cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hk0tf00
title: Data from: Plastic limit bearing calculation of blasting-roof in deep hole mining and its applications

description: In order to solve the problem that blasting-roof thickness was hard to
 determine in deep hole mining, the plastic bearing calculation method of
 blasting-roof was proposed. Aim at typical boundary conditions of
 blasting-roof, mechanical analysis model of plastic bearing was built. The
 external work and internal work of blasting-roof under plastic limit state
 were calculated. Based on virtual work principle, the limit bearing
 formulas of blasting-roof under various boundary conditions were derived.
 Taking a VCR stope as the object, the safe blasting-roof thickness was
 determined as 6m by derived formula (considering safety coefficient).
 Numerical model of stope was constructed by Surpac-Flac3D technique, while
 blasting-roof stability was simulated under different thickness. The
 variation of simulated indexes (stress, plastic zone volume) prove that
 theoretical calculation is reliable. The plastic bearing calculation
 method can provide a new way for determining blasting-roof thickness in
 deep hole mining.
description: Rock mechanics
 parametersRock mechanics
 parameters for simulation in the paper.
DOI: 10.5061/dryad.km7dc4t
title: Data from: Water as a resource, stress and disturbance shaping tundra vegetation

description: Water is crucial for plant productivity and survival as a fundamental
 resource, but water conditions can also cause physiological stress and
 mechanical disturbance to vegetation. However, these different influences
 of water on vegetation patterns have not been evaluated simultaneously.
 Here, we demonstrate the importance of three water aspects (spatial and
 temporal variation of soil moisture and fluvial disturbance) for three
 ecologically and evolutionary distinct taxonomical groups (vascular
 plants, mosses, and lichens) in Fennoscandian mountain tundra. Fine-scale
 plant occurrence data for 271 species were collected from 378 x 1 m2 plots
 sampled over broad environmental gradients (water, temperature, radiation,
 soil pH, cryogenic processes, and the dominant allelopathic plant
 species). While controlling all other key environmental variables, water
 in its different aspects proved to be a crucial environmental driver,
 acting on individual species and on community characteristics. The
 inclusion of the water variables significantly improved our models. In
 this high-latitude system, the importance of spatial variability of water
 exceeds the importance of temperature for the fine-scale distribution of
 species from the three taxonomical groups. We found differing responses to
 the three water variables between and within the taxonomical groups. Water
 as a resource was the most important water-related variable in species
 distribution models across all taxonomical groups. Both water resource and
 disturbance were strongly related to vascular plant species richness,
 whereas for moss species richness, water resources had the highest
 influence. For lichen species richness, water disturbance was the most
 influential water-related variable. These findings demonstrate that water
 variables are not only independent properties of tundra hydrology, but
 also that water is truly a multifaceted driver of vegetation patterns at
 high-latitudes.
description: Kemppinen et al. (2019).
 Water as a resource, stress and disturbance shaping tundra
 vegetationHere, are the data, on
 which the analyses of Kemppinen et al. (2019) were based on. The first
 column is the plot identification number. After which are the eight
 environmental variables, namely temperature, radiation, soil pH, cryogenic
 processes, and biotic interactions, as well as the three water variables:
 water as a resource, stress, and disturbance. The environmental variables
 are followed by the species richness of three taxonomical groups, namely
 vascular plants, mosses, and lichens. The rest of the columns are the
 coverage data on the 271 species, on which this research was based on. For
 a detailed description on the data and for full species names, please see
 Kemppinen et al. (2019).Kemppinen_et_al_2019_Oikos.csv
DOI: 10.5061/dryad.73d9482
title: Data from: How accurately do behavioural observations predict reproductive success in free-ranging lizards?

description: Behavioural ecologists often use data on patterns of male-female
 association to infer reproductive success of free-ranging animals. For
 example, a male seen with several females during the mating season is
 predicted to father more offspring than a male not seen with any females.
 We explored the putative correlation between this behaviour and actual
 paternity (as revealed by microsatellite data) from a long-term study on
 sand lizards (Lacerta agilis), including behavioural observations of 574
 adult males and 289 adult females, and paternity assignment of
 &gt;2500 offspring during 1998-2006. The number of males that
 contributed paternity to a female’s clutch was correlated with the number
 of males seen accompanying her in the field, but not with the number of
 copulation scars on her body. The number of females that a male
 accompanied in the field predicted the number of females with whom he
 fathered offspring, and his annual reproductive success (number of
 progeny). Although behavioural data explained less than one-third of total
 variance in reproductive success, our analysis supports the utility of
 behavioural-ecology studies for predicting paternity in free-ranging
 reptiles.
description: BehavProxiesDataCorrelative data between pairs and true genetic reproductive success
DOI: 10.5061/dryad.59f10v7
title: Data from: Testing the Distraction Hypothesis: do extrafloral nectaries reduce ant‐pollinator conflict?

description: 1. Ant guards protect plants from herbivores, but can also hinder
 pollination by damaging reproductive structures and/or repelling
 pollinators. Natural selection should favour the evolution of plant traits
 that deter ants from visiting flowers during anthesis, without waiving
 their defensive services. The Distraction Hypothesis posits that rewarding
 ants with extrafloral nectar could reduce their visitation of flowers,
 reducing ant-pollinator conflict while retaining protection of other
 structures. 2. We characterised the proportion of flowers occupied by ants
 and the number of ants per flower in a Mexican ant-plant, Turnera
 velutina. We clogged extrafloral nectaries on field plants and observed
 the effects on patrolling ants, pollinators and ants inside flowers, and
 quantified the effects on plant fitness. Based on the Distraction
 Hypothesis we predicted that preventing extrafloral nectar secretion
 should result in fewer ants active at extrafloral nectaries, more ants
 inside flowers and a higher proportion of flowers occupied by ants,
 leading to ant-pollinator conflict, with reduced pollinator visitation and
 reduced plant fitness. 3. Overall ant activity inside flowers was low.
 Preventing extrafloral nectar secretion through clogging reduced the
 number of ants patrolling extrafloral nectaries, significantly increased
 the proportion of flowers occupied by ants from 6.1% to 9.7%, and reduced
 plant reproductive output through a 12% increase in the probability of
 fruit abortion. No change in the numbers of ants or pollinators inside
 flowers was observed. This is the first support for the Distraction
 Hypothesis obtained under field conditions, showing ecological and plant
 fitness benefits of the distracting function of extrafloral nectar during
 anthesis. 4. Synthesis: Our study provides the first field experimental
 support for the Distraction Hypothesis, suggesting that extrafloral
 nectaries located close to flowers may bribe ants away from reproductive
 structures during the crucial pollination period, reducing the probability
 of ant-occupation of flowers, reducing ant-pollinator conflict, and
 increasing plant reproductive success.
description: Clogging Experiments
 DataIncludes in the tabs
 within the excel file the following datasets: 1) data short term clogging
 experiment; 2) data for long term clogging experiment; 3) fitness (seeds)
 data for short term clogging experiment; 4) details of ant species and
 abundance visiting flowers and EFN (used for supplementary material
 analyses).CloggingExpJEcolData.xls
DOI: 10.5061/dryad.244nt37
title: Data from: Coordination of rapid cholinergic and dopaminergic signaling in striatum during spontaneous movement

description: Interplay between dopaminergic and cholinergic neuromodulation in the
 striatum is crucial for movement control, with prominent models proposing
 pro-kinetic and anti-kinetic effects of dopamine and acetylcholine
 release, respectively. However, the natural, movement-related signals of
 striatum cholinergic neurons and their relationship to simultaneous
 variations in dopamine signaling are unknown. Here, functional optical
 recordings in mice were used to establish rapid cholinergic signals in
 dorsal striatum during spontaneous movements. Bursts across the
 cholinergic population occurred at transitions between movement states and
 were marked by widespread network synchronization which diminished during
 sustained locomotion. Simultaneous cholinergic and dopaminergic recordings
 revealed distinct but coordinated sub-second signals, suggesting a new
 model where cholinergic population synchrony signals rapid changes in
 movement states while dopamine signals the drive to enact or sustain those
 states.
description: Bi5_003Representative bilateral DA/ChI photometry traces with treadmill velocity from a single session. Please contact for details on variable names and units.AllBinned.matBi5_004Representative bilateral DA/ChI photometry traces with treadmill velocity from a single session. Please contact for details on variable names and units.AllBinned.matBi5_005Representative bilateral DA/ChI photometry traces with treadmill velocity from a single session. Please contact for details on variable names and units.AllBinned.matBi5_003,Sesh2Representative bilateral DA/ChI photometry traces with treadmill velocity from a single session. Please contact for details on variable names and units.AllBinned.matacq8_2_motcorr_byHandROIsDF/F traces and treadmill velocity from a representative 2-photon imaging session (Data included in examples in Fig 4). Please contact authors for details on variable names and units.IR1_1Representative dorsal striatum ChI photometry traces with treadmill velocity from a single session. Please contact for details on variable names and units.AllBinned.mat
DOI: 10.5061/dryad.5hr25nv
title: Data from: Tip rates, phylogenies, and diversification: what are we estimating, and how good are the estimates?

description: 1. Species-specific diversification rates, or “tip rates”, can be computed
 quickly from phylogenies and are widely used to study diversification rate
 variation in relation to geography, ecology, and phenotypes. These tip
 rates provide a number of theoretical and practical advantages, such as
 the relaxation of assumptions of rate homogeneity in trait-dependent
 diversification studies. However, there is substantial confusion in the
 literature regarding whether these metrics estimate speciation or net
 diversification rates. Additionally, no study has yet compared the
 relative performance and accuracy of tip rate metrics across simulated
 diversification scenarios. 2. We compared the statistical performance of
 three model-free rate metrics (inverse terminal branch lengths; node
 density metric; DR statistic) and a model-based approach (BAMM). We
 applied each method to a large set of simulated phylogenies that had been
 generated under different diversification processes. We summarized
 performance in relation to the type of rate variation, the magnitude of
 rate heterogeneity and rate regime size. We also compared the ability of
 the metrics to estimate both speciation and net diversification rates. 3.
 We show decisively that model-free tip rate metrics provide a better
 estimate of the rate of speciation than of net diversification. Error in
 net diversification rate estimates increases as a function of the relative
 extinction rate. In contrast, error in speciation rate estimates is low
 and relatively insensitive to extinction. Overall, and in particular when
 relative extinction was high, BAMM inferred the most accurate tip rates
 and exhibited lower error than non-model-based approaches. DR was highly
 correlated with true speciation rates but exhibited high error variance,
 and was the best metric for very small rate regimes. 4. We found that, of
 the metrics tested, DR and BAMM are the most useful metrics for studying
 speciation rate dynamics and trait-dependent diversification. Although
 BAMM was more accurate than DR overall, the two approaches have
 complementary strengths. Because tip rate metrics are more reliable
 estimators of speciation rate, we recommend that empirical studies using
 these metrics exercise caution when drawing biological interpretations in
 any situation where the distinction between speciation and net
 diversification is important.
description: tipRatesDataScriptsR scripts and data files needed to reproduce all analyses and figures.tipRates_dryad.tar.gztreesForTipRatesDirectory of all phylogenies used to evaluate tip rate metrics.
DOI: 10.5061/dryad.q8d17km
title: Data from: Lowland tapirs facilitate seed dispersal in degraded Amazonian forests

description: The forests of southeastern Amazonia are highly threatened by disturbances
 such as fragmentation, understory fires and extreme climatic events.
 Large-bodied frugivores such as the lowland tapir (Tapirus terrestris)
 have the potential to offset this process, supporting natural forest
 regeneration by dispersing a variety of seeds over long distances to
 disturbed forests. However, we know little about their effectiveness as
 seed dispersers in degraded forest landscapes. Here, we investigate the
 seed dispersal function of lowland tapirs in Amazonian forests subject to
 a range of human (fire, fragmentation) and natural (extreme droughts,
 windstorms) disturbances, using a combination of field observations,
 camera traps, and Light Detection and Ranging (LiDAR) data. Tapirs travel
 and defecate more often in degraded forests, dispersing much more seeds in
 these areas [9,822 seeds per ha/yr (CI95% = 9,106; 11,838)] than in
 undisturbed forests [2,950 seeds per ha/yr (CI95% = 2,961; 3,771)]. By
 effectively dispersing seeds across disturbed forests, tapirs may
 contribute to natural forest regeneration – the cheapest and usually the
 most feasible way to achieve large-scale restoration of tropical forests.
 Through the dispersal of large-seeded species that eventually become large
 trees, such frugivores also contribute indirectly to maintaining forest
 carbon stocks. These functions may be critical in helping tropical
 countries to achieve their goals to maintain and restore biodiversity and
 its ecosystem services. Ultimately, preserving these animals along with
 their habitats may help in the process of natural recovery of degraded
 forests throughout the tropics.
description: R script – estimate of
 seed dispersal and correctionThis R script shows how
 we estimated the number of seeds dispersed by tapirs per ha/year in our
 study area. Additionally, it shows how we adjusted our estimate to account
 for the fact that we sampled just 10 pellets per dung
 clump.Seed_dispersion_ha.yr.calculation.RmdAdditional clumps dataThis file contains data from the additional sampling of clumps we did to correct our estimate of the number of seeds dispersed per ha/year. It is necessary to run the R script with this estimate analysisadditional_clumps.csvRaw dataThis file contains all raw data collected in the field used in the analyses of this study. Abbreviations of the 'Treatment plot' column are as follows, according to the article: B1yr = burned annually; B3yr = burned triennially.master_Paolucci_et.al.csv
DOI: 10.5061/dryad.j3p00pc
title: Data from: A liquid-like organelle at the root of motile ciliopathy

description: Motile ciliopathies are characterized by specific defects in cilia beating
 that result in chronic airway disease, subfertility, ectopic pregnancy,
 and hydrocephalus. While many patients harbor mutations in the dynein
 motors that drive cilia beating, the disease also results from mutations
 in so-called Dynein Axonemal Assembly Factors (DNAAFs) that act in the
 cytoplasm. The mechanisms of DNAAF action remain poorly defined. Here, we
 show that DNAAFs concentrate together with axonemal dyneins and chaperones
 into organelles that form specifically in multiciliated cells, which we
 term DynAPs, for Dynein Axonemal Particles. These organelles display
 hallmarks of biomolecular condensates, and remarkably, DynAPs are enriched
 for the stress granule protein G3bp1, but not for other stress granule
 proteins or P-body proteins. Finally, we show that both the formation and
 the liquid-like behaviors of DynAPs are disrupted in a model of motile
 ciliopathy. These findings provide a unifying cell biological framework
 for a poorly understood class of human disease genes and add motile
 ciliopathy to the growing roster of human diseases associated with
 disrupted biological phase separation.
description: Image Data for
 Co-localization studiesThis ZIP file contains
 image stacks in Zeiss LSM format, which can be opened with Fiji/ImageJ (or
 other visualization software such as Imaris). All images compare
 localization of a test protein against the localization of KTU. File names
 indicate the tested protein.colocalization_with_Ktu_raw_data.zip
DOI: 10.5061/dryad.tr3dq8c
title: Data from: The interplay among intraspecific leaf trait variation, niche breadth and species abundance along light and soil nutrient gradients

description: It is assumed that widespread, generalist species have high phenotypic
 variation, but we know little about how intraspecific trait variation
 (ITV) relates to species abundance and niche breadth. In the temperate
 rainforest of southern Chile, we hypothesized that species with wide niche
 breadth would exhibit 1) high among-plot ITV, 2) a strong relationship
 between trait values and the environment, and 3) a close fit between
 traits and local environment trait optima. We measured leaf functional
 traits (leaf area, LMA, leaf N and P concentrations) of saplings in woody
 species, and compared the relative abundance of each species with its
 niche breadth, measured as the range of light, soil N and P availability.
 We used the slope of the linear regression of species’ trait-environment
 relationships to assess the strength and direction of these relationships,
 and measured the degree to which species’ trait values track the
 environmental optimum across plots. In some cases, species having wide
 niche breadth had high ITV in leaf N and also matched traits (LMA and leaf
 P) to local optima along the light gradient; they also had high ITV in
 general and matched leaf P to local optima along the soil P gradient. The
 relationship between species with wide niche breadth and the strength of
 intraspecific trait-environment relationships was generally weak and
 varied depending on the niche dimension and trait in question. Species
 varied considerably in the strength of trait-environment relationships and
 total magnitude of ITV, and this variation was not generally strongly
 related to species abundances or niche breadth patterns. In conclusion,
 trait variation at the community level is not driven by a few abundant,
 widely distributed species, but depends on the aggregate trait responses
 of both abundant and rare species. This makes it difficult to scale
 individual species trait responses up to the community level.
description: patagonia_itv_data3_Sept2018Leaf trait values (LMA, leaf size, leaf N and leaf P concentrations) of saplings of species belonging to the temperate rainforest of southern Chile.
DOI: 10.5061/dryad.4pg1vv4
title: Data from: Rigorous monitoring of a large-scale marine stock enhancement program demonstrates the need for comprehensive management of fisheries and nursery habitat

description: Release of captively-bred individuals into the wild is one of the most
 popular tools in fisheries, forestry, and wildlife management, and
 introgression of hatchery-reared animals into wild populations is of
 global concern. However, research and monitoring of impacts on wild
 populations are generally lacking, and the benefit of hatcheries for
 long-term fisheries and conservation goals is unclear. Using
 spatio-temporal genetic monitoring and a four-dacade time series of catch
 data, we quantified the effects on the size and genetic diversity of wild
 populations of one of the world’s largest marine stock enhancement
 programs--the red sea bream (Pagrus major) in Kagoshima Bay, Japan. Our
 analyses found that the stock enhancement program reduced genetic
 diversity of the population, but the genetic effect diminished with
 increased size of the wild population. Increases to the seaweed
 communities and reduced fishing efforts were the primary factors
 associated with the wild population recovery; effects of aquaculture were
 much smaller. Our results represent crucial evidence that hatcheries for
 enhancement and conservation of populations cannot be successful over the
 long term unless sufficient efforts are also made to reduce harvest rates
 and rehabilitate natural habitats.
description: Bream_genepop_datThis Genepop format file includes genotypes for 8 samples totalling 642 red sea bream (Pagrus major) from six geographical regions collected between 2002 and 2011 (497 wild, 45 hatchery, and 100 farmed fish).RedSeaBream_genepop_dat.txt