cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b8v656
title: Raw data for: Phosphate deprivation-induced changes in tomato are mediated by an interaction between brassinosteroid signaling and zinc

description: Inorganic phosphate (Pi) is a necessary macronutrient for basic biological
 processes. Plants modulate their root system architecture (RSA) and
 cellular processes to adapt to Pi deprivation albeit with a growth
 penalty. Excess application of Pi fertilizer, on the other hand, leads to
 eutrophication and has a negative environmental impact. We compared RSA,
 root hair elongation, acid phosphatase activity, metal ion accumulation,
 and brassinosteroid hormone levels of Solanum lycopersicum (tomato) and
 Solanum pennellii, which is a wild relative of tomato, under Pi
 sufficiency and deficiency conditions to understand the molecular
 mechanism of Pi deprivation response in tomato. We showed that Solanum
 pennellii is partially insensitive to phosphate deprivation. Furthermore,
 it mounts a constitutive response under phosphate sufficiency. We
 demonstrate that activated brassinosteroid signaling through a tomato BZR1
 ortholog gives rise to the same constitutive phosphate deficiency
 response, which is dependent on zinc over-accumulation. Collectively,
 these results reveal an additional strategy by which plants can adapt to
 phosphate starvation.
DOI: 10.5061/dryad.fqz612jxd
title: Industry funding of patient organisations in the United Kingdom: A retrospective study of commercial determinants, funding concentration and disease prevalence

description: Objectives – To assess the relationship between UK-based patient
 organisation funding and companies’ commercial interests in rare and
 non-rare diseases in 2020. Design – Retrospective analysis of the value
 and volume of payments from pharmaceutical companies to patient
 organisations in the UK matched with data on the conditions supported by
 patient organisations and drugs in companies’ approved portfolios and
 research and development pipelines. Setting – UK. Participants – 74
 pharmaceutical companies making payments to 341 UK-based patient
 organisations. Main outcome measures – Alignment between the commercial
 interests of pharmaceutical companies and the disease area focus of
 patient organisations; difference in the volume and value of payments to
 patient organisations broken down by prevalence of conditions; industry
 funding concentration, measured as the number of companies funding each
 patient organisations, the share of overall industry funding coming from
 each contributing company and the share of industry funding of each
 organisation comprised by the single highest payments. Results – 1,422
 payments were made by 74 companies to 341 patient organisations. Almost
 all funds (90%) from pharmaceutical companies were directed to patient
 organisations that are aligned with companies’ approved drug portfolios
 and research and development pipelines. Despite rare diseases affecting
 less than 5% of the UK population, more than 20% of all payments were
 directed to patient organisations which target such conditions. Patient
 organisations focusing on rare diseases relied on payments from fewer
 companies (p-value = 0.0031) compared to organisations focusing on
 non-rare diseases. Conclusions – Companies predominantly funded patient
 organisations operating in therapeutic areas relevant to companies’
 portfolio or drug development pipeline. Patient organisations focusing on
 rare diseases received more funding relative to the number of patients
 affected by these conditions and relied more heavily on payments from
 fewer companies compared to organisations targeting non-rare diseases.
 Increased independence of patient organisations could help avoiding
 conflicts of interest.
DOI: 10.5061/dryad.jwstqjqfp
title: Climate-driven decline in the habitat of the endemic spiny babbler (Turdoides nipalensis)

description: Climate change could amplify the extinction risk of endemic species, and
 the risk is even greater for the species occupying high elevations and
 mountain ranges. In this study, we assessed the climatically suitable
 habitat of the only endemic Nepalese bird species, the spiny babbler
 (Turdoides nipalensis), and predicted the extent of the future (2050 and
 2070) habitat of this species under two climate change scenarios (SSP2-4.5
 and SSP5-8.5). We used georeferenced occurrence points alongside
 ecologically meaningful climatic and topographic variables to develop an
 ensemble suitable habitat model using different species distribution
 modeling algorithms in BIOMOD2. We identified 22,488.83 km2 (15%) of
 Nepal's total land area as suitable habitat for this endemic species,
 where the non-protected regions incorporated the largest extent of
 suitable habitat (88%), with a majority of this suitable area within the
 central Mid-Hill region. Under the SSP2-4.5 scenario, 21.58% and 34.08% of
 the current suitable habitat range are projected to be lost by 2050 and
 2070, respectively. Whereas under the SSP5-8.5 scenario, our projections
 suggest that 40.45% and 52.18% of habitat will be lost by 2050 and 2070,
 respectively. Habitat suitability increased with a rise in warmest quarter
 precipitation (above 1000 mm), coldest quarter precipitation between 50
 and 100 mm, and warmest quarter temperature between 20 and 30°C. Given our
 results, it is crucial to review the conservation policy of non-protected
 areas and to formulate a spiny babbler-specific conservation action plan
 with a special focus on protecting their primary habitat in the
 human-dominated landscapes and non-protected areas. 
description: The TSS value of accurracy was generated through the ensemble
 modeling approach.
DOI: 10.5061/dryad.0vt4b8h40
title: Single fathers sacrifice their broods and re-mate quickly in a socially monogamous cichlid

description: When one of two parents disappears in the midst of caring for offspring,
 the remaining parent is left with several options. They can
 either i) desert the brood, ii) continue caring on their own and
 reject propositions from new potential partners, or iii) continue caring
 but remain receptive to re-mating opportunities. The presence of a brood
 may increase re-mating success of single parents, either because brood
 care is perceived as a signal of partner quality, or because prospective
 mates perceive the brood as a potential energy source. In this
 field experiment, we used the socially monogamous, biparental cichlid fish
 Variabilichromis moorii to examine the re-mating strategy of males with or
 without dependent offspring after the loss of their female partner.
 Partner vacancies were filled quickly by new females, and these females
 engaged in high levels of affiliative behavior with the males. The new
 females engaged in territorial defense but focused primarily against
 intruding conspecifics, likely as a means to repel rivals. The males, in
 turn, took over the majority of territorial defense against intruding
 heterospecifics. Interestingly, males that still had offspring from their
 previous partnerships did not show aggression towards their new female
 partners, even when those females were infanticidal and cannibalizing the
 males’ previous offspring. Overall, our experiment shows that single
 fathers of a biparental species will re-mate quickly even at the detriment
 of their current offspring.
description: Word, Excel, R
DOI: 10.5061/dryad.r4xgxd2js
title: Density-dependent changes in elk resource selection over successional time scales following forest disturbance

description: There is an increasing need to understand how animals respond to
 modifications of their habitat following landscape-scale disturbances such
 as wildfire or timber harvest. Such disturbances can promote increased use
 by herbivores due to changes in plant community structure that improve
 forage conditions, but can also cause avoidance if other habitat functions
 provided by cover are substantially reduced or eliminated. Quantifying the
 total effects of these disturbances, however, is challenging because they
 may not fully be apparent unless observed at successional timescales.
 Further, the effects of disturbances that improve habitat quality may be
 density dependent such that the benefits are 1) less valuable to
 high-density populations because the per-capita benefits are reduced when
 shared among more users, or alternatively, 2) more valuable to animals
 living in high densities because resources may be more depleted from
 greater intraspecific competition. We used 30 years of telemetry data on
 elk occurring at two distinct population densities to quantify changes in
 space use at diel, monthly, and successional timescales following timber
 harvest. Elk selected for logged areas at night only, with selection
 strongest during mid-summer, and peak selection occurring 14 years
 post-harvest but persisting for 26–33 years. This pattern of increased
 selection at night following a reduction in overhead canopy cover is
 consistent with elk exploiting improved nutritional conditions for
 foraging. The magnitude of selection for logged areas was 73% higher for
 elk at low population density, consistent with predictions from the ideal
 free distribution. Yet elk avoided these same areas during daytime up to
 28 years post-logging and instead selected for untreated forest,
 suggesting a role for cover to meet other life history requirements. Our
 results demonstrate that while landscape-scale disturbances can lead to
 increased selection by large herbivores suggesting the improvement in
 foraging conditions can persist over short-term successional timescales,
 the magnitude of the benefits may not be equal across population
 densities. Further, the enduring avoidance of logging treatments during
 daytime indicates a need for structurally-intact forest and suggests that
 a mosaic of forest patches of varying successional stages and structural
 completeness will likely be most beneficial to large herbivores.
DOI: 10.5061/dryad.p5hqbzktp
title: User preference optimization for control of ankle exoskeletons using sample efficient active learning

description: A major challenge to the widespread success of augmentative exoskeletons
 is accurately adjusting the controller to provide cooperative assistance
 with their wearer. Often, the controller parameters are
 ``tuned'' to optimize a physiological or biomechanical
 objective. However, these approaches are resource-intensive, while
 typically only enabling optimization of a single objective. In reality,
 the exoskeleton user experience is derived from many factors, including
 comfort and stability, among others. This work introduces an approach to
 conveniently tune four parameters of the exoskeleton controller that
 maximize user preference. We use an evolutionary algorithm to recommend
 potential parameters, which are ranked by a neural network that is
 pre-trained with previously collected preference data. The controller
 parameters that have the highest preference ranking are provided to the
 exoskeleton, and the wearer provides feedback as forced-choice
 comparisons. Our approach was able to converge on controller parameters
 preferred by the wearer compared to randomized parameters with an accuracy
 of 88% on average. The result indicates that the proposed algorithm was
 able to identify users' preferences while requiring less than 50
 queries to users. This work demonstrates user preference can be used to
 tune high-dimensional controller spaces easily and accurately, which shows
 the potential of translating lower-limb wearable technologies into our
 daily lives.
description: The data includes subjects' selections of control parameters
 throughout the experiment. The experiment consists of two sessions, which
 is the main optimization session and the validation session. The data
 shows users' selection process between two parameters (parent,
 offspring), which is composed of exploration / selection, and confirmation
 of the parameters they preferred throughout the session. There are a total
 of 13 subjects and each subject went through 3 trials of experiment. The
 speed of the treadmill was fixed to 1.2 m/s across all subjects. Please
 see the details of the protocol in the manuscript. The readme.txt
 describes the content of the data in each Excel file. 
description: Microsoft Excel, Python
DOI: 10.5061/dryad.w6m905qv3
title: Data from: using camera traps and N-mixture models to estimate population abundance: model selection really matters

description: Estimating the abundance or density of wildlife populations is a critical
 part of species conservation and management, but estimates can vary
 greatly in precision and accuracy according to the data collection and
 statistical methods, sampling and ecological variation, and sample size.
 N-mixture models are a common method which has been applied to a wide
 range of taxa for estimating population abundance from non-invasive data
 representing the distribution of the species. We used population estimates
 from an aerial survey of moose and videos from camera traps to assess the
 sensitivity of N-mixture models to ecological conditions, the spatial
 scale at which they were measured, the criteria used to define independent
 detections, and model choice based on the common statistical criterion of
 parsimony. The most parsimonious N-mixture models were considerably
 biased, producing implausibly large and considerably imprecise estimates
 of the abundance of moose. Most of the other models produced estimates of
 abundance that were ecologically realistic and relatively accurate. The
 accuracy of population estimates produced by N-mixture models were not
 overly sensitive to the formulation of models, the scale at which
 ecological conditions were measured, or the criteria used to define
 independent detection and by extension sample size. Our results suggest
 that parsimony was a poor measure of the predictive accuracy of the
 population estimates produced with the N-mixture model. Collecting and
 processing data from the aerial survey was less expensive and took less
 time, but data from camera traps can provide valuable information on
 behavior of the target species as well as insights into multiple species
 in the community.
description: # Data from: using camera traps and N-mixture models to estimate
 population abundance: model selection really matters --- ## Description of
 the data and file structure **Sheet 1: aerial survey data for three
 strata**\ total cells: number of cells in stratum\ sampled cells: number
 of cells in stratum that were surveyed\ total area: area (km2) of all
 cells in stratum\ sampled area: area (km2) of surveyed cells in stratum\
 cell ID: unique identifier for each cell\ count: number of bulls, cows,
 and calves detected in each cell\ area: area (km2) of each cell **Sheets
 2-4: camera trap data**\ camera: unique identifier for each camera\ All
 other columns are the number of moose detections on each camera for each
 day.\ NAs represent days in which the camera was not active (dead battery
 or full memory card)
DOI: 10.5061/dryad.pk0p2ngt7
title: Density dependence of seed dispersal and fecundity profoundly alters the spread dynamics of plant populations

description: Plant population spread has fundamental ecological and evolutionary
 importance. Both determinants of plant population spread, fecundity and
 dispersal, can be density-dependent, which should cause feedback between
 population densities and spread dynamics. Yet it is poorly understood how
 density-dependence affects key characteristics of spread: spread rate at
 which the location of the furthest forward individual moves, edge depth
 (the geographical area over which individuals contribute to spread) and
 population continuity (occupancy of the spreading population). We present
 a general modelling framework for analysing the effects of
 density-dependent fecundity and dispersal on population spread and
 parameterize this framework with experimental data from a common-garden
 experiment using five wind-dispersed plant species grown at different
 densities.  Our model shows that density-dependent fecundity and
 dispersal strongly affect all three population spread characteristics for
 both exponential and lognormal dispersal kernels. Spread rate and edge
 depth are strongly correlated but show weaker correlations with population
 continuity. Positive density-dependence of fecundity increases all three
 spread characteristics. Increasingly positive density-dependence of
 dispersal increases spread rate and edge depth but generally decreases
 population continuity. Density-dependent fecundity and dispersal are
 largely additive in their effect on spread characteristics. For population
 continuity, the joint effects of density-dependent fecundity and dispersal
 are somewhat contingent on the dispersal kernel. The common-garden
 experiment and the experimentally parameterized mechanistic dispersal
 model revealed density-dependent fecundity and dispersal across study
 species. All study species exhibited negative density-dependent fecundity,
 but they differed qualitatively in the density-dependence of dispersal
 distance and probability of long-distance dispersal. The negative
 density-dependence of fecundity and dispersal found for three species
 reinforced each other in reducing spread rate and edge depth. The
 positively density-dependent dispersal found for two species markedly
 increased spread rate and edge depth. Population continuity was hardly
 affected by population density in all study species except Crepis sancta
 in which it was strongly reduced by negatively density-dependent
 fecundity. Synthesis. Density-dependent fecundity and seed dispersal
 profoundly alter population spread. In particular, positively
 density-dependent dispersal should promote the spread and genetic
 diversity of plant populations migrating under climate change but also
 complicate the control of invasive species.
description: Data of fecundity and dispersal traits were measured from a
 common garden experiment from March to
 October 2019 at the Heidfeldhof research station (48.71°N, 9.19°E, 389 m
 a.s.l), University of Hohenheim, Germany.
description: The data can be read with Excel or R.
DOI: 10.5061/dryad.0gb5mkm6b
title: Test case selection through novel methodologies for software application developments

description: Test case selection is to minimize the time and effort spent for software
 testing in real time practice. During the course of software testing, the
 software firms are in want of techniques to finish the testing in a
 stipulated time, whilst uncompromising on quality. The motto is to select
 subset of test cases rather to take up all available test cases to uncover
 most of the bugs. Clustering of test cases using ranking and also based on
 similarity coefficients is to be implemented. The experimented results
 have to show up the techniques proposed improving the catching up of
 errors in a comparatively shorter duration. In this research, eleven
 different features were considered in order to cluster the test cases.
 There are two methodologies implemented. In the first methodology, each
 cluster will cover set of specific features to a certain percentage.
 Depending on the feature’s coverage, cluster of test cases can be
 selected. These clusters were formed using ranking methodology. In the
 second methodology, similarity among test cases based on eleven features
 is found. Then max-min composition is used to find fuzzy equivalences,
 upon which clusters are formed. Most similar test cases are clustered.
DOI: 10.5061/dryad.f1vhhmh28
title: Data From: Rapid expansion and visual specialisation of learning and memory centers in the brains of Heliconiini butterflies

description: Changes in the abundance and diversity of neural cell types, and their
 connectivity, shape brain composition and provide the substrate for
 behavioral evolution. Although investment in sensory brain regions is
 understood to be largely driven by the relative ecological importance of
 particular sensory modalities, how selective pressures impact the
 elaboration of integrative brain centers has been more difficult to
 pinpoint. Here, we provide evidence of extensive, mosaic expansion of an
 integration brain center among closely related species, which is not
 explained by changes in sites of primary sensory input. By building new
 datasets of neural traits among a tribe of diverse Neotropical
 butterflies, the Heliconiini, we detected several major evolutionary
 expansions of the mushroom bodies, central brain structures pivotal for
 insect learning and memory. The genus Heliconius, which exhibits a unique
 dietary innovation, pollen-feeding, and derived foraging behaviors reliant
 on spatial memory, shows the most extreme enlargement. This expansion is
 primarily associated with increased visual processing areas and coincides
 with increased precision of visual processing, and enhanced long-term
 memory. These results demonstrate that selection for behavioral innovation
 and enhanced cognitive ability occurred through expansion and localized
 specialization in integrative brain centers.
description: See associated article for full methodological information.
DOI: 10.5061/dryad.2z34tmprk
title: The structure and ecological function of the interactions between plants and arbuscular mycorrhizal fungi through multilayer networks

description: Arbuscular mycorrhizas are one of the most frequent mutualisms in
 terrestrial ecosystems. Although studies on plant mutualistic interaction
 networks suggest that they may leave their imprint on plant community
 structure and dynamics, this has not been explicitly assessed. Thus, in
 the context of plant-fungi interactions, studies explicitly linking
 plant-mycorrhizal fungi interaction networks with key ecological functions
 of plant communities, such as recruitment, are lacking.  In this
 study, we analyse, in two Mediterranean forest communities of southern
 Iberian Peninsula, how plant-AMF networks modulate plant-plant recruitment
 interaction networks. We use a new approach integrating plant-AMF and
 plant recruitment networks into a single multilayer structure. We also
 develop a new metric (Interlayer Node Neighbourhood Integration, INNI) to
 explore the impact of a given node on the structure across layers.
 Similarity of plant species in their AMF communities is positively related
 to the observed frequency of recruitment interactions in the field.
 Results reveal that properties of plant-AMF networks, such as plant degree
 and centrality, contribute to explaining properties of the plant
 recruitment network, such as in- and out-degree (i.e. sapling bank and
 canopy service) and its modular structure. However, these relationships
 differed between the two forest communities. Finally, we identify
 particular AMF that contribute to integrating the neighbourhood of
 recruitment interactions between plants. This multilayer network approach
 is useful to explore the role of plant-AMF interactions on recruitment, a
 key ecosystem function enhanced by fungi. Results provide evidence that
 the complex structure of plant-AMF interactions impacts functional and
 structurally plant-plant interactions, which in turn may potentially
 influence plant community dynamics, through their effects on the structure
 of the recruitment network.