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352 results for “Data Enrichment”
Data from: Tree performance in a biodiversity enrichment experiment in an oil palm landscape
1. Large-scale conversion of tropical forests into oil palm monocultures has led to dramatic losses of biodiversity and ecosystem functions. While ecological restoration is urgently needed in many oil palm landscapes, there is a lack of scientific knowledge of sustainable management strategies. 2. We established experimental tree islands of varying sizes (25 m2 to 1600 m2) and diversity levels (1, 2, 3 and 6 species) in an oil palm plantation in Sumatra, Indonesia. Six native multi-purpose tree species including Jengkol (Archidendron pauciflorum), Durian (Durio zibethinus), Petai (Parkia speciosa), Meranti (Shorea leprosula), Sungkai (Peronema canescens), and Jelutung (Dyera polyphylla) were planted between living and felled oil palms. Here, we analyze the controlling factors of tree growth and survival during the first four years at the level of local neighborhood and tree island. 3. We found a significant effect of diversity levels on tree productivity, i.e. basal area was higher in mixed-species than in single-species tree islands. This overyielding was attributed to enhanced tree growth, while mortality had no effect. In the local neighborhood, tree species richness had a positive effect on tree growth during the first year only, indicating that selection and dominance of well-performing species at high level of diversity are most likely driving overyielding. 4. Trees grew better away from living oil palms, suggesting tree-palm competition. Proximity to felled oil palms increased growth especially during the first years, during which the planted trees might have benefited from the additional available space and resources. Despite positive edge effects from the conventional oil palm management in the surrounding, tree island size had an overall positive effect on tree growth. 5. Synthesis and applications. We planted multiple native trees in an oil palm plantation following a tree island pattern. The establishment success differed widely among species. The selection of particular species is a decisive factor to foster a positive relationship between diversity andtree growth. Planting larger tree islands (e.g. 1'600 square meters) is a better option to enhance tree growth, but tree-palm competition implies a trade-off between tree growth and palm oil production locally.
Data from: CO2 enrichment and soil type additively regulate grassland productivity
Atmospheric CO2 enrichment usually increases aboveground productivity (ANPP) of grassland vegetation, but the magnitude of the ANPP-CO2 response differs among ecosystems. Soil properties affect ANPP via multiple mechanisms and vary over topographic to geographic gradients, but have received little attention as potential modifiers of the ANPP-CO2 response. We assessed effects of three soil types, sandy loam, silty clay, and clay, on the ANPP response of perennial C3/C4 grassland communities to a subambient to elevated CO2 gradient over 10 years in Texas, USA. We predicted an interactive, rather than additive, effect of CO2 and soil type on ANPP. Contrary to prediction, CO2 and soil additively influenced grassland ANPP. Increasing CO2 by 250 μL L-1 increased ANPP by 170 g m-2 across soil types. Increased clay content from 10% to 50% among soils reduced ANPP by 50 g m-2. CO2 enrichment increased ANPP via a predominant direct effect accompanied by a smaller indirect effect mediated by successional shift to increased dominance of the C4 tallgrass Sorghastrum nutans. Our results indicate a large, positive influence of CO2 enrichment on grassland productivity that resulted from direct physiological benefits of CO2 augmented by species succession and was expressed similarly across soils of differing physical properties.
Data from: Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901
The mygalomorph family Ctenizidae has a world-wide distribution and currently contains nine genera and 135 species. However, the monophyly of this group has long been questioned on both morphological and molecular grounds. Here, we use Anchored Hybrid Enrichment (AHE) to gather hundreds of loci from across the genome for reconstructing the phylogenetic relationships among the nine genera and test the monophyly of the family. We also reconstruct the possible ancestral ranges of the most inclusive clade recovered. Using AHE, we generate a supermatrix of 565 loci and 115,209 bp for 27 individuals. For the first time, analyses using all nine genera produce results definitively establishing the non-monophyly of Ctenizidae. A lineage formed exclusively by representatives of South African Stasimopus was placed as the sister group to the remaining taxa in the tree, and the Mediterranean Cteniza and Cyrtocarenum were recovered with high support as sister to exemplars of Euctenizidae, Migidae, and Idiopidae. All the remaining genera—Bothriocyrtum, Conothele, Cyclocosmia, Hebestatis, Latouchia, and Ummidia—share a common ancestor. Based on these results, we formally elevate this clade to the level of family. Our results definitively establish both the non-monophyly of the Ctenizidae and non-validity of the subfamilies Ummidiinae and Ctenizinae. In order to establish the placement of the remaining three ctenizid genera, Cteniza, Cyrtocarenum, and Stasimopus, thorough analyses within the context of a complete mygalomorph phylogenetic framework are needed. We formally describe the family Halonoproctidae Pocock 1901 and infer that the family's most recent common ancestor was likely distributed in western North America and Asia.
Data from: Assessing the effects of iron enrichment across holobiont compartments reveals reduced microbial nitrogen fixation in the Red Sea coral Pocillopora verrucosa
The productivity of coral reefs in oligotrophic tropical waters is sustained by an efficient uptake and recycling of nutrients. In reef-building corals, the engineers of these ecosystems, this nutrient recycling is facilitated by a constant exchange of nutrients between the animal host and endosymbiotic photosynthetic dinoflagellates (zooxanthellae), bacteria, and other microbes. Due to the complex interactions in this so-called coral holobiont, it has proven difficult to understand the environmental limitations of productivity in corals. Among others, the micronutrient iron has been proposed to limit primary productivity due to its essential role in photosynthesis and bacterial processes. Here, we tested the effect of iron enrichment on the physiology of the coral Pocillopora verrucosa from the central Red Sea during a 12-day experiment. Contrary to previous reports, we did not see an increase in zooxanthellae population density or gross photosynthesis. Conversely, respiration rates were significantly increased, and microbial nitrogen fixation was significantly decreased. Taken together, our data suggest that iron is not a limiting factor of primary productivity in Red Sea corals. Rather, increased metabolic demands in response to iron enrichment, as evidenced by increased respiration rates, may reduce carbon (i.e., energy) availability in the coral holobiont, resulting in reduced microbial nitrogen fixation. This decrease in nitrogen supply in turn may exacerbate the limitation of other nutrients, creating a negative feedback loop. Thereby, our results highlight that the effects of iron enrichment appear to be strongly dependent on local environmental conditions and ultimately may depend on the availability of other nutrients.
Data from: A proteomic method to extract, concentrate, digest, and enrich peptides from fossils with colored (humic) substances for mass spectrometry analyses
Humic substances are break-down products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution, and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content, and remove humics, producing clean samples easily analyzed by mass spectrometry (MS). This method includes: 1) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; 2) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; 3) centrifugal stage-tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (~800¬–1000 yr) dark with humic content, generating colorless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics, and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.
Data from: CO2 alters community composition and response to nutrient enrichment of freshwater phytoplankton
Nutrients can limit the productivity of ecosystems and control the composition of the communities of organisms that inhabit them. Humans are causing atmospheric CO2 concentrations to reach levels higher than those of the past millions of years while at the same time propagating eutrophication through the addition of nutrients to lakes and rivers. We studied the effect of elevated CO2 concentrations, nutrient addition and their interaction in a series of freshwater mesocosm experiments using a factorial design. Our results highlight the important role of CO2 in shaping phytoplankton communities and their response to nutrient addition. We found that CO2 greatly magnified the increase in phytoplankton growth caused by the increased availability of nutrients. Elevated CO2 also caused changes in phytoplankton community composition. As predicted from physiology and laboratory experiments, the taxonomic group that was most limited by current day CO2 concentrations, chlorophytes, increased in relative frequency at elevated CO2. This predictable change in community composition with changes in CO2 is not altered by changes in the availability of other nutrients.
Data from: Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome
Heterochromatic regions of the genome are repeat-rich and poor in protein coding genes, and are therefore underrepresented in even the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization in D. melanogaster, we develop an assembly strategy involving the in silico enrichment of heterochromatic long single-molecule reads and use these reads to create targeted de novo assemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends the D. melanogaster reference genome by 11.9 Mb, closes 43.8% of the gaps, and improves overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted us to study the organization of repeats and genes along the Y chromosome. We detected a high rate of duplication to the pericentric regions of the Y chromosome from other regions in the genome. Most of these duplicated genes exist in multiple copies. We detail the evolutionary history of one sex-linked gene family—crystal-Stellate. While the Y chromosome does not undergo crossing over, we observed high gene conversion rates within and between members of the crystal-Stellate gene family, Su(Ste), and PCKR, compared to genome-wide estimates. Our results suggest that gene conversion and gene duplication play an important role in the evolution of Y-linked genes.
Data from: Teasing apart plant community responses to N enrichment: the roles of resource limitation, competition and soil microbes
Although ecologists have documented the effects of nitrogen enrichment on productivity, diversity and species composition, we know little about the relative importance of the mechanisms driving these effects. We propose that distinct aspects of environmental change associated with N enrichment (resource limitation, asymmetric competition, and interactions with soil microbes) drive different aspects of plant response. We test this in greenhouse mesocosms, experimentally manipulating each factor across three ecosystems: tallgrass prairie, alpine tundra and desert grassland. We found that resource limitation controlled productivity responses to N enrichment in all systems. Asymmetric competition was responsible for diversity declines in two systems. Plant community composition was impacted by both asymmetric competition and altered soil microbes, with some contributions from resource limitation. Results suggest there may be generality in the mechanisms of plant community change with N enrichment. Understanding these links can help us better predict N response across a wide range of ecosystems.
Data from: Warming reduces the effects of enrichment on stability and functioning across levels of organization in an aquatic microbial ecosystem
Warming and nutrient enrichment are major environmental factors shaping ecological dynamics. However, cross-scale investigation of their combined effects by linking theory and experiments is lacking. We collected data from aquatic microbial ecosystems investigating the interactive effects of warming (constant and rising temperatures) and enrichment across levels of organization and contrasted them with community models based on metabolic theory. We found high agreement between our observations and theoretical predictions: we observed in many cases the predicted antagonistic effects of high temperature and high enrichment across levels of organization. Temporal stability of total biomass decreased with warming but did not differ across enrichment levels. Constant and rising temperature treatments with identical mean temperature did not show qualitative differences. Overall, we conclude that model and empirical results are in broad agreement due to robustness of the effects of temperature and enrichment, that the mitigating effects of temperature on effects of enrichment may be common, and that models based on metabolic theory provide qualitatively robust predictions of the combined ecological effects of enrichment and temperature.
Data from: Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates
Recent studies have advocated biomonitoring using DNA techniques. In this study, two high-throughput sequencing (HTS)-based methods were evaluated: amplicon metabarcoding of the cytochrome C oxidase subunit I (COI) mitochondrial gene and gene enrichment using MYbaits (targeting nine different genes including COI). The gene-enrichment method does not require PCR amplification and thus avoids biases associated with universal primers. Macroinvertebrate samples were collected from 12 New Zealand rivers. Macroinvertebrates were morphologically identified and enumerated, and their biomass determined. DNA was extracted from all macroinvertebrate samples and HTS undertaken using the illumina miseq platform. Macroinvertebrate communities were characterized from sequence data using either six genes (three of the original nine were not used) or just the COI gene in isolation. The gene-enrichment method (all genes) detected the highest number of taxa and obtained the strongest Spearman rank correlations between the number of sequence reads, abundance and biomass in 67% of the samples. Median detection rates across rare (<1% of the total abundance or biomass), moderately abundant (1–5%) and highly abundant (>5%) taxa were highest using the gene-enrichment method (all genes). Our data indicated primer biases occurred during amplicon metabarcoding with greater than 80% of sequence reads originating from one taxon in several samples. The accuracy and sensitivity of both HTS methods would be improved with more comprehensive reference sequence databases. The data from this study illustrate the challenges of using PCR amplification-based methods for biomonitoring and highlight the potential benefits of using approaches, such as gene enrichment, which circumvent the need for an initial PCR step.
Data from: Hierarchical Hybrid Enrichment: multi-tiered genomic data collection across evolutionary scales, with application to chorus frogs (Pseudacris)
Determining the optimal targets of genomic sub-sampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for sub-sampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first we compare the benefits of target loci developed for deep- and shallow-scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography) and within a hybrid zone (population genomics). Specifically, we target evolutionary conserved loci that are appropriate for deep phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer longstanding evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels, we (a) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis-testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; (b) estimate the phylogeographic history of P. feriarum, which reveals five independent invasions of sympatry by this species to form replicated reinforcement contact zones with P. nigrita with ongoing gene flow into sympatry; and (c) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is much lower than previously found by microsatellite-based studies. We find that the hierarchical hybrid enrichment approach offers an efficient, multi-tiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales.
Data from: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life
Background: Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Results: Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. Conclusions: The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
Data from: Selective increases in inter-individual variability in response to environmental enrichment in female mice
One manifestation of individualization is a progressively differential response of individuals to the non-shared components of the same environment. Individualization has practical implications in the clinical setting, where subtle differences between patients are often decisive for the success of an intervention, yet there has been no suitable animal model to study its underlying biological mechanisms. Here we show that enriched environment (ENR) can serve as a model of brain individualization. We kept 40 isogenic female C57BL/6JRj mice for 3 months in ENR and compared these mice to an equally sized group of standard-housed control animals, looking at the effects on a wide range of phenotypes in terms of both means and variances. Although ENR influenced multiple parameters and restructured correlation patterns between them, it only increased differences among individuals in traits related to brain and behavior (adult hippocampal neurogenesis, motor cortex thickness, open field and object exploration), in agreement with the hypothesis of a specific activity-dependent development of brain individuality.
16S rRNA gene data for aerobic BTEX-degrading enrichments exposed to sulfonamide polyfluorinated substances in fire-fighting foams and transformation products
<p>Per- and polyfluoroalkyl substances (PFASs) from aqueous film forming foams (AFFFs) can hinder bioremediation of co-contaminants, such as trichloroethene (TCE) and benzene, toluene, ethylbenzene, and xylene (BTEX). Anaerobic dechlorination can require bioaugmentation of <em>Dehalococcoides</em> and for BTEX, oxygen is often sparged to stimulate in-situ aerobic biodegradation. We tested PFAS inhibition to TCE and BTEX bioremediation by exposing an anaerobic TCE-dechlorinating co-culture, an aerobic BTEX-degrading enrichment culture, and an anaerobic toluene-degrading enrichment culture to n-dimethyl perfluorohexane sulfonamido amine (AmPr-FHxSA), perfluorohexane sulfonamide (FHxSA), perfluorohexane sulfonic acid (PFHxS), or non-fluorinated surfactant sodium dodecyl sulfate (SDS). The anaerobic TCE-dechlorinating co-culture was resistant to individual PFASs exposures but was inhibited by >1,000x diluted AFFF. FHxSA and AmPr-FHxSA inhibited the aerobic BTEX-degrading enrichment. The anaerobic toluene-degrading enrichment was not inhibited by AFFF or individual PFASs. Increases in amino acids in the anaerobic TCE-dechlorinating co-culture compared to the control indicated stress response, while the BTEX culture exhibited lower concentrations of all amino acids upon exposure to most surfactants (both fluorinated and non-fluorinated) compared to the control. These data suggest the main mechanisms of microbial toxicity are related to interactions with cell membrane synthesis as well as protein stress signaling.</p>
Investigating the utility of Anchored Hybrid Enrichment data to resolve the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes
<p>The Killifishes (Blenniiformes: Cyprinodontoidea) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to resolve the phylogenetic relationships among the families within the Superfamily Cyprinodontoidea (formerly the Cyprindontiformes). This study included more than 100 individuals, representing all sixteen families within Cyprinodontoidea, including many recently diagnosed families. We recovered an average of 244 loci per individual. These data were submitted to phylogenetic analyses (RaxML and ASTRAL) and although we recovered many of the same relationships as in previous studies of the group, several novel sets of relationships for other families also were recovered. In addition, two well-established clades were recovered as monophyletic and are in agreement with most previous studies. We also assessed the degree of gene tree discordance in our dataset to evaluate support for alternative topological hypotheses for interfamilial relationships within the Cyprinodontoidea using a variety of different analyses. The results from this study will provide a robust, historical framework needed to investigate a plethora of biogeographic, taxonomic, ecological, and physiological questions for this group of fishes.</p>
Data for Individual and combined impacts of carbon dioxide enrichment, heatwaves, flow velocity variability and fine sediment deposition on stream invertebrate communities
Open the record for dataset details and reuse information.
Data from: Arbuscular mycorrhizal communities respond to nutrient enrichment and plant invasion in phosphorus-limited eucalypt woodlands
<p>Arbuscular mycorrhizal fungi (AMF) facilitate ecosystem functioning through provision of plant hosts with phosphorus (P), especially where soil P is limiting. Changes in soil nutrient regimes are expected to impact AMF, but the direction of the impact may depend on context. We predicted that nitrogen (N)-only enrichment promotes plant invasions and exacerbates their P limitation, increasing the utility of AMF and promoting AMF diversity. We expected that enrichment with N, P and other nutrients similarly promotes plant invasions, but decreases the benefit and diversity of AMF because P is readily available for both native and exotic plants. We tested these hypotheses in eucalypt woodlands of south-western Australia, that occur on soils naturally low in P. We evaluated AMF communities within three modified ground-layer states representing different types of nutrient enrichment and associated plant invasions. We compared these modified states to near-natural reference woodlands. AMF richness varied across ground-layer states. The moderately invaded/N-enriched state showed the highest AMF richness, while the highly invaded/NP-enriched state showed the lowest AMF richness. The reference state and the weakly invaded/enriched state were intermediate. AMF richness and colonisation were higher in roots of exotic than native plant species. AMF community composition differed among ground-layer states, with the highly invaded/NP-enriched state being most distinct. Distinctions among states were often driven by family-level patterns. Reference and moderately invaded/N-enriched states each supported distinct groups of zero-radius operational taxonomic units (zOTUs) in Acaulosporaceae, Gigasporaceae and Glomeraceae, whereas Gigasporaceae and Glomeraceae were nearly absent from the highly invaded/NP-enriched state. Further, Diversisporaceae and Glomeraceae were most diverse in the moderately invaded/N-enriched state.</p> <p> Synthesis. Both the nature of soil nutrient enrichment and plant provenance matter for AMF. N-only enrichment of low-P soils increased AMF richness, likely due to introduction of AMF-dependent exotic plant species and exacerbation of their P-limitation. In contrast, multi-nutrient enrichment, decreased AMF richness potentially due to a decrease in host dependence on AMF, regardless of host provenance. The changes in AMF community composition with nutrient enrichment and plant invasion warrants further research into predicting the functional implications of these changes.</p>
Data for: Akhund-Zade et al The effect of environmental enrichment on behavioral variability depends on genotype, behavior, and type of enrichment
<p>Data and analysis scripts for the manuscript entitled "The effect of environmental enrichment on behavioral variability depends on genotype, behavior, and type of enrichment" by Jamilla Akhund-Zade et al. </p>
enriched_piles_paper_data_archive
<p>Archive for data from:<br> Effects of heat-producing elements on the stability of deep mantle thermochemical piles<br> R.I. Citron, D.L. Lourenco, A.J. Wilson, A.G. Grima, S.A. Wipperfurth, M.L Rudolph, S. Cottaar, L. Montesi</p>
Supplementary Material for "Integrating Security-Enriched Data Flow Diagrams Into Architecture-Based Confidentiality Analysis"
<p>Supplementary material for the paper "Integrating Security-Enriched Data Flow Diagrams Into Architecture-Based Confidentiality Analysis". For more information, please see the README.md. For even more information please visit https://dataflowanalysis.org</p>
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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.