cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b8gtht7cr
title: Data from: Rich resource environment of fish farms facilitates phenotypic variation and virulence in an opportunistic fish pathogen

description: Phenotypic variation is suggested to facilitate the persistence of
 environmentally growing pathogens under environmental change. Here we
 hypothesized that the intensive farming environment induces higher
 phenotypic variation in microbial pathogens than natural environment,
 because of high stochasticity for growth and stronger survival selection
 compared to the natural environment. We tested the hypothesis with an
 opportunistic fish pathogen Flavobacterium columnare isolated either from
 fish farms or from natural waters. We measured growth parameters of two
 morphotypes from all isolates in different resource concentrations and two
 temperatures relevant for the occurrence of disease epidemics at farms and
 tested their virulence using a zebrafish (Danio rerio) infection model.
 According to our hypothesis, isolates originating from the fish farms had
 higher phenotypic variation in growth between the morphotypes than the
 isolates from natural waters. The difference was more pronounced in higher
 resource concentrations and the higher temperature, suggesting that
 phenotypic variation is driven by the exploitation of increased
 outside-host resources at farms. Phenotypic variation of virulence was not
 observed based on isolate origin but only based on morphotype. However,
 when in contact with the larger fish, the less virulent morphotype of some
 of the isolates also had high virulence. As the less virulent morphotype
 also had higher growth rate in outside-host resources, the results suggest
 that both morphotypes can contribute to F. columnare epidemics at fish
 farms, especially with current prospects of warming temperatures. Our
 results suggest that higher phenotypic variation per se does not lead to
 higher virulence, but that environmental conditions at fish farms could
 select isolates with high phenotypic variation in bacterial population and
 hence affect evolution in F. columnare at fish farms. Our results
 highlight the multifaceted effects of human-induced environmental
 alterations in shaping epidemiology and evolution in microbial pathogens.
  
description: The archived data comprises three data files: growth.xlsx,
 morphotype_stability.xlsx and challenge_test.xlsx and a README-file with
 infromation on data collection and lists of variables.
DOI: 10.5061/dryad.z08kprrcx
title: Data from: Life-history responses of a freshwater rotifer to copper pollution

description: In organisms with dormant stages, life-history responses to past pollution
 can be studied retrospectively. Here, we study such responses in a rotifer
 (Brachionus calyciflorus) from the once heavily copper-polluted Lake Orta
 (Italy). We extracted resting eggs from sediments, established clonal
 lineages from hatchlings, and exposed newborns of these lineages to one of
 three copper concentrations that each mimicked a specific period in the
 lake’s pollution history. For each rotifer, we daily collected life-table
 data. We then estimated treatment-specific vital rates and used a
 stage-structured population model to project population growth rate λ. We
 also estimated elasticities of λ to vital rates and contributions of vital
 rates to observed Δλ between copper treatments. As expected, λ decreased
 with increasing copper concentration. This decrease resulted mostly from a
 decline in juvenile survival rate (SJ) and partly from a decline in the
 survival rate of asexually reproducing females (SA). Maturation rate, and
 with one exception fecundity, also declined but did not contribute
 consistently to Δλ. λ was most elastic to SJ and SA, indicating that
 survival rates were under stronger selection than maturation rate and
 fecundity. Together, our results indicate that variation in juvenile
 survival is a key component in the rotifers’ copper response. The
 consistent decrease in SJ with increasing copper stress and the
 sensitivity of λ to that decrease also suggest that juvenile survival is a
 useful indicator of population performance under environmental pollution.
description: We exposed each experimental rotifer individually for the entire
 lifetime to either 0, 40, or 80 µg Cu L<sup>–1</sup>, added as
 copper sulphate pentahydrate, and a food density of 1 ×
 10<sup>6</sup> algal cells mL<sup>–1</sup>. We
 recorded daily whether a given rotifer was still alive, how many female
 offspring it had produced, and whether it was mictic or amictic.
description: “id” is rotifer identity; “run” is experimental run number;
 “population” (“contemporary”, “recovery”, “peak”) is population identity
 (post-pollution population, recovery population, peak-pollution
 population); “copper” is Cu concentration in µg per litre; “stage” (“juv”,
 “amictic_ad”, “mictic_ad”) is life stage (juvenile, amictic adult, mictic
 adult); “age” is rotifer age in days; “survival” (“1” or “0” mean the
 rotifer survived or died, respectively); “fecundity” is number of
 offspring; “NA”: not available.
DOI: 10.15468/dl.98vy2h
title: Occurrence Download

description: A dataset containing 681 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cryptostegia madagascariensis"
 ]
}

 The dataset includes 681 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002865-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.v15dv41w9
title: A non-native earthworm shifts the seed predation dynamics of a native weed

description: Seed predators both consume and disperse seeds, with important
 consequences for the population dynamics of many plant species. 
 The net effect of multiple seed predators depends on the relative
 proportion of the seed pool each predator obtains, and this proportion
 should reflect species-specific habitat preferences.  We studied
 the effect of the non-native earthworm, Lumbricus terrestris, on seed loss
 dynamics in the native weed, Ambrosia trifida (giant ragweed). 
 Giant ragweed seeds are predated by mice, but L. terrestris may protect
 the seeds against rodent predation by caching them in its
 burrows.  We investigated these interactions, as well as how
 environmental factors affected net seed losses by competing seed
 predators. A two-year field study was conducted in which we measured
 removal of experimentally dispersed giant ragweed seeds by earthworms and
 mice in habitats varying in plant cover.  We analyzed the
 relative proportion of seeds taken by each species under the varying
 experimental conditions.    Species-specific responses
 to abiotic conditions and plant cover drove variation in the share of
 seeds taken by earthworms versus mice, with earthworms gaining relatively
 more seeds under warmer, wetter conditions and low plant cover habitats,
 and mice obtaining more seeds under colder, drier conditions and high
 plant cover habitats.  Plant cover and weather conditions also
 determined which predator species accessed seeds first, and this conferred
 a competitive advantage that was compounded over time. Earthworms cached
 some seeds under all experimental conditions, suggesting that L.
 terrestris can act mutualistically with giant ragweed by making seeds
 inaccessible to rodent seed predators.  Synthesis and
 applications. Our results support the view that interactions
 among the environment and competing seed predators determine the fate of
 seed pools.  The data also support the hypothesis that L.
 terrestris facilitates giant ragweed by competing with mice for giant
 ragweed seeds, likely contributing to its spread across the landscape and
 hindering effective weed management.  Lumbricus
 terrestris is prevalent throughout temperate regions and may similarly
 affect seed predation dynamics of other large-seeded species, impacting
 plant communities across a range of habitats.
description: A
 two-year field study was conducted in which we measured removal of
 experimentally dispersed giant ragweed seeds by earthworms and mice in
 habitats varying in plant cover.  We analyzed the relative proportion of
 seeds taken by each species under the varying experimental
 conditions.
DOI: 10.5061/dryad.9ghx3ffhn
title: Data from: Direct and indirect effects of landscape and field management intensity on carabids through trophic resources and weeds

description: Carabids are important biological control agents of weeds and other pests
 in agricultural fields. The carabid community is built upon direct and
 indirect ecological effects of landscape complexity, field management
 intensity and biotic components that in interaction make any prediction of
 community size and composition challenging. We analyse a large-scale
 sample of 60 European cereal fields using Structural Equation Modelling to
 quantify the direct effects of field management intensity and the
 surrounding landscape, and their indirect effect via biotic components, on
 carabid diversity. Our results highlight that direct and indirect effects
 of increasing landscape complexity, mediated by trophic resources, mainly
 affect carabids positively. Field management intensity only ever affects
 carabids through indirect effects that are generally negative, by
 suppressing standing weeds and weed seeds. Indirect effects on granivore
 carabid species depended on weed seed availability whereas omnivores
 depended on the availability of both weed seeds and animal prey. Synthesis
 and applications: A consideration of both the direct and indirect effects
 of landscape and field management is necessary for predicting carabid
 communities and with interactions. These effects, mediated via trophic
 resources, supports the diversity and abundance of carabid communities and
 their provision of ecosystem services. Our results show that promoting
 crop diversity and connectivity to semi-natural habitats will directly
 enhance carabid communities in farmland by manipulating their migration
 from source habitats. A reduction in field management intensity will
 preserve local standing weeds and weed seeds, and indirectly support
 carabid communities. These local and landscape modifications could
 contribute to improve the natural regulation of pests and weeds by
 carabids.
description: Read the material and method of the article entitled "Direct
 and indirect effects of landscape and field management intensity on
 carabids through trophic resources and weeds".
description: This dataset consists of 4 files:<br> -a weather data file
 (Carbonne_JAE_Weather_Data)<br> -a file containing biological,
 landscape and management data (Carbonne_JAE_Data)<br> -a file
 describing each variable (Carbonne_JAE_Data_Labels)<br> -a file with
 the R code (Carbonne_JAE_R_code)
DOI: 10.5061/dryad.05qfttf34
title: Clinging ability is related to particular aspects of foot morphology in salamanders

description: The interaction between morphology, performance, and ecology has long been
 studied in order to explain variation in the natural world. Within
 arboreal salamanders, diversification in foot morphology and microhabitat
 use are thought to be linked by the impact of foot size and shape on
 clinging and climbing performance, resulting in an ability to access new
 habitats. We examine whether various foot shape metrics correlate with
 stationary cling performance and microhabitat to explicitly quantify this
 performance gradient across 14 species of salamander, including both
 arboreal and non-arboreal species. Clinging performance did not correlate
 with foot shape, as quantified by landmark-based geometric morphometrics,
 nor with microhabitat use. Mass-corrected foot centroid size and foot
 contact area, on the other hand, correlated positively with clinging
 performance on a smooth substrate. Interestingly, these foot variables
 correlated negatively with clinging performance on rough substrates,
 suggesting the use of multiple clinging mechanisms dependent upon the
 texture of the surface. These findings demonstrate that centroid size and
 foot contact area are more functionally relevant for clinging in
 salamanders than foot shape, suggesting that foot shape need not converge
 in order to achieve convergent performance. More broadly, our results
 provide an example of how the quantification of the performance gradient
 can provide the appropriate lens through which to understand the
 macroevolution of morphology and ecology.
description: Included is an R script used for all analyses, a tps file
 including the foot shape data as quantified by 2d geometric morphometrics,
 a csv with cling data, and a phy file which is a phylogeny from Bonett and
 Blair 2017, pruned to match the species used in this study.
 See Baken and O'Donnell 2021 for methodological
 details. Baken, E. K., and M. K. O'Donnell.
 2021.  Bonett, R., and A. Blair. 2017. Evidence for complex life cycle constraints on salamander body form diversification. Proceedings of the National Academy of Sciences 114(37):9936-9941.
DOI: 10.5061/dryad.9kd51c5h7
title: Time-Optimal Planning for Quadrotor Waypoint Flight

description: Quadrotors are amongst the most agile flying robots. However, planning
 time-optimal trajectories at the actuation limit through multiple
 waypoints remains an open problem. This is crucial for applications such
 as inspection, delivery, search and rescue, and drone racing. Early works
 used polynomial trajectory formulations, which do not exploit the full
 actuator potential due to their inherent smoothness.  Recent
 works resorted to numerical optimization, but require waypoints to be
 allocated as costs or constraints at specific discrete times. However,
 this time-allocation is a priori unknown and renders previous works
 incapable of producing truly time-optimal trajectories. To generate truly
 time-optimal trajectories, we propose a solution to the time allocation
 problem while exploiting the full quadrotor's actuator potential. We
 achieve this by introducing a formulation of progress along the
 trajectory, which enables the simultaneous optimization of the
 time-allocation and the trajectory itself. We compare our method against
 related approaches and validate it in real-world flights in one of the
 world's largest motion-capture systems, where we outperform human
 expert drone pilots in a drone-racing task.
description: This data contains drone flight tracks of two professional human
 pilots and a proposed planning approach, flown in a drone racing
 environment in one of the worlds largest flight arenas equipped with a
 VICON motion capture system.
description: All data is provided as is and can be evaluated using the
 included analysis scripts.
DOI: 10.5061/dryad.hqbzkh1gm
title: Long-term effect of regular physical activity and exercise habits in patients with early parkinson disease

description: Objective: Owing to the lack of long-term observations and/or
 comprehensive adjustment for confounding factors, reliable conclusions
 regarding long-term effects of exercise and regular physical activity in
 Parkinson’s disease (PD) have yet to be drawn. Here, using data from the
 Parkinson’s Progression Markers Initiative study that includes
 longitudinal and comprehensive evaluations of many clinical parameters, we
 examined the long-term effects of regular physical activity and exercise
 habits on the course of PD. Methods: In this observational cohort study,
 we primarily used the multivariate linear mixed-effects models to analyze
 the interaction effects of their regular physical activity and
 moderate-to-vigorous exercise levels, measured through the Physical
 Activity Scale for the Elderly questionnaire, on the progression of
 clinical parameters, after adjusting for age, sex, levodopa-equivalent
 dose, and disease duration. We also calculated bootstrapping 95%
 confidence intervals (CIs), and conducted sensitivity analyses using the
 multiple imputation method and subgroup analyses using the propensity
 score matching to match for all baseline background factors. Results: 237
 early PD patients [median (interquartile range); age, 63.0 (56.0–70.0)
 years; Male, 69.2%; follow-up duration, 5.0 (4.0–6.0) years] were
 included. Regular physical activity and moderate-to-vigorous exercise
 levels at the baseline did not significantly affect the subsequent
 clinical progression of PD. However, average regular overall physical
 activity levels over time were significantly associated with slower
 deterioration of postural and gait stability [standardized fixed-effects
 coefficients of the interaction term (βinteraction) = -0.10 (95% CI, -0.14
 to -0.06)], activities of daily living [βinteraction = 0.08 (95% CI, 0.04
 to 0.12)], and processing speed [βinteraction = 0.05 (95% CI, 0.03 to
 0.08)] in PD patients. Moderate-to-vigorous exercise levels were
 preferentially associated with slower decline of postural and gait
 stability [βinteraction = -0.09 (95% CI, -0.13 to -0.05)] and work-related
 activity levels were primarily associated with slower deterioration of
 processing speed [βinteraction = 0.07 (95% CI, 0.04 to 0.09)]. Multiple
 imputation and propensity score matching confirmed the robustness of our
 results. Conclusions: In the long-term, the maintenance of high regular
 physical activity levels and exercise habits was robustly associated with
 better clinical course of PD, with each type of physical activity having
 different effects.
description: This is an R code that aims to make the analysis done in this
 study transparent.
DOI: 10.5061/dryad.9kd51c5h8
title: GPR84 and GPR119 in the central regulation of food intake in rainbow trout

description: We evaluated the role of GPR84 and GPR119 in food intake regulation in
 fish using rainbow trout (Oncorhynchus mykiss) as a model. In a first
 experiment, we assessed the effects on food intake of
 intracerebroventricular treatment with agonists of these receptors. In a
 second experiment, we assessed in hypothalamus and hindbrain the impact of
 the same treatments on mRNA abundance of neuropeptides involved in the
 metabolic control of food intake (npy, agrp1, pomca1, and cartpt) as well
 as in changes in parameters related to signaling pathways and
 transcription factors involved in the integrative response leading to
 neuropeptide production. Treatment with both agonists elicited an
 anorectic response in rainbow trout attributable to changes observed in
 the mRNA abundance of the four neuropeptides. Changes in neuropeptides
 relate to changes observed in mRNA abundance and phosphorylation status of
 the transcription factor Foxo1. These changes occurred in parallel with
 changes in phosphorylation status of Ampkα and Akt, mRNA abundance of mTOR
 as well as in signaling pathways related to PLCβ and IP3. These results
 allow us to suggest that 1) at least part of the capacity of fish brain to
 sense MCFA like octanoate depends on the function of GPR84, and 2) the
 capacity of fish brain to sense NAE or triglyceride-derived molecules
 through binding of these ligands to GPR119
description: qPCR, Western Blot, spectrophotometric analysis
DOI: 10.34740/kaggle/dsv/14646357
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.bk3j9kdcc
title: Sequestration of defenses against predators drives specialized host plant associations in preadapted milkweed bugs (Heteroptera: Lygaeinae)

description: Host plant specialization across herbivorous insects varies dramatically,
 but while the molecular mechanisms of host-plant adaptations are
 increasingly known, we often lack a comprehensive understanding of the
 selective forces that favor specialization. The milkweed bugs
 (Heteroptera: Lygaeinae) are engaged in ancestrally specialized
 associations with plants of the Apocynaceae from which they commonly
 sequester cardiac glycosides for defense, facilitated by resistant
 Na+/K+-ATPases and adaptations for transport, storage and discharge of
 toxins. Here, we show that three Lygaeinae species independently colonized
 four novel non-apocynaceous hosts that convergently produce cardiac
 glycosides. A fourth species shifted to a new source of toxins by
 tolerating and sequestering alkaloids from meadow saffron (Colchicum
 autumnale, Colchicaceae). Across three milkweed bug species tested,
 feeding on seeds containing toxins did not improve growth or speed of
 development, and even impaired growth and development in two species, but
 sequestration mediated protection of milkweed bugs against two natural
 predators: lacewing larvae and passerine birds. We conclude that
 physiological preadaptations and convergent phytochemistry facilitated
 novel specialized host associations. Since toxic seeds did not improve but
 either impaired growth or at most had neutral effects, selection by
 predators on sequestration of defenses, rather than the exploitation of
 additional profitable dietary resources, can lead to obligatory
 specialized host associations in otherwise generalist insects.
description: Details on data collection are described in detail in the
 manuscript. All data are unprocessed. Data transformation is described in
 the manuscript.
description: All archived files are listed in a text-file (_README_general)
 comprising the metadata for each dataset alongside with an explanation of
 all variables. Datasets are presented in individual csv-files and are
 named with consecutive numbers (e.g.,
 1_growth_3_weeks, 2_growth_continuous, 3_development, etc.). Text-files
 with corresponding R-codes are named accordingly (e.g.,<strong>
 </strong>2_growth_continuous, 2_growth_continuous_R-code). In
 addition all outputs from the statistical analyses computed with JMP are
 compiled in a pdf named 14_JMP_outputs. Furthermore, a text-file named
 14_README_JMP_outputs is provided containing all scripts exported from JMP
 (JMP v. 13, SAS Institute, Cary, NC, USA) as well as some additional
 information on excluded outliers.
DOI: 10.5061/dryad.wstqjq2mp
title: Raw images for: The narrowing of dendrite branches across nodes follows a well-defined scaling law

description: The systematic variation of diameters in branched networks has tantalized
 biologists since the discovery of da Vinci’s rule for trees. Da Vinci’s
 rule can be formulated as a power law with exponent two: the square of the
 mother branch’s diameter is equal to the sum of the squares of those of
 the daughters. Power laws, with different exponents, have been proposed
 for branching in circulatory systems (Murray’s law with exponent 3) and in
 neurons (Rall’s law with exponent 3/2). The laws have been derived
 theoretically, based on optimality arguments, but, for the most part, have
 not been tested rigorously. Using super-resolution methods to measure the
 diameters of dendrites in highly
 branched Drosophila Class IV sensory neurons, we have
 found that these types of power laws do not hold. In their place, we have
 discovered a different diameter-scaling law: the cross-sectional area is
 proportional to the number of dendrite tips supported by the branch plus a
 constant, corresponding to a minimum diameter of the terminal
 dendrites. The area proportionality accords with a requirement for
 microtubules to transport materials and nutrients for dendrite tip growth.
 The minimum diameter may be set by the force, on the order of a
 few piconewtons, required to bend membrane into the highly curved surfaces
 of terminal dendrites. Because the observed scaling differs from
 Rall’s law, we propose that cell biological constraints
 such as intracellular transport and protrusive forces generated by the
 cytoskeleton are important in determining the branched morphology of these
 cells.
description: Raw images were taken using Spinning disk confocal microscope
 equipped with 60X WI NA 1.2 objective. The step size along axial direction
 is 0.2μm.