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7,195 results for “SET”
Data from: Incongruence between morphological data sets: an example from the evolution of endoparasitism among parasitic wasps (Hymenoptera: Braconidae)
Phylogenetic analyses of molecular and morphological data sets for a group of parasitic wasps (Hymenoptera: Braconidae) give strikingly different results. The molecular data indicate that the major life history transition from ectoparasitism to endoparasitism has occurred independently several times within the family while the morphological data indicate a single origin. Similar incongruent topologies are obtained if the morphological data are partitioned by either of two methods: distinguishing (1) characters of the larval stage and female reproductive system, or (2) characters selected individually by the authors prior to the analysis as likely to be mechanistically associated with endo/ectoparasitism. This result is supported by significant differences in tests of incongruence, and we propose that it is caused by convergence among morphological characters resulting from a shared life history strategy.
Data from: A fuzzy-set-theory-based approach to analyze species membership in DNA barcoding
Reliable assignation of an unknown query sequence to its correct species remains a methodological problem for the growing field of DNA barcoding. While great advances have been achieved recently, species identification from barcodes can still be unreliable if the relevant biodiversity has been insufficiently sampled. We here propose a new notion of species membership for DNA barcoding - fuzzy membership, based on fuzzy set theory - and illustrate its successful application to four real datasets (bats, fishes, butterflies and flies) with more than 5000 random simulations. Two of the datasets comprise especially dense species/population level samples. In comparison with current DNA barcoding methods, the newly proposed minimum distance (MD) plus fuzzy set approach, and another computationally simple method, "best close match", outperform two computationally sophisticated Bayesian and BootstrapNJ methods. The new method proposed here has great power in reducing false positive species identification compared with other methods when conspecifics of the query are absent from the reference database.
Data from: Does local conspecific density and floral display size influence fruit set via pollinator visitation in Orchis militaris?
Plant density varies naturally, from isolated plants to clumped individuals, and can influence pollinator foraging behaviour and plant reproductive success. The effect of conspecific density could depend on the pollination system, and deceptive species differ from rewarding ones in this regard, a high density being often associated with low fruit set in deceptive plants. In our study, we aimed to determine how local conspecific density and floral display size (i.e. number of flowers per plant) affect fruit set in a deceptive orchid (Orchis militaris) through changes in pollinator visitation. We measured fruit set in a natural population and recorded pollinator abundance and foraging behaviour within plots of different O. militaris densities. Detailed data were recorded for the most abundant potential pollinators of O. militaris, i.e. solitary bees. Floral display size was negatively correlated to fruit set in medium-density plots, but uncorrelated in low- and high-density plots. Plot density had no effect on solitary bee abundance and visitation, which may be due to low pollinator abundance within the study site. The proportion of visited flowers per inflorescence was negatively influenced by floral display size, which is in line with previous studies. In addition, solitary bees spent decreasing time in successive flowers within an inflorescence, and the time spent per flower was negatively affected by ambient temperature. Our results suggest that pollinator behaviour during visitation is poorly linked to pollen deposition and reproductive success in O. militaris.
Data from: Multiple molecular data sets suggest independent origins of highly eusocial behavior in bees (Hymenoptera:Apinae)
Different views of the pattern of social evolution among the highly eusocial bees have arisen as a result of discordance between past molecular and morphology-based phylogenies. Here we present new data and taxa for four molecular data sets and reassess the morphological characters available to date. We show that there is no significant character incongruence between four molecular data sets (two nuclear and two mitochondrial) but that there is highly significant character incongruence, which leads to topological incongruence, between the molecular and morphological data. We investigate the effects of using different outgroup combinations to root the estimated tree. We also consider various ways in which biases in the sequence data could be misleading, employing several maximum likelihood models, LogDet corrections, and spectral analyses. Ultimately, we concede that there is strong discordance between the molecular and morphological data partitions, and that the conditional combination approach is appropriately applied in this case. We also find for the molecular trees that there are two equally well supported placements of the root, one supported by 16S and 28S sequences, the other supported by cyt b and opsin. The strength of the evidence leads us to accept two equally well supported hypotheses based on analyses of the molecular data sets. These are the most rigorously supported hypotheses of corbiculate bee relationships at this time, and frame our argument that highly eusocial behavior within the corbiculate bees evolved twice independently.
Data from: Social setting, intuition and experience in laboratory experiments interact to shape cooperative decision-making
Recent studies suggest that cooperative decision-making in one-shot interactions is a history-dependent dynamic process: promoting intuition versus deliberation typically has a positive effect on cooperation (dynamism) among people living in a cooperative setting and with no previous experience in economic games on cooperation (history dependence). Here, we report on a laboratory experiment exploring how these findings transfer to a non-cooperative setting. We find two major results: (i) promoting intuition versus deliberation has no effect on cooperative behaviour among inexperienced subjects living in a non-cooperative setting; (ii) experienced subjects cooperate more than inexperienced subjects, but only under time pressure. These results suggest that cooperation is a learning process, rather than an instinctive impulse or a self-controlled choice, and that experience operates primarily via the channel of intuition. Our findings shed further light on the cognitive basis of human cooperative decision-making and provide further support for the recently proposed social heuristics hypothesis.
Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
Data from: Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms
To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and three outgroups. Separate data sets of 18S rDNA (1,855 bp), rbc L (1,428 bp), and atp B (1,450 bp) sequences were combined into a single matrix 4,733 bp in length. Analyses of the combined data set show great improvements in computer run times compared to those of the separate data sets and of the data sets combined in pairs. Six searches of the 18S rDNA rbc L atp B data set were conducted; in all cases TBR branch swapping was completed, generally within a few days. In contrast, TBR branch swapping was not completed for any of the three separate data sets, or for the pairwise combined data sets. These results illustrate that it is possible to conduct a thorough search of tree space with large data sets, given sufficient signal. In this case, and probably most others, sufficient signal for a large number of taxa can only be obtained by combining data sets. The combined data sets also have higher internal support for clades than the separate data sets, and more clades receive bootstrap support of 50% in the combined analysis than in analyses of the separate data sets. These data suggest that one solution to the computational and analytical dilemmas posed by large data sets is the addition of nucleotides, as well as taxa.
Data from: Phylogenetic Congruence and Discordance Among One Morphological and Three Molecular Data Sets from Pontederiaceae
A morphological data set and three sources of data from the chloroplast genome (two genes and a restriction-site survey) were used to reconstruct the phylogenetic history of the Pickerelweed family Pontederiaceae. The chloroplast data are converging to a single tree, presumably the true chloroplast phylogeny of the family. Unrooted trees estimated from the three chloroplast data sets were identical or extremely similar in shape to each other, mostly robustly supported and there was no evidence of significant heterogeneity among them. The few topological differences seen among unrooted trees from each chloroplast data set are probably artifacts of sampling error on short branches. Despite well documented differences in rates of evolution for different characters in individual data sets, equally weighted parsimony therefore permits accurate reconstructions of chloroplast relationships in Pontederiaceae. A separate morphology-based data set yielded trees that were very different from the chloroplast trees. While there was substantial support by the morphological evidence for several major clades supported by chloroplast trees, most of the conflicting phylogenetic structure on the morphology trees was not robust. Nonetheless, several statistical tests of incongruence indicate significant heterogeneity between molecules and morphology. The source of this apparent incongruence appears to be a low ratio of phylogenetic signal to noise in the morphological data.
Data from: Silver nanoparticles as a medical device in healthcare settings: a five-step approach for candidate screening of coating agents
Silver nanoparticle-based antimicrobials can promote a long lasting bactericidal effect without detrimental toxic side effects. However, there is not a clear and complete protocol to define and relate the properties of the particles (size, shape, surface charge, ionic content) with their specific activity. In this paper, we propose an effective multi-step approach for the identification of a 'purpose-specific active applicability window' to maximize the antimicrobial activity of medical devices containing silver nanoparticles (Ag NPs) (such as surface coaters), minimizing any consequent risk for human health (safety by design strategy). The antimicrobial activity and the cellular toxicity of four types of Ag NPs, differing in their coating composition and concentration have been quantified. Through the implementation of flow-field flow fractionation, Ag NPs have been characterized in terms of metal release, size and shape. The particles are fractionated in the process while being left unmodified, allowing for the identification of biological particle-specific contribution. Toxicity and inflammatory response in vitro have been assessed on human skin models, while antimicrobial activity has been monitored with both non-pathogenic and pathogenic Escherichia coli. The main benefit associated with such approach is the comprehensive assessment of the maximal effectiveness of candidate nanomaterials, while simultaneously indexing their properties against their safety.
Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them
Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group.
Evaluation Data Set
<p>Evaluation data set of dissertation:</p> <p>Kersch, Mike, Evaluation von Trading-Algorithmen unter realen Marktbedingungen: Ansätze zur praktischen Anwendbarkeit, Anforderungen, Implementierung, Dissertation, Universität des Saarlandes, 2015.</p>
Reason for encounter: a superior description of the epidemiology and the management of flu syndromes in the Italian family medicine setting.
<p>Dataset of the research.</p>
The Silva taxonomic training set formatted for DADA2
<p>These DADA2-formatted training fastas were derived from Silva version 123. They are available under the Silva dual-licensing model for academia and commercial users: https://www.arb-silva.de/silva-license-information/</p>
Set of basic stimuli used for our experiments
<p>Set of basic stimuli used for our experiments. Including a short description</p>
Open Turbulent Image Set (OTIS) Grayscale-PNG Version
<p>This the grayscale version of the OTIS dataset saved in PNG format</p>
Open Turbulent Image Set (OTIS) Color-PNG Version
<p>This the colored version of the OTIS dataset saved in PNG format</p>
Open Turbulent Image Set (OTIS) Grayscale-Matlab Version
<p>This the grayscale version of the OTIS dataset saved in Matlab format</p>
Open Turbulent Image Set (OTIS) Color-Matlab Version
<p>This the colored version of the OTIS dataset saved in Matlab format</p>
Data set
<p>Normalised residual levels under different test conditions.</p>
ASD specific data set An. aging
<p>These are the *.asd specific files from the spectrometer.</p>
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.