical attributes. We posit unprecedented innovations for tumor remediation by precisely modulating these physical properties, eschewing conventional chemical interventions. Leveraging rigorous mathematical derivations, reproducible Python simulations grounded in empirical data from published literature, advanced sensitivity analyses including Sobol indices, Bayesian inference, uncertainty quantification, and falsifiability criteria, we substantiate the conceptual feasibility and prospective impact. A multi-phased roadmap from experimental validation to industrial manufacturing is articulated, augmented by high-fidelity TikZ visualizations and comparative tabular analyses. Applications in nuclear and radiation medicine are expounded, alongside ethical deliberations and a comprehensive literature review. This manuscript is self-contained, with all requisite data embedded therein. The framework is positioned as a hypothesis-generating theoretical study, with detailed methodological descriptions to facilitate reproducibility and future empirical testing.
DOI: 10.5061/dryad.p4f5v
title: Data from: The Hercules beetles (subgenus Dynastes, genus Dynastes, Dynastidae): a revisionary study based on the integration of molecular, morphological, ecological, and geographic analyses

description: The taxonomic treatment of Hercules beetles (subgenus Dynastes of the
 genus Dynastes MacLeay, 1819) is revised, with the recognition of two
 major species groups and 15 species. The following 10 taxa, originally
 designated as subspecies, have been elevated to full species status:
 Dynastes moroni Nagai, 2005 (REVISED STATUS); Dynastes bleuzeni Silvestre
 & Dechambre, 1995 (NEW STATUS); Dynastes ecuatorianus Ohaus, 1913
 (NEW STATUS); Dynastes lichyi Lachaume, 1985 (NEW STATUS); Dynastes
 morishimai Nagai, 2002 (NEW STATUS); Dynastes occidentalis Lachaume, 1985
 (NEW STATUS); Dynastes paschoali Grossi & Arnaud, 1993 (NEW
 STATUS); Dynastes reidi Chalumeau, 1977 (NEW STATUS); Dynastes
 septentrionalis Lachaume, 1985 (NEW STATUS); and Dynastes trinidadensis
 Chalumeau & Reid, 1995 (NEW STATUS). The use of the species name
 Dynastes hercules (Linnaeus, 1758) is restricted to only two island
 populations from Guadeloupe and Dominica. This taxonomic revision is
 accompanied by discussions of the basis for these taxonomic changes, i.e.
 based on differences in genetic, phenotypic, and ecological data and on
 estimates of geographic overlap. An updated Dynastes beetle phylogeny
 based on Illumina sequencing data is also presented for a discussion of
 the evolutionary relationships among the species.
description: Dynastes_unlinkedSNPsunlinked SNP dataset for species tree reconstructionTreemix_GHtreemix input for Giant Hercules beetlesTreemix_WHTreemix input for White Hercules beetlesmorphological_dataOutline coordinates for shape analyses
DOI: 10.5061/dryad.11j13
title: Data from: Temporal variability in the environmental and geographic predictors of spatial-recruitment in nearshore rockfishes

description: Geography and habitat availability may be key drivers underlying spatial
 patterns of larval supply and recruitment success of nearshore marine
 fishes, but they are poorly understood. We assessed spatial recruitment
 patterns of nearshore young-of-the-year Pacific rockfishes Sebastes spp.
 in kelp forest and eelgrass meadow habitats from 2004 to 2014 on the west
 coast of Vancouver Island, British Columbia. Our sites varied in habitat
 area, wave exposure, sea surface temperature, and distance from the open
 coast. We observed recruitment of several species of rockfish, including
 black rockfish S. melanops, bocaccio rockfish S. paucispinis, and a
 complex of copper, quillback, and brown rockfishes (S. caurinus, S.
 maliger, and S. auriculatus; CQB). For black rockfish, the species
 recruiting in highest abundances, we found that although the environmental
 variables that predicted recruitment were temporally variable, in some
 years recruitment was higher at sites with colder sea surface temperature,
 higher tidal velocity, higher fetch, and higher salinity. In contrast, CQB
 rockfish recruitment was consistently higher at sites with higher fetch
 but lower tidal velocity, and this relationship was stable through time.
 Interactions among environmental variables and habitat area explained the
 counterintuitive observation of higher recruitment in smaller eelgrass
 meadows but larger kelp forests. Moreover, sites in or on the boundary of
 a rockfish conservation area experienced the lowest recruitment during an
 exceptionally strong black rockfish recruitment event in 2006. These
 results suggest that temporal variability in the ability of environmental
 variables to predict the spatial distribution of young-of-the-year
 rockfishes should be considered in models of population connectivity.
description: R_AnalysisThis zip file contains all data and scripts needed to reproduce the results in the paper.
DOI: 10.5061/dryad.5p6kr
title: Data from: Functional responses in animal movement explain spatial heterogeneity in animal-habitat relationships

description: 1. Understanding why heterogeneity exists in animal-habitat spatial
 relationships is critical for identifying the drivers of animal
 distributions. Functional responses in habitat selection – whereby animals
 adjust their habitat selection depending on habitat availability – are
 useful for describing animal-habitat spatial heterogeneity. However, they
 could be yielded by different movement tactics, involving contrasting
 inter-specific interactions. 2. Identifying functional responses in animal
 movement, rather than in emergent spatial patterns like habitat selection,
 could disentangle the effects of different movement behaviours on spatial
 heterogeneity in animal-habitat relationships. This would clarify how
 functional responses in habitat selection emerge and provide a general
 tool for understanding the mechanistic drivers of animal distributions. 3.
 We tested this approach using data from GPS-collared woodland caribou
 (Rangifer tarandus), a prey species under top-down control. We tested how
 caribou selected and moved with respect to a key resource (lichen-conifer
 stands) as a function of the availability of surrounding refuge land-cover
 (closed-conifer stands), using step selection functions. 4. Caribou
 selected resource patches more strongly in areas richer in refuge
 land-cover – a functional response in habitat selection. However,
 adjustments in multiple movement behaviours could have generated this
 pattern: stronger directed movement towards resources patches and/or
 longer residency within resource patches, in areas richer in refuges.
 Different contributions of these behaviours would produce contrasting
 forager spatial dynamics. 5. We identified functional responses in both
 movement behaviours: caribou were more likely to move towards resource
 patches in areas richer in refuge land-cover, and to remain in these
 patches during movement steps. This tactic enables caribou to spend longer
 foraging in safer areas where they could rapidly seek refuge in dense
 cover when predators are detected. 6. Our study shows that functional
 responses in movement can expose the context-dependent movement decisions
 that generate heterogeneity in animal-habitat spatial relationships. We
 used these functional responses to characterise anti-predator movement
 tactics employed by a large herbivore, but they could be applied in many
 different scenarios. The movement rules from functional responses in
 movement are well-suited to integration in spatial explicit
 individual-based models for forecasting animal distributions in landscapes
 undergoing environmental change.
description: Caribou movement and
 habitat selection dataData on the movement and
 habitat selection of woodland caribou for fitting step selection
 functions. Data are from 23 adult female caribou, collected during winter
 in the Côte-Nord region of Québec, Canada, between 2005 and
 2012.caribou.RData
DOI: 10.5061/dryad.54qr4
title: Data from: Characterization of unexplored deadwood mycobiome in highly diverse subtropical forests using culture-independent molecular technique

description: The deadwood mycobiome, also known as wood-inhabiting fungi (WIF), are
 among the key players in wood decomposition, having a large impact on
 nutrient cycling in forest soils. However, our knowledge of WIF richness
 and distribution patterns in different forest biomes is limited. Here, we
 used pyrotag sequencing of the fungal internal transcribed spacer (ITS2)
 region to characterize the deadwood mycobiome of two tree species with
 greatly different wood characteristics (Schima superba and Pinus
 massoniana) in a Chinese subtropical forest ecosystem. Specifically, we
 tested (i) the effects of tree species and wood quality properties on WIF
 OTU richness and community composition; (ii) the role of biotic and
 abiotic factors in shaping the WIF communities; and (iii) the relationship
 between WIF OTU richness, community composition and decomposition rates.
 Due to different wood chemical properties, we hypothesized that the WIF
 communities derived from the two tree species would be correlated
 differently with biotic and abiotic factors. Our results show that
 deadwood in subtropical forests harbors diverse fungal communities
 comprising six ecological functional groups. We found interesting
 colonization patterns for this subtropical biome, where Resinicium spp.
 were highly detected in both broadleaved and coniferous deadwood. In
 addition, the members of Xylariales were frequently found in Schima. The
 two deadwood species differed significantly in WIF OTU richness (Pinus
 &gt; Schima) and community composition (P &lt; 0.001). Variations
 in WIF community composition of both tree species were significantly
 explained by wood pH and ecological factors (biotic: deadwood species,
 basal area and abiotic: soil pH), but the WIF communities derived from
 each tree species correlated differently with abiotic factors.
 Interestingly, we found that deadwood decomposition rate significantly
 correlated with WIF communities and negatively correlated with WIF OTU
 richness. We conclude that the pattern of WIF OTU richness and community
 composition are controlled by multiple interacting biotic and abiotic
 factors. Overall, our study provides an in-depth picture of the deadwood
 mycobiome in this subtropical forest. Furthermore, by comparing our
 results to results from temperate and boreal forests we contribute to a
 better understanding of patterns of WIF communities across different
 biomes and geographic locations.
description: Bioinformatics
 scriptsThis script describes
 bioinformatics procedure to produce an operational taxonomic unit (OTU)
 table of this study "Characterization of unexplored deadwood
 mycobiome in highly diverse subtropical forests using culture-independent
 molecular technique".script_bioinformatic.BEF_CSP_deadwood_ITS.txtBIOM TableThe representative sequences and taxonomic assignment of the abundant fungal OTUs as well as the full OTU table in BIOM format.BEF_CSP_deadwood_ITS.json.biom
DOI: 10.5061/dryad.171q5
title: Data from: Genetic characterization of dog personality traits

description: The genetic architecture of behavioural traits in dogs is of great
 interest to owners, breeders and professionals involved in animal welfare,
 as well as to scientists studying the genetics of animal (including human)
 behaviour. The genetic component of dog behaviour is supported by
 between-breed differences and some evidence of within-breed variation.
 However, it is a challenge to gather sufficiently large datasets to
 dissect the genetic basis of complex traits such as behaviour, which are
 both time-consuming and logistically difficult to measure, and known to be
 influenced by non-genetic factors. In this study, we exploited the
 knowledge that owners have of their dogs to generate a large dataset of
 personality traits in Labrador Retrievers. While accounting for key
 environmental factors, we demonstrate that genetic variance can be
 detected for dog personality traits assessed using questionnaire data. We
 identified substantial genetic variance for several traits, including
 fetching tendency and fear of loud noises, while other traits revealed
 negligibly small heritabilities. Genetic correlations were also estimated
 between traits, however, due to fairly large standard errors, only a
 handful of trait pairs yielded statistically significant estimates.
 Genomic analyses indicated that these traits are mainly polygenic, such
 that individual genomic regions have small effects, and suggested
 chromosomal associations for six of the traits. The polygenic nature of
 these traits is consistent with previous behavioural genetics studies in
 other species, for example in mouse, and confirms that large datasets are
 required to quantify the genetic variance and to identify the individual
 genes that influence behavioural traits.
description: archive.tarCompressed plink files for 885 dogs (see README file for description)all_traits_1975dogs_dryadbehavioural traits and fixed effects for 1975 dogs
DOI: 10.5061/dryad.m82qm
title: Data from: Maternal and nourishment factors interact to influence offspring developmental trajectories in social wasps

description: The social and nutritional environments during early development have the
 potential to affect offspring traits, but the mechanisms and molecular
 underpinnings of these effects remain elusive. We used Polistes fuscatus
 paper wasps to dissect how maternally controlled factors (vibrational
 signals and nourishment) interact to induce different caste developmental
 trajectories in female offspring, leading to worker or reproductive (gyne)
 traits. We established a set of caste phenotype biomarkers in P. fuscatus
 females, finding that gyne-destined individuals had high expression of
 three caste-related genes hypothesized to have roles in diapause and
 mitochondrial metabolism. We then experimentally manipulated maternal
 vibrational signals (via artificial ‘antennal drumming’) and nourishment
 levels (via restricted foraging). We found that these caste-related
 biomarker genes were responsive to drumming, nourishment level or their
 interaction. Our results provide a striking example of the potent
 influence of maternal and nutritional effects in influencing
 transcriptional activity and developmental outcomes in offspring.
description: Jandt et al: Polistes
 drumming and foraging restriction results, Data ArchiveSheet 1: Individual wasp
 data (weight, lipid, gene expression); Sheet 2: Colony data (averaged
 individual data used in analyses); Sheet 3: Colony Growth
 DataJandt
 et al AD Data Archive.xlsx
DOI: 10.5061/dryad.82qd0
title: Data from: Bias correction of bounded location errors in presence-only data

description: 1. Location error occurs when the true location is different than the
 reported location. Because habitat characteristics at the true location
 may be different than those at the reported location, ignoring location
 error may lead to unreliable inference concerning species-habitat
 relationships. 2. We explain how a transformation known in the spatial
 statistics literature as a change of support (COS) can be used to correct
 for location errors when the true locations are points with unknown
 coordinates contained within arbitrary shaped polygons. 3. We illustrate
 the flexibility of the COS by modeling the resource selection of Whooping
 Cranes (Grus americana) using citizen contributed records with locations
 that were reported with error. We also illustrate the COS with a
 simulation experiment. 4. In our analysis of Whooping Crane resource
 selection, we found that location error can result in up to a five-fold
 change in coefficient estimates. Our simulation study shows that location
 error can result in coefficient estimates that have the wrong sign, but a
 COS can efficiently correct for the bias.
description: ReadMe for Hefley et. al
 (2017)Land cover
 data2011 National Land Cover
 Database for the Platte River Recovery Implementation
 ProgramNLCD.2011.tifPublic land survey system shapefileShapefile of sections in Nebraska as designated from the Public land survey system. Original file obtained from ftp://dnrftp.dnr.ne.gov/pub/data/state/SectionsUTM.zipSectionsUTM.zip
DOI: 10.5061/dryad.bc434
title: Data from: Pragmatic analysis of the electric submerged arc furnace continuum

description: A transient mathematical model was developed for the description of fluid
 flow, heat transfer and electromagnetic phenomena involved in the
 production of ferronickel in electric arc furnaces. The key operating
 variables considered were the thermal and electrical conductivity of the
 slag and the shape, immersion depth and applied electric potential of the
 electrodes. It was established that the principal stimuli of the
 velocities in the slag bath were the electric potential and immersion
 depth of the electrodes and the thermal and electrical conductivities of
 the slag. Additionally, it was determined that, under the set of operating
 conditions examined, the maximum slag temperature ranged between 1756 and
 1825 K, which is in accordance with industrial measurements. Moreover, it
 was affirmed that contributions to slag stirring due to Lorentz forces and
 momentum forces due to the release of carbon monoxide bubbles from the
 electrode surface were negligible
description: ANYS Fluent input
 fileANSYS Fluent v15 input
 file.case.cas.gz
DOI: 10.5061/dryad.mp32f
title: Data from: Genome-wide analysis of allele frequency change in sunflower crop-wild hybrid populations evolving under natural conditions

description: Crop-wild hybridization occurs in numerous plant species, and could alter
 the genetic structure and evolutionary dynamics of wild populations.
 Studying crop-derived alleles in wild populations is also relevant to
 assessing/mitigating the risks associated with transgene escape. To date,
 crop-wild hybridization has generally been examined via short-term
 studies, typically within a single generation, focusing on few traits or
 genetic markers. Little is known about patterns of selection on
 crop-derived alleles over multiple generations, particularly at a
 genome-wide scale. Here, we documented patterns of natural selection in an
 experimental crop × wild sunflower population that was allowed to evolve
 under natural conditions for two generations at two locations. Allele
 frequencies at a genome-wide collection of SNPs were tracked across
 generations, and a common garden experiment was conducted to compare trait
 means between generations. These data allowed us to identify instances of
 selection on crop-derived alleles/traits and, in concert with QTL mapping
 results, test for congruence between our genotypic and phenotypic results.
 We found that natural selection overwhelmingly favors wild alleles and
 phenotypes. However, crop alleles in certain genomic regions can be
 favored, and these changes often occurred in parallel across locations. We
 did not, however, consistently observe close agreement between our
 genotypic and phenotypic results. For example, when a trait evolved
 towards the wild phenotype, wild QTL alleles associated with that trait
 did not consistently increase in frequency. We discuss these results in
 the context of crop allele introgression into wild populations and
 implications for the management of GM crops.
description: G1 and G3 SNP
 genotypesSNP
 genotypesInputfilerg0g3lg05Sample data file for the 'Python script for simulation of selection drift recombination with linked loci.py'.IOWA2011RData were collected in Decorah, IA and Fargo, ND in 2011ND2011RData were collected in Decorah, IA and Fargo, ND in 2011lg05dInput used by the 'Python script for simulation of selection drift recombination with linked loci.py'python script for simulation of selection drift recombination with linked locipython script for simulation of selection drift recombination with linked locipython script for simulation of selection without linkagepython script for simulation of selection without linkageR script for analysis of 2011 common garden data setsR script for data analysis of sunflower phenotypic datarilfreqInput file used for 'python sript for simulation of selection without linkage.py'.RIL genotypes - generation 0RIL genotypes - generation 0SNP loci used sorted by map positionSNP loci used sorted by map positionSNP 278Sequences of the 278 SNP used
DOI: 10.5061/dryad.69dh9
title: Data from: Effects of the group’s mix of sizes and personalities on the emergence of alternative mating systems in water striders

description: Although much work has analysed how individual behavioural plasticity and
 adaptations to ecological conditions (e.g. density, sex-ratio, resource
 distribution) shape mating systems, few studies have assessed the relative
 importance of multiple factors in explaining why mating systems vary from
 one sub-population to the next even in the same ecological conditions.
 Differences among groups in their phenotypic composition, such as their
 average phenotype, within-group variation in phenotype, or the phenotype
 of individuals occupying key social roles might shape the mating system
 emerging at the group level and explain some portion of mating system
 variability. Here, we take advantage of the mating system flexibility of
 stream water striders (Aquarius remigis) to investigate how phenotypic
 composition affects the mating system emerging at the group level. Groups
 exhibited stable mating systems varying from scramble polygyny with
 intense sexual conflict, to systems with a clear dominant male guarding a
 “harem” of females. We found that male size asymmetries and the
 personality of the largest individuals within groups had important effects
 on the group’s mating system. The group’s average male and female
 personality, size, and social plasticity also explained some of the
 variation in mating systems. Our study is one of the first to quantify
 significant relationships between group phenotypic composition and mating
 system variability.
description: data.stridersThis file contains all the scan observations on all individuals during the experiment. Read the metadata file for more details.R script used to generate all results and figuresThis script provides all the results presented in the paper and generates all the figures it contains.script.r