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914 results for “filtered”
Filtered SNPs for wild Paspalum vaginatum and Paspalum distichum
<p>Filtered SNP calls in .ped format from "Hybridization, polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (<em>Paspalum vaginatum</em>)". We used GBS to genotype 218 <em>P. vaginatum </em>and <em>P. distichum</em> accessions collected from the US Gulf and Atlantic coasts plus available USDA germplasm. We confirm that <em>P. vaginatum </em>and <em>P. distichum </em>are genetically distinct and that the coarse-textured ecotype of <em>P. vaginatum </em>is composed of hybrids between fine-textured accessions and an unidentified paspalum species. These hybrids vary in ploidy and subgenome composition which may influence their geographic patterns of adaptation to saline environments.</p>
Data from: Choosing wavelet methods, filters, and lengths for functional brain network construction
Wavelet methods are widely used to decompose fMRI, EEG, or MEG signals into time series representing neurophysiological activity in fixed frequency bands. Using these time series, one can estimate frequency-band specific functional connectivity between sensors or regions of interest, and thereby construct functional brain networks that can be examined from a graph theoretic perspective. Despite their common use, however, practical guidelines for the choice of wavelet method, filter, and length have remained largely undelineated. Here, we explicitly explore the effects of wavelet method (MODWT vs. DWT), wavelet filter (Daubechies Extremal Phase, Daubechies Least Asymmetric, and Coiflet families), and wavelet length (2 to 24)—each essential parameters in wavelet-based methods—on the estimated values of graph metrics and in their sensitivity to alterations in psychiatric disease. We observe that the MODWT method produces less variable estimates than the DWT method. We also observe that the length of the wavelet filter chosen has a greater impact on the estimated values of graph metrics than the type of wavelet chosen. Furthermore, wavelet length impacts the sensitivity of the method to detect differences between health and disease and tunes classification accuracy. Collectively, our results suggest that the choice of wavelet method and length significantly alters the reliability and sensitivity of these methods in estimating values of metrics drawn from graph theory. They furthermore demonstrate the importance of reporting the choices utilized in neuroimaging studies and support the utility of exploring wavelet parameters to maximize classification accuracy in the development of biomarkers of psychiatric disease and neurological disorders.
Data from: Dense dwarfs versus gelatinous giants: the trade-offs and physiological limits determining the body plan of planktonic filter feeders
Most marine plankton have a high energy (carbon) density, but some are gelatinous with approximately hundred times more watery bodies. How do those distinctly different body plans emerge and what are the trade-offs? We address this question by modeling the energy budget of planktonic filter feeders across life forms from micron-sized unicellular microbes like choanoflagellates to centimeter-sized gelatinous tunicates such as salps. We find two equally successful strategies, one being small with high energy density (dense dwarf), and the other being large with low energy density (gelatinous giant). The constraint that forces large - but not small - filter feeders to be gelatinous is identified as a lower limit to the size-specific filter area, below which the energy costs lead to starvation. A further limit is found from the maximum size-specific motor force that restricts the access to optimum strategies. The quantified constraints are discussed in the context of other resource acquisition strategies. We argue that interception feeding strategies can only be accessed by large organisms if they are gelatinous. On the other hand, organisms that use remote prey sensing do not need to be gelatinous, even if they are large.
Data from: Depth image super-resolution reconstruction based on a modified joint trilateral filter
Depth image super-resolution (SR) is a technique that utilizes signal processing technology to enhance the resolution of a low-resolution (LR) depth image. Generally, the external database or high-resolution (HR) images are needed for acquiring the priori information to support the SR reconstruction. To overcome the limitation, a depth image SR method which does not need the reference of any external images is proposed. In the paper, a high-quality edge map is firstly constructed using a sparse coding method, which uses a dictionary learned from the original images themselves at different scales. Then, the high-quality edge map is used to guide the interpolation for depth images by a modified joint trilateral filter. During the interpolation, some information of gradient and structural similarity (SSIM) are added to preserve the detailed information and suppress the noise. The proposed method not only can preserve the sharpness of image edge, but also can avoid the dependence on database. Experimental results show the proposed method is superior to some state-of-the-art depth image SR methods.
Data from: Habitat filtering determines the functional niche occupancy of plant communities worldwide
How the patterns of niche occupancy vary from species-poor to species-rich communities is a fundamental question in ecology that has a central bearing on the processes that drive patterns of biodiversity. As species richness increases, habitat filtering should constrain the expansion of total niche volume, while limiting similarity should restrict the degree of niche overlap between species. Here, by explicitly incorporating intraspecific trait variability, we investigate the relationship between functional niche occupancy and species richness at the global scale. We assembled 21 datasets worldwide, spanning tropical to temperate biomes and consisting of 313 plant communities representing different growth forms. We quantified three key niche occupancy components (the total functional volume, the functional overlap between species and the average functional volume per species) for each community, related each component to species richness, and compared each component to the null expectations. As species richness increased, communities were more functionally diverse (an increase in total functional volume), and species overlapped more within the community (an increase in functional overlap) but did not more finely divide the functional space (no decline in average functional volume). Null model analyses provided evidence for habitat filtering (smaller total functional volume than expectation), but not for limiting similarity (larger functional overlap and larger average functional volume than expectation) as a process driving the pattern of functional niche occupancy. Synthesis. Habitat filtering is a widespread process driving the pattern of functional niche occupancy across plant communities and coexisting species tend to be more functionally similar rather than more functionally specialized. Our results indicate that including intraspecific trait variability will contribute to a better understanding of the processes driving patterns of functional niche occupancy.
Data from: Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference
Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms.
Data from: Both trait-neutrality and filtering effects are validated by the vegetation patterns detected in the functional recovery of sand grasslands
Neutral theory of species assembly means that species assembly is governed by stochastic dispersal processes and fluctuations in established populations. An alternative theory suggests that assembly is strongly determined by functional trait filtering governed by abiotic and biotic filtering selecting species from the local species pool. To test these assumptions, in the current paper we analysed vegetation changes in the first 12 years of succession after heavy goose grazing on acidic sand. With trait-based analyses using permanent plots we addressed the following hypotheses: (i) High fluctuations in the trait values are typical in the first years; later a temporally divergent change in the trait patterns of sites with different vertical position became characteristic. (ii) In the functional diversity of regenerative and vegetative traits we expected different temporal patterns. We confirmed the first hypothesis, as in the first few years most traits displayed high fluctuations with no clear patterns. Our findings weakly supported the second hypothesis; while there were distinct patterns detected in the functional richness of traits, functional divergence and evenness displayed no clear distinctive patterns. We can conclude that both trait neutrality and filtering effects operate in the vegetation changes of the first period of secondary succession.
Data from: Process-based species pools reveal the hidden signature of biotic interactions amid the influence of temperature filtering
A persistent challenge in ecology is to tease apart the influence of multiple processes acting simultaneously and interacting in complex ways to shape the structure of species assemblages. We implement a heuristic approach that relies on explicitly defining species pools and permits assessment of the relative influence of the main processes thought to shape assemblage structure: environmental filtering, dispersal limitations and biotic interactions. We illustrate our approach using data on the assemblage composition and geographic distribution of hummingbirds, a comprehensive phylogeny and morphological traits. The implementation of several process-based species pool definitions in null models suggests that temperature, but not precipitation or dispersal limitation, acts as the main regional filter of assemblage structure. Incorporating this environmental filter directly into the definition of assemblage-specific species pools revealed an otherwise hidden pattern of phylogenetic evenness, indicating that biotic interactions might further influence hummingbird assemblage structure. Such hidden patterns of assemblage structure call for a reexamination of a multitude of phylogenetic- and trait-based studies that did not explicitly consider potentially important processes in their definition of the species pool. Our heuristic approach provides a transparent way to explore patterns and refine interpretations of the underlying causes of assemblage structure.
The application of filter based assembly model to develop best practices for Pannonian sand grassland restoration
<p>Data used for a manuscript sent to JAE in 2015.</p>
DOHH2 hg38 H3K4me1 ChIP-seq Dataset filtered for Unique Multiread Mappability
<p>DOHH2 hg38 H3K4me1 ChIP-seq Dataset filtered for Unique Multiread Mappability</p>
Data for manuscript "Integrated microwave photonic notch filter using a heterogeneously integrated Brillouin and active-silicon photonic circuit"
<p>Experimental data and scripts to plot results for manuscript "Integrated microwave photonic notch filter using a heterogeneously integrated Brillouin and active-silicon photonic circuit"</p>
Raw data associated to the paper "Analysis of species pair associations combined with functional traits reveals the effects of environmental filtering and biotic interactions in an unmanaged temperate forest"
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Online repository for: "Sorting microparticle mixtures by multiple properties in a single dielectrophoretic filter"
<p>Please consult the Data_Overview file for information on the content of this online repository.</p>
Figure 3 from: Mesa-Varona O, Plaza-Rodríguez C, Valentin L, Filter M (2024) WarenstromInfo: a tool for the easy extraction and visualisation of trade flow data. Research Ideas and Outcomes 10: e112227. https://doi.org/10.3897/rio.10.e112227
Figure 3 WI User Interfaces: UI3. In the UI3, countries involved in the query can be selected (I and J). Input data from UI3 are included in the query by clicking "Next" (K).
Figure 5 from: Mesa-Varona O, Plaza-Rodríguez C, Valentin L, Filter M (2024) WarenstromInfo: a tool for the easy extraction and visualisation of trade flow data. Research Ideas and Outcomes 10: e112227. https://doi.org/10.3897/rio.10.e112227
Figure 5 A screenshot of the BACI SQLite database builder workflow. The workflow presented here is organised into two main sections, with interconnected KNIME nodes displayed in each section. The yellow-boxed nodes are responsible for creating and loading the database where the data are stored. The green-boxed section shows: Locate BACI csv files (BACI files must have been previously downloaded and stored in a folder that is pointed in the "List Files/Folders" KNIME node). Split the files according to the HS data provided and Load csv files, filtering and storage in SQLite database (carried out in each consecutive metanode). In this last section, the user can decide not to filter the data or customise the filter criteria of the BACI database, including more types of data apart from those agrifood data that are included in the default configuration of the workflow. Variable flow connections (red lines) can be removed in the second green-boxed section, if an HPC (High Performance Computing) service is available. This will allow the workflow to run much faster as the nodes will not be executed one after the other, but all at the same time.
Figure 4 from: Mesa-Varona O, Plaza-Rodríguez C, Valentin L, Filter M (2024) WarenstromInfo: a tool for the easy extraction and visualisation of trade flow data. Research Ideas and Outcomes 10: e112227. https://doi.org/10.3897/rio.10.e112227
Figure 4 WI User Interfaces: UI4. The UI4 provides an overview of the final WI outputs, displaying a list with the initial input variables (L), three maps displaying trade flows (a world map, a world map focused on Europe and an European map) (M), download options (N), slide filter bars for value and weight preview (O) and trade flow data in the preview table (P).
Figure 1 from: Mesa-Varona O, Plaza-Rodríguez C, Valentin L, Filter M (2024) WarenstromInfo: a tool for the easy extraction and visualisation of trade flow data. Research Ideas and Outcomes 10: e112227. https://doi.org/10.3897/rio.10.e112227
Figure 1 WI User Interfaces: UI1. In the UI1, users can select the desired database (EUROSTAT/BACI) (A). The database selection is concluded by clicking "Next" (B), which will lead the user to the following UI.
Figure 2 from: Mesa-Varona O, Plaza-Rodríguez C, Valentin L, Filter M (2024) WarenstromInfo: a tool for the easy extraction and visualisation of trade flow data. Research Ideas and Outcomes 10: e112227. https://doi.org/10.3897/rio.10.e112227
Figure 2 User Interfaces: UI2. In the UI2, the following input options can be selected: standard selection (C), time range of the search (D), the email option (E), the pre-filter option (F) and the table with the embedded live filter (G). Input data from UI2 are processed by clicking "Next" (H).
PanRBPNet ENCODE Dataset (filtered by min max-positional CL count of 5, across eCLIP and SMInput)
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PanRBPNet ENCODE Dataset (filtered by min max-positional CL count of 3, across eCLIP and SMInput)
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ScienceDex guides
Understand access before you commit
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.