cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.qsuj56
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus corniculatus",
 "Year 1900-2026"
 ]
}

 The dataset includes 20 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002171-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fttdz08p7
title: What are the most crucial soil variables for predicting the distribution of mountain plant species? a comprehensive study in the Swiss Alps

description: Aim: To investigate the potential of a large range of soil variables to
 improve topo-climatic models of plant species distributions in a temperate
 mountain region encompassing complex relief. Location: The western Swiss
 Alps. Methods: Fitting topo-climatic models for &gt;60 plant species
 across &gt;250 sites with and without added soil predictor variables
 (&gt;30). Testing included: (i) which soil variables improve plant
 species distribution models; (ii) whether an optimal subset of soil
 variables can improve models for the majority of species and habitat
 types; and (iii) how much variation in plant species distributions soil
 variables alone explain. Results: Geochemical variables (i.e., CaO, pH and
 inorganic carbon) and a drainage indicator (i.e., bulk soil water content)
 improved the predictive abilities of the models across the large majority
 of alpine plant species. The improvement of the models after the addition
 of soil information varied strongly between plant species and habitat
 types, but a trade-off was found between the number of soil variables and
 the associated gain in model performance. Finally, across all species, one
 specific combination of soil variables–bulk soil water content + total
 phosphorus + δ13C–outperformed the commonly used topo-climatic variables.
 Main conclusions: Several soil variables significantly increased the
 predictive power of plant species distribution models in the temperate
 mountain region. Geochemical and drainage variables proved most important.
DOI: 10.5061/dryad.866t1g1mv
title: Herbivore phenology can predict response to changes in plant quality by livestock grazing

description: Livestock grazing can have a strong impact on herbivore abundance,
 distribution and community. However, not all species of herbivores respond
 the same way to livestock grazing, and we still have a poor understanding
 of the underlying mechanisms driving these differential responses. Here,
 we investigate the effect of light intensity cattle grazing on the
 abundance of two grasshoppers (Euchorthippus cheui and E. unicolor) that
 co-occur in the same grasslands and feed on the same food plant (the
 dominant grass Leymus chinensis). The two grasshopper species differ in
 phenology so that their peak abundances are separated into early- and
 late-growing seasons. We used an exclosure experiment to monitor
 grasshopper abundance and food quality in the field under grazed and
 ungrazed conditions, and performed feeding trials to examine grasshopper
 preference for grazed or ungrazed food plants in the laboratory. We found
 that the nitrogen content of L. chinensis leaves continuously declined in
 the ungrazed areas, but was significantly enhanced by cattle grazing over
 the growing season. Cattle grazing facilitated the early-season
 grasshopper E. cheui, whereas it suppressed the late-season grasshopper E.
 unicolor. Moreover, feeding trials showed that E. cheui preferred L.
 chinensis from grazed plots, while E. unicolor preferred the leaves from
 ungrazed plots. We conclude that livestock grazing has opposite effects on
 the two grasshopper species, and that these effects may be driven by
 grazing-induced chagnes in plant nutrient content and the unique
 nutritional niches of the grasshoppers. These results suggest that insects
 that belong to the same guild can have opposite nutrient requirements,
 related to their distinct phenologies, and that this can ultimately affect
 their response to cattle grazing. Our results show that phenology may link
 insect physiological needs to local resource availabilities, and should be
 given more attention in future work on interactions between large
 herbivores and insects.
DOI: 10.5061/dryad.msbcc2fv2
title: Data from: Stoichiometric constraints modulate the effects of temperature and nutrients on biomass distribution and community stability

description: Temperature and nutrients are two of the most important drivers of global
 change. Both can modify the elemental composition (i.e. stoichiometry) of
 primary producers and consumers. Yet their combined effect on the
 stoichiometry, dynamics, and stability of ecological communities remains
 largely unexplored. To fill this gap, we extended the Rosenzweig-MacArthur
 consumer-resource model by including thermal dependencies, nutrient
 dynamics, and stoichiometric constraints on both the primary producer and
 the consumer. We found that stoichiometric constraints dampen the paradox
 of enrichment and increased persistence at high nutrient levels.
 Nevertheless, they also reduced consumer persistence at extreme
 temperatures. Finally, we also found that stoichiometric constraints can
 strongly influence biomass distribution across trophic levels by
 modulating consumer assimilation efficiency and resource growth rates
 along the environmental gradients. In the Rosenzweig-MacArthur model,
 consumer biomass exceeded resource biomass for most parameter values
 whereas, in the stoichiometric model, consumer biomass was strongly
 reduced and sometimes lower than resource biomass. Our findings highlight
 the importance of accounting for stoichiometric constraints as they can
 mediate the temperature and nutrient impact on the dynamics and
 functioning of ecological communities.
description: Directions for running code in R 1. Place all
 R codes in your working directory<br> 2. run the R code
 "generate starting values" to produce the starting values for
 the simulations<br> 3. run the R code "Models" for the
 simulations with the RM and SRM models<br> 4. Plot the results using
 the R code "Models". For more information see
 Sentis, A., B. Haegeman and J. M. Montoya. "Stoichiometric
 constraints modulate the effects of temperature and nutrients on biomass
 distribution and community stability." on Biorxiv.
DOI: 10.5061/dryad.stqjq2c0d
title: Imperfect detection alters the outcome of management strategies for protected areas

description: Designing protected areas configurations to maximize biodiversity is a
 critical conservation goal. The configuration of protected areas can
 significantly impact the richness and identity of the species found there;
 one large patch supports larger populations but can facilitate competitive
 exclusion. Conversely, many small habitats spreads risk but may exclude
 predators that typically require large home ranges. Identifying how best
 to design protected areas is further complicated by monitoring programs
 failing to detect species. Here we test the consequences of different
 protected area configurations using multi-trophic level experimental
 microcosms. We demonstrate that for a given total size, many small patches
 generate higher species richness, are more likely to contain predators,
 and have fewer extinctions compared to single large patches. However, the
 relationship between the size and number of patches and species richness
 was greatly affected by insufficient monitoring, and could lead to
 incorrect conservation decisions, especially for higher trophic levels.
description: The data set was collected using custom-built 3D printed
 microcosms to house protist communities. The data on abundances of
 different species were collected by counting on a disecting microscope.
 The protected area portfolios used in the manuscript were produced from
 the raw data using numerical simulations. 
description: There are no missing values, the numbers in each column represent
 the abundance of each species in the entire well.
DOI: 10.5061/dryad.nzs7h44n7
title: Ultrasound dataset for head model speed-of-sound derived from segmented MRI (MIDA model)

description: Dataset generated using a finite-difference acoustic wave propagator.
description: This is an in-silico dataset.
description: The format of the file is 'unformatted fortran'. The
 first line in the file contains the number of emitters (integer), number
 of receivers (integer), the total number of time-steps used in the
 modelling(integer), and the time-sampling (float). The remaining lines
 contain the emitter number id (integer), the receiver number id (integer),
 and the time series corresponding to the emitter-receiver pair at the
 beginning of the line (array of floats).
DOI: 10.5061/dryad.cnp5hqc20
title: Identifying and characterizing stress pathways of concern for consumer safety in next generation risk assessment

description: Many substances for which consumer safety risk assessments need to be
 conducted are not associated with specific toxicity modes of action but
 rather exhibit non-specific toxicity leading to cell stress. In this work,
 a cellular stress panel is described, consisting of 36 biomarkers
 representing mitochondrial toxicity, cell stress and cell health, measured
 predominantly using high content imaging. To evaluate the panel, data were
 generated for thirteen substances at exposures consistent with typical
 use-case scenarios. These included some that have been shown to cause
 adverse effects in a proportion of exposed humans and have a toxicological
 mode-of-action associated with cellular stress (e.g. doxorubicin,
 troglitazone, diclofenac), and some that are not associated with adverse
 effects due to cellular stress at human-relevant exposures (e.g. caffeine,
 niacinamide and phenoxyethanol).  For each substance,
 concentration response data were generated for each biomarker at three
 time points. A Bayesian model was then developed to quantify the evidence
 for a biological response, and if present, a credibility range for the
 estimated point of departure (PoD) was determined. PoDs were compared with
 the plasma Cmax associated with the typical substance exposures and
 indicated a clear differentiation between ‘low’ risk and ‘high’ risk
 chemical exposure scenarios. Developing robust methods to characterize the
 in vitro bioactivity of xenobiotics is an important part of non-animal
 safety assessment. The results presented show that the cellular stress
 panel can be used, together with other new approach methodologies, to
 identify chemical exposures that are protective of consumer health.
DOI: 10.5061/dryad.ffbg79cqx
title: Environmental stress maintains trioecy in nematode worms

description: Sex is determined by chromosomes in mammals but it can be influenced by
 the environment in many worms, crustaceans and vertebrates. Despite this,
 there is little understanding of the relationship between ecology and the
 evolution of sexual systems. The nematode Auanema freiburgensis has a
 unique sex determination system in which individuals carrying one X
 chromosome develop into males while XX individuals develop into females in
 stress-free environments and self-fertile hermaphrodites in stressful
 environments. Theory predicts that trioecious populations with coexisting
 males, females and hermaphrodites should be unstable intermediates in
 evolutionary transitions between mating systems. In this article we study
 a mathematical model of reproductive evolution based on the unique life
 history and sex determination of A. freiburgensis. We develop the model in
 two scenarios, one where the relative production of hermaphrodites and
 females is entirely dependent on the environment and one based on
 empirical measurements of a population that displays incomplete, ‘leaky’
 environmental dependence. In the first scenario environmental conditions
 can push the population along an evolutionary continuum and result in the
 stable maintenance of multiple reproductive systems. The second ‘leaky’
 scenario results in the maintenance of three sexes for all environmental
 conditions. Theoretical investigations of reproductive system transitions
 have focused on the evolutionary costs and benefits of sex. Here, we show
 that the flexible sex determination system of A. freiburgensis may
 contribute to population-level resilience in the microscopic nematode’s
 patchy, ephemeral natural habitat. Our results demonstrate that life
 history, ecology and environment may play defining roles in the evolution
 of sexual systems.
description: Matlab model files for parameter exploration, Anderson Bubrig
 Fierst 2020 Evolution
DOI: 10.5061/dryad.jwstqjq5d
title: Data from: User experience methods and maturity in academic libraries

description: This article presents a mixed-methods study of the methods and maturity of
 user experience (UX) practice in academic libraries. The authors apply
 qualitative content analysis and quantitative statistical analysis to a
 research dataset derived from a survey of UX practitioners. Results reveal
 the type and extent of UX methods currently in use by practitioners in
 academic libraries. Themes extracted from the survey responses also reveal
 a set of factors that influence the development of UX maturity. Analysis
 and discussion focuses on organizational characteristics that influence UX
 methods and maturity. The authors conclude by offering a library-focused
 maturity scale with recommended practices for advancing UX maturity in
 academic libraries. 
description: See README for additional information
DOI: 10.5061/dryad.9ghx3ffdf
title: Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases

description: Genetic diversity among metastases is poorly understood but contains
 important information about disease evolution at secondary sites. Here we
 investigate inter- and intra-lesion heterogeneity for two types of
 metastases that associate with different clinical outcomes: lymph node and
 distant organ metastases in human colorectal cancer. We develop a rigorous
 mathematical framework for quantifying metastatic phylogenetic diversity.
 Distant metastases are typically monophyletic and genetically similar to
 each other. Lymph node metastases, in contrast, display high levels of
 inter-lesion diversity. We validate these findings by analyzing 317
 multi-region biopsies from an independent cohort of 20 patients. We
 further demonstrate higher levels of intra-lesion heterogeneity in lymph
 node than in distant metastases. Our results show that fewer primary tumor
 lineages seed distant metastases than lymph node metastases, indicating
 that the two sites are subject to different levels of selection. Thus,
 lymph node and distant metastases develop through fundamentally different
 evolutionary mechanisms.
DOI: 10.5061/dryad.cjsxksn2n
title: Evaluation of the silkworm lemon mutant as an invertebrate animal model for human sepiapterin reductase deficiency

description: Human sepiapterin reductase deficiency is an inherited disease caused by
 SPR gene mutations and is a monoamine neurotransmitter disorder. Here, we
 investigated whether the silkworm lemon mutant could serve as a model of
 sepiapterin reductase deficiency. A point mutation in the BmSPR gene led
 to a five amino acid deletion at the carboxyl terminus in the lemon
 mutant. In addition, classical phenotypes seen in sepiapterin reductase
 deficient patients were observed in the lemon mutant, including a normal
 phenylalanine level, a decreased dopamine and serotonin content, and an
 increased neopterin level. A recovery test showed that replenishment of
 L-dopa significantly increased the dopamine level in the lemon mutant. The
 silkworm lemon mutant also showed negative behavioral abilities. These
 results suggest that the silkworm lemon mutant has an appropriate genetic
 basis and meets the biochemical requirements to be a model of sepiapterin
 reductase deficiency. Thus, the silkworm lemon mutant can serve as a
 candidate animal model of sepiapterin reductase deficiency, which may be
 helpful in facilitating accurate diagnosis and effective treatment options
 of sepiapterin reductase deficiency.
description: These gene sequences were collected from NCBI.
DOI: 10.5061/dryad.pvmcvdnh3
title: Mutations in the tail domain of MYH3 contributes to atrial septal defect

description: Atrial septal defect (ASD) is one of the most common congenital heart
 defects (CHDs) diagnosed in children. Sarcomeric genes has been attributed
 to ASD and knockdown of MYH3 functionally homologues gene in chick models
 indicated abnormal atrial septal development. Here, we report for the
 first time, a case-control study investigating the role of MYH3 among
 non-syndromic ASD patients in contributing to septal development. Four
 amplicons which will amplifies the 40 kb MYH3 were designed and amplified
 using long range-PCR. The amplicons were then sequenced using indexed
 paired-end libraries on the MiSeq platform. The STREGA guidelines were
 applied for planning and reporting. The non-synonymous c. 3574G&gt;A
 (p.Ala1192Thr) [p=0.001, OR=2.36 (1.36-4.11)] located within the tail
 domain indicated a highly conserved protein region. The mutant model of c.
 3574G&gt;A (p.Ala1192Thr) showed high root mean square deviation
 (RMSD) values compared to the wild model.  To our knowledge, this
 is the first study to provide compelling evidence on the pathogenesis of
 MYH3 variants towards ASD hence, suggesting the crucial role of
 non-synonymous variants in the tail domain of MYH3 towards atrial septal
 development. It is hoped that these genes can be used as panel for
 diagnosis of ASD in future.
description: This is a genotyping data generated by sequencing patinets with
 atrial septal defect, using the  Nextera XT DNA Sample Preparation
 Kit (Illumina, San Diego, CA) according to the manufacturer's
 protocol. A fragment length of the libraries was ascertained using the
 High Sensitivity DNA kit (Agilent Technologies,Santa Clara, CA) on the
 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Normalized
 libraries were subjected to a 300-cycle 153 sequencing run with MiSeq
 Reagent<br> Nano Kit v2 (Illumina, San Diego, CA) on the MiSeq
 (Illumina, San Diego, CA), were carried out the Genetic Laboratory,
 faculty of Science, University of Malaya.
DOI: 10.5061/dryad.1jwstqjr5
title: Community-wide trait means and variations affect biomass in a biodiversity experiment with tree seedlings

description: The structure of a plant community in terms of functional traits can
 strongly affect community productivity. Two components may contribute to
 this, community-wide trait means (mass-ratio hypothesis) or community-wide
 trait variations (diversity hypothesis) across species and individuals. We
 compared the explanatory power of the two hypotheses for explaining
 biomass variation among individuals and communities as measures of
 productivity. We set up experimental communities of tree seedlings that
 ranged in species richness from 1‒8. We measured above- and belowground
 biomass, leaf area, specific leaf area and height of all individuals
 separately after 16 months of growth and calculated species-level values
 by averaging across all individuals of each species grown in monoculture.
 Using species- and individual-level trait data, we calculated community-
 (CWM) and neighbourhood-weighted mean (NWM) values to assess the
 mass-ratio hypothesis and community functional dissimilarity (FD) and
 average trait dissimilarity of target individuals to neighbours (ATD),
 i.e. trait variations, to assess the diversity hypothesis. CWMs explained
 much more variation in community biomass than did species richness or FD,
 supporting the mass-ratio hypothesis. The explanatory power of CWMs
 increased when calculated with individual-level data, demonstrating
 positive effects of trait adjustments of individuals in response to
 species richness, i.e. plasticity in the broad sense. FD calculated with
 individual-level data also increased community biomass, lending some
 support to the diversity hypothesis. The effects of trait means and
 variations on community biomass were related to effects of trait means and
 variations on the biomass of individuals. Overall, our results suggest
 that trait means rather than trait variations may drive community biomass
 productivity at the earliest stage of forest development.
description: We assembled experimental communities of eight tree seedlings
 with four species richness levels (one, two, four or eight species). We
 measured above- and belowground biomass, leaf area, specific leaf area and
 height of all individuals separately after 16 months of growth.
DOI: 10.5061/dryad.573n5tb42
title: The signal detection problem of aposematic prey revisited: integrating prior social and personal experience

description: Data collected during three separate experiments using
 the "novel world" (Alatalo & Mappes, Nature
 1996) approach to test how social information changes predator
 discrimination of novel aposematic prey from a cryptic palatable
 alternative. Experiments were conducted with great tits (Parus major),
 captured from the wild and released afterwards, at the University
 of Jyväskylä Research Station, Konnevesi, Finland (62.6° N, 26.3° E)
 during three winters (2013-2014, 2016-2017, 2017-2018). Social information
 was provided by video playback of a demonstrator (adult male) showing an
 aversive behavioural response to a novel prey signal before observers
 (juveniles, adults, males, females) searched for prey signals against a
 background in either an aviary or in a "miniature novel world"
 in an experimental holding box.
description: The dataset includes 21 variables, with no data processing. See
 ReadMe for details.
description: There are missing values in covariates. See ReadMe for
 details.