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885 results for “data strategy”
Data from: Life history strategy and everyday word use
Research by Sherman et al. (Journal of Personality and Social Psychology, 105, 873–888, 2013) has shown that, in speech during clinical-style interviews, life history strategy (LHS) was correlated with variation in the use of 16–19 word categories from the Linguistic Inquiry and Word Count program. However, links between individual difference variables and word use have been shown to vary as a function of communication context. Therefore, I sought to replicate their results using speech recorded during participants' daily life via the Electronically Activated Recorder. I also used (1) observer ratings rather than self-ratings of the California Adult Q-Sort (CAQ) items as a measure of LHS, (2) the self-report Arizona Life History Battery (ALHB) as an additional measure of LHS, and (3) Bayesian multi-level aggregated binomial regressions as a complementary analytical technique to conventional correlations. In general, the Sherman et al. results were replicated, particularly with respective to distinctive (corrected for normativeness) LHS. People pursuing a slower distinctive LHS produced proportionately fewer swear words, sexual words, and affect words (particularly negative emotion and anger words), and more work-related words. They also produced fewer words overall. After controlling for distinctive LHS, women were more talkative than men. Associations between the ALHB and word use were weaker than those between the CAQ and word use.
Data from: Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls
Independent or convergent evolution can underlie phenotypic similarity of derived behavioural characters. Determining the underlying neural and neuromuscular mechanisms sheds light on how these characters arose. One example of evolutionarily derived characters is a temporally simple advertisement call of male African clawed frogs (Xenopus) that arose at least twice independently from a more complex ancestral pattern. How did simplification occur in the vocal circuit? To distinguish shared from divergent mechanisms, we examined activity from the calling brain and vocal organ (larynx) in two species that independently evolved simplified calls. We find that each species uses distinct neural and neuromuscular strategies to produce the simplified calls. Isolated Xenopus borealis brains produce fictive vocal patterns that match temporal patterns of actual male calls; the larynx converts nerve activity faithfully into muscle contractions and single clicks. In contrast, fictive patterns from isolated Xenopus boumbaensis brains are short bursts of nerve activity; the isolated larynx requires stimulus bursts to produce a single click of sound. Thus, unlike X. borealis, the output of the X. boumbaensis hindbrain vocal pattern generator is an ancestral burst-type pattern, transformed by the larynx into single clicks. Temporally simple advertisement calls in genetically distant species of Xenopus have thus arisen independently via reconfigurations of central and peripheral vocal neuroeffectors.
Data from: Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes
The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as Phytophthora species, Hyaloperonospora arabidopsidis, and Pythium ultimum var. ultimum. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in Phytophthora species and an over-representation of genes involved in proteolytic degradation and signal transduction in Pythium species. A complete lack of classical RxLR effectors was observed in the seven surveyed Pythium genomes along with an overall reduction of pathogenesis-related gene families in H. arabidopsidis. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in Pythium species and H. arabidopsidis as compared to Phytophthora species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven Pythium species with the closely related oomycetes, Phytophthora species and H. arabidopsidis, and distantly related diatoms provide insight into genes that underlie virulence.
Data from: Contemporary evolution of plant reproductive strategies under global change is revealed by stored seeds
Global change is expected to impose new selection pressures on natural populations. Phenotypic responses, such as earlier phenology in response to climate warming, have been repeatedly observed in the field. The recent pollinator decline is also expected to change selection on reproductive traits in flowering plants. However, it remains unclear whether short-term adaptation of plant reproductive strategies occurs in response to global change. In this study, we report the evolution of some important reproductive traits of the annual self-incompatible weed Centaurea cyanus. In a common garden experiment we germinated stored seeds, sampled 18 years apart from the same location, in a region where warmer springs and indices of pollinator decline have been reported. Compared to the ancestral population (1992), our results showed that plants of the descendant population (2010) flowered earlier and also produced larger capitula with longer receptivity and a larger floral display. QST -FST comparisons indicated that natural selection has likely contributed to the evolution of some of the traits investigated. Lower FST within temporal samples than among spatial samples further suggests a limited role of gene flow from neighboring populations. We therefore propose that trait shifts could partly be due to adaptation to global change.
Data from: Fruiting strategies of perennial plants: a resource budget model to couple mast seeding to pollination efficiency and resource allocation strategies
Masting, a breeding strategy common in perennial plants, is defined by seed production that is highly variable over years and synchronized at the population level. Resource budget models (RBMs) proposed that masting relies on two processes: (i) the depletion of plant reserves following high fruiting levels, which leads to marked temporal fluctuations in fruiting; and (ii) outcross pollination that synchronizes seed crops among neighboring trees. We revisited the RBM approach to examine the extent to which masting could be impacted by the degree of pollination efficiency, by taking into account various logistic relationships between pollination success and pollen availability. To link masting to other reproductive traits, we split the reserve depletion coefficient into three biological parameters related to resource allocation strategies for flowering and fruiting. While outcross pollination is considered to be the key mechanism that synchronizes fruiting in RBMs, our model counterintuitively showed that intense masting should arise under low-efficiency pollination. When pollination is very efficient, medium-level masting may occur, provided that the costs of female flowering (relative to pollen production) and of fruiting (maximum fruit set and fruit size) are both very high. Our work highlights the powerful framework of RBMs, which include explicit biological parameters, to link fruiting dynamics to various reproductive traits and to provide new insights into the reproductive strategies of perennial plants.
Data From: Getting cited early: influence of visibility strategies, structure, and focal system on early citation rates
<p>Elucidating factors that contribute to citation rates of scientific articles can help scientists write manuscripts that have a stronger influence on their scientific field and wildlife management, and are accessible to a broad audience. Using a cohort of 778 articles published in <i>The Journal of Wildlife Management</i> from 2011–2015, we examined how visibility strategies (e.g., open access, increasing the Atlmetric Attention Score, self-citations), article structure, and focal system – all factors authors can predominantly control – influenced the accumulation of citations over various time frames within the first 5 years after publication, and the number of days until an article received its first citation. Visibility strategies influenced the number of citations accrued within the first year following publication. Our model explained less of the variation in number of citations received 1 year post-publication compared to 5 years post-publication (R<sup>2</sup> increased from 0.12 to 0.57 from years 1 to 5). Two years post-publication, factors associated with an article's visibility increased citation counts, and factors associated with article structure and focal system became important. Our analyses suggest citation rates, within wildlife ecology, are influenced by a number of controllable factors and that the influence of an article on science and management can be increased by authors pursuing a variety of visibility strategies.</p>
Data from: Is increased male flower production a strategy for avoidance of predispersal seed predation in andromonoecious plants?
<p>Floral gender in angiosperms often varies within and among populations. We conducted a field survey to test how predispersal seed predation affects sex allocation in an andromonoecious alpine herb <i>Peucedanum multivittatum</i>. We compared plant size, male and perfect flower production, fruit set, and seed predation rate over three years among nine populations inhabiting diverse snowmelt conditions in alpine meadows. Flowering period of individual populations varied from mid-July to late August reflecting the snowmelt time. Although perfect flower and fruit productions increased with plant size, size-dependency of male flower production was less clear. The number of male flowers was larger in the early-flowering populations, while the number of perfect flowers increased in the late-flowering populations. Thus, male-biased sex allocation was common in the early-flowering populations. Fruit-set rates varied among populations and between years, irrespective of flowering period. Fruit-set success of individual plants increased with perfect flower number, but independent of male flower number. Seed predation by lepidopteran larvae was intense in the early-flowering populations, whereas predation damage was absent in the late-flowering populations, reflecting the extent of phenological matching between flowering time of host plants and oviposition period of predator moths. Seed predation rate was independent of male and perfect flower numbers of individual plants. Thus, seed predation is a stochastic event in each population. There was a clear correlation between the proportion of male flowers and the intensity of seed predation among populations. These results suggest that male-biased sex allocation could be a strategy to reduce seed predation damage but maintain the effort as a pollen donor under intensive seed predation.</p>
Data for WarpX milestone ECP-ADSE06.FY21.2: Assessment of dynamic load-balancing strategies on available exascale systems.
<p>This dataset includes the inputs, outputs, job submission scripts, and data analysis scripts used to prepare the WarpX milestone report for "Assessment of dynamic load-balancing strategies on available exascale systems." The code versions of WarpX, AMReX, and PICSAR used are stored in the outputs file for each run. </p>
Data from: Thriving in a hostile world: insights from the dietary strategy of two allopatric, closely-related tepui summit endemic amphibians
<p>To date, there has been no published investigation on the trophic diversity in any tepui summit vertebrate. In this paper we analysed the dietary composition of a tepui summit endemic toad, <i>Oreophrynella quelchii</i> from Roraima-tepui, and compared it with that of <i>O. nigra</i>, to examine to what extent diet differs between these two sister species across isolated, although neighbouring, tepui tops. The digestive tracts of a total of 197 toads were dissected: 111 from <i>O. quelchii</i> and 86 from <i>O. nigra</i>. The diet composition of <i>O. quelchii</i> was relatively diverse, with 13 major prey categories; mites (Acari, 36.5%) and beetles (Coleoptera, 21.0%) numerically dominated its diet. Despite occurring on two different tepui summits, <i>O. quelchii </i>and <i>O. nigra</i> exhibited a similar diet composition, although in <i>O. nigra</i> mites (Acari, 42.4%) and hymenopterans (especially ants, 16.9%) numerically dominated the diet. The present data suggest that tepui summit <i>Oreophrynella</i> species are flexible in their diet and are active foragers that also feed on aquatic arthropods, successful strategies in tepui competitive environments.</p>
Data from: Incorporating single-step strategy into random regression model to enhance genomic prediction of longitudinal trait
In prediction of genomic values, single-step method has been demonstrated to outperform multi-step methods. In statistical analyses of longitudinal traits, random regression test-day model (RR-TDM) has clear advantages over other models. Our goal in this study was to evaluate the performance of the model integrating both single-step and RR-TDM prediction methods, called single-step random regression test-day model (SS RR-TDM), in comparison with the pedigree-based RR-TDM and genomic best linear unbiased prediction (GBLUP) model. We performed extensive simulations to exploit potential advantages of SS RR-TDM over the other two models under various scenarios with different level of heritability, the number of QTL as well as the selection scheme. SS RR-TDM was found to achieve the highest accuracy and unbiasedness under all scenarios, exhibiting robust prediction ability in longitudinal trait analyses. Moreover, SS RR-TDM showed better persistency of accuracy over generations than GBLUP model. In addition, we also found that the SS RR-TDM had advantages over RR-TDM and GBLUP in terms of a real dataset of human contributed by the GAW18 workshop. The findings in our study firstly proved the feasibility and advantages of the SS RR-TDM, and further enhanced strategies for the genomic prediction of longitudinal traits in the future.
Data for: Warm night temperature alters paternal allocation strategy in a North temperate zone butterfly
<p class="CxSpFirst">Warming temperatures are greatly impacting wild organisms across the globe. Some of the negative impacts of climate change can be mitigated behaviorally, for example, by changes in habitat and oviposition site choice. Temperatures are reportedly warming faster at night than during the day, yet studies assessing the impacts of increasing night temperature are rare. We used the Finnish Glanville fritillary butterfly (<i>Melitaea cinxia</i>) as study species and exposed adult butterflies of both sexes to warmer night conditions. Under a semi-natural outdoor enclosure, we assessed whether females base their oviposition choices primarily on habitat site characteristics (open, suggestive of dry meadows <i>vs</i> covered by a coarse canopy, suggestive of pastures) or on plant condition (dry <i>vs</i> lush), and if their choice is altered by the thermal conditions experienced at night. As exposure to warmer environmental conditions is expected to increase resting metabolic rate and potentially reduce life expectancy, we further assessed the fitness implications of warm night temperatures. We found that females prefer open sites for oviposition and that females do not switch their oviposition strategy based on the thermal conditions they experienced at night prior to the reproductive event. Exposure to warm nights did not influence female lifespan, but the egg hatching success of their offspring was reduced. In addition, we found that males exposed to warm nights sired larger clutches with higher hatching rate. As warm night exposure reduced male lifespan, this may imply a switch in male resource allocation strategy towards increased offspring quality. The present work adds on to the complex implications of climate warming and highlights the importance of the often-neglected role of males in shaping offspring performance.</p>
Supplementary material 1 from: Runnel V, Wetzel F, Groom Q, Koch W, Pe'er I, Valland N, Panteri E, Kõljalg U (2016) Summary report and strategy recommendations for EU citizen science gateway for biodiversity data. Research Ideas and Outcomes 2: e11563. https://doi.org/10.3897/rio.2.e11563
Species occurrence data sources metadata
Figure 6 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 6 - Automated creation of data paper manuscripts from Ecological Metadata Language (EML) metadata in the ARPHA Writing Tool.
Figure 5 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 5 - The metadata from the GBIF Integrated Publishing Toolkit (IPT) can be downloaded as RTF or EML files and submitted to Pensoft's journals as data paper manuscripts.
Figure 3 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 3 - The user interface of the ARPHA Writing Tool through which single or multiple specimen records from GBIF, BOLD, iDigBio and PlutoF are imported through records identifiers.
Figure 1 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 1 - Recommendation of Dryad to cite both the original article in association with which the data were published and the data themselves.
Figure 7 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 7 - Selection of the journal and "Data Paper (Biosciences)" template in the ARPHA Writing Tool.
Figure 4 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 4 - Occurrence records and taxonomic treatments (if present in the article), published in the Biodiversity Data Journal, are exported in two separate Darwin Core Archives (DwC-A) and are available for direct download or harvesting via web services.
Figure 4 from: Runnel V, Wetzel F, Groom Q, Koch W, Pe'er I, Valland N, Panteri E, Kõljalg U (2016) Summary report and strategy recommendations for EU citizen science gateway for biodiversity data. Research Ideas and Outcomes 2: e11563. https://doi.org/10.3897/rio.2.e11563
Figure 4 - European Starling Sturnus vulgaris (Linnaeus, 1758) occurrences visualized in GBIF portal (A), distribution map in Fauna Europaea (B) and occurrences in Latvian national observation portal dabastati.lv (C).
Figure 3 from: Runnel V, Wetzel F, Groom Q, Koch W, Pe'er I, Valland N, Panteri E, Kõljalg U (2016) Summary report and strategy recommendations for EU citizen science gateway for biodiversity data. Research Ideas and Outcomes 2: e11563. https://doi.org/10.3897/rio.2.e11563
Figure 3 - Peacock Butterfly Aglais io (Linnaeus, 1758) occurrences visualized in GBIF portal (A), distribution map in Fauna Europaea (B) and occurrences in Latvian national observation portal dabastati.lv (C).
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.