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235 results for “Redundancy”
Non-redundant metagenome-assembled genomes of activated sludge reactors at different disturbances and scales
<p>Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenomic data and can be assigned to known taxa or lead to uncovering novel ones. MAGs can provide insights into how microbes interact with the environment. Here, we performed genome-resolved metagenomics on sequencing data from four studies using sequencing batch reactors at microcosm (~25 mL) and mesocosm (~4 L) scales inoculated with sludge from full-scale wastewater treatment plants. These studies investigated how microbial communities in such plants respond to two environmental disturbances: the presence of toxic 3-chloroaniline and changes in organic loading rate. We report 839 non-redundant MAGs with at least 50% completeness and 10% contamination (MIMAG medium-quality criteria). From these, 399 are of putative high-quality, while sixty-seven meet the MIMAG high-quality criteria. MAGs in this catalogue represent the microbial communities in sixty-eight laboratory-scale reactors used for the disturbance experiments, and in the full-scale wastewater treatment plant which provided the source sludge. This dataset can aid meta-studies aimed at understanding the responses of microbial communities to disturbances, particularly as ecosystems confront rapid environmental changes.</p>
Dataset: Redox-Activated Proton Transfer through a Redundant Network in the Qo Site of Cytochrome bc1
<p>This dataset contains initial molecular configurations and an example script used with the pDynamo3 library to obtain the results published in the paper "Redox-Activated Proton Transfer through a Redundant Network in the Qo Site of Cytochrome bc1" by Guilherme M. Arantes (USP, Brazil).</p>
Supplementary Figures 1 and 2, research article "Can Moving in a Redundant Workspace Accelerate Motor Adaptation?"
<p><strong>Supplementary Figures 1 and 2. Movement endpoints during the priming phase (figure 1) and test phase (figure 2), shown separately for each target location (colors) and target shape (background shading). </strong>Each panel shows movement endpoints for a different subjects (the order of subjects is identical in figure 1 and 2). The home position is at (0,0). Movements to different target locations are indicated by different colors (purple = left target, green = center targer, red = right target). Thick outlines around movement endpoints indicate outliers excluded from all analyses.</p>
Supplementary information for: Redundancy analysis, genome-wide association studies, and the pigmentation of brown trout (Salmo trutta L.)
<p><span>The association of molecular variants to phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multi-trait GWAS to explore the molecular basis of pigmentation variation in brown trout (<em>Salmo</em> <em>trutta</em>) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multi-trait GWAS allowed us to extract 337 independent "colour patterning loci" (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (<em>i</em>) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (<em>ii</em>) were found associated with</span><span> 218 </span><span>candidate genes, including 197 genes </span><span>formerly mentioned in the literature dealing with skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (<em>Onchorhynchus</em> <em>mykiss</em>)</span><span>, and (<em>iii</em>) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.</span></p>
Low redundancy and complementarity shape ecosystem functioning in a low-diversity ecosystem
<p>Data used in the publication of "Low redundancy and complementarity shape ecosystem functioning in a low-diversity ecosystem" in the Journal of Animal Ecology.</p>
MGBC-26640: high quality, non-redundant genome annotations (part 2)
<p>Genome annotations (GenBank flat files, .gbk) for the 26,640 non-redundant, high-quality genomes of the MGBC (part 2: MGBC130000 to MGBC167528).</p> <p>Please note that due to the 50Gb file size limit, part 1 of the MGBC annotations can be found at DOI: 10.5281/zenodo.5534741.</p>
MGBC-26640: high quality, non-redundant genome annotations (part 1)
<p>Genome annotations (GenBank flat files, .gbk) for the 276 genomes of the MCC and the 26,640 non-redundant, high-quality genomes of the MGBC (part 1: MGBC000001 to MGBC129999).</p> <p>Please note that due to the 50Gb file size limit, part 2 of the MGBC annotations can be found at DOI: 10.5281/zenodo.5532847.</p>
FI, Remote Driving, Remote driving in a redundant network environment
<p>Use Case Category: <strong>Remote Driving</strong><br> User Story: <strong>Remote driving in a redundant network environment</strong><br> Location: Finnish (FI) trial site</p> <p>According to 3GPP TS 22.186 R16, Remote Driving “enables a remote driver or a V2X application to operate a remote vehicle for those passengers who cannot drive themselves or a remote vehicle located in dangerous environments. For a case where variation is limited, and routes are predictable, such as public transportation, driving based on cloud computing can be used. In addition, access to cloud-based back-end service platform can be considered for this use case group”.</p> <p>User Story: <strong>Remote driving in a redundant network environment</strong></p> <p>The remote driving of an SAE L4 vehicle is enabled by a V2N connection between the vehicular Onboard Unit (OBU) and a remote server hosting V2N applications, in this case the remote driving application is used by the remote human operator. The V2N connection transfers the sensor data feed (high resolution</p> <p>perception data) from the vehicle to the remote human operator (in the uplink direction). The sensor data provides the human operator a “driver’s view” allows the human operator to send appropriate command messages (e.g. command trajectories) back to the L4 vehicle (in the downlink direction).</p> <p>The remote control/driving of vehicle presents stringent requirements on connection between the vehicle and the Remote Operations Centre (ROC). These requirements include the need to ensure that human operator always maintains connectivity to the vehicle they control, the latency minimized to ensure timeliness of the downlink control messages from the human operator; and the uplink capacity is guaranteed for the transmission of the sensor data feeds from the vehicle. The whole control loop needs to keep tight. The accumulated delay from: sensor reading, sensor data processing, uplink, data visualization, manual control, control signal reading, downlink, and control signal processing to control must be kept low for direct control (depending on speed and dynamics of the vehicle). Furthermore, the vehicle should be aware of any latency issues, so that the operational speed could be adjusted accordingly.</p> <p>Remote driving (and other V2X use cases) will occur in multi-operator scenarios in legacy 4G [3GPP TR 36.885]4 and future 5G [3GPP 38.885]5 contexts, whereby, the L4 vehicle trajectory is an area covered by multiple public land mobile networks (PLMNs) or transitions between two PLMN coverage areas.</p> <p>The remote driving user story also underlines safety aspects and need for the L4 vehicle to maintain reliable/uninterrupted V2N connectivity. In practice, a vehicle’s home PLMN (original serving network) may have locations with poor or non-existent coverage, or then experience V2N connection degradation or failure due to overloading, network failure etc. To guarantee availability V2N connectivity for critical L4 vehicle services (such as, remote driving), the possibility of the vehicle to seamlessly switch to (or simultaneously utilise) a visited PLMN ensures safer operation of the vehicle regardless of instantaneous network conditions.</p>
Mapping trait versus species turnover reveals spatiotemporal variation in functional redundancy and network robustness in a plant‐pollinator community
<p>1. Functional overlap among species (redundancy) is considered important in shaping competitive and mutualistic interactions that determine how communities respond to environmental change. Most studies view functional redundancy as static, yet traits within species – which ultimately shape functional redundancy – can vary over seasonal or spatial gradients. We therefore have limited understanding of how trait turnover within and between species could lead to changes in functional redundancy or how loss of traits could differentially impact mutualistic interactions depending on where and when the interactions occur in space and time.</p> <p>2. Using an Arctic bumblebee community as a case study, and 1,277 individual measures from 14 species over three annual seasons, we quantified how inter- and intraspecific body-size turnover compared to species turnover with elevation and over the season. Coupling every individual and their trait with a plant visitation, we investigated how grouping individuals by a morphological trait or by species identity altered our assessment of network structure and how this differed in space and time. Finally, we tested how the sensitivity of the network in space and time differed when simulating extinction of nodes representing either morphological trait similarity or traditional species groups. This allowed us to explore the degree to which trait-based groups increase or decrease interaction redundancy relative to species-based nodes.</p> <p>3. We found that i) groups of taxonomically and morphologically similar bees turn over in space and time independently from each other, with trait turnover being larger over the season; ii) networks composed of nodes representing species versus morphologically similar bees were structured differently; and iii) simulated loss of bee trait groups caused faster coextinction of bumblebee species and flowering plants than when bee taxonomic groups were lost. Crucially, the magnitude of these effects varied in space and time, highlighting the importance of considering spatiotemporal context when studying the relative importance of taxonomic and trait contributions to interaction network architecture.</p> <p>4. Our finding that functional redundancy varies spatiotemporally demonstrates how considering the traits of individuals within networks is needed to understand the impacts of environmental variation and extinction on ecosystem functioning and resilience.</p>
Data from: Functionally redundant multimodal predator cues elicit changes in prey foraging behavior
<p><span>Many prey species can assess the risk of predation from information acquired through different sensory systems. For many animals, this information is detected with sensory organs specialized for visual (sight) or chemical (smell or taste) stimuli. It is unclear, however, whether information acquired through multiple sensory systems is functionally redundant or interchangeable, especially if the message is the same. Here we assess prey response to unimodal visual and chemical cues as well as multimodal (visual + chemical) cues. We specifically test if a foraging individual shows a stronger behavioral response to risk when they can perceive that risk through multimodal versus unimodal cues. To do this, we measured the functional response (prey abundance-foraging rate relationship) of Tibellus oblongus spiders foraging on midges while exposing them to visual stimuli, chemical stimuli, or a combination of both visual and chemical stimuli from potential predators. We then determined if the spider's functional response for the multimodal treatment differed more strongly from a control treatment than from either unimodal treatment. We found that under any simulated predation risk (multimodal and both unimodal), T. oblongus spiders showed longer handling times than in control groups without risk. </span><span>However, we saw no elevated anti-predator response in the multimodal treatment, suggesting that information from visual and chemical modalities is interchangeable and sufficient to indicate reliably predation risk. </span></p>
Global variation in unique and redundant mammal functional diversity across the daily cycle
<p>(1) Data S1: Excel file consisting of</p> <p>‘1_Data’ Trait data containing both missing values and imputed data, with data sources as a ‘2_Metadata’ sheet in the excel file. Activity patterns were extracted from our recently compiled database for mammals (Cox et al., 2021)<em>.</em> ‘3_Updated activity patterns’: Here, we updated activity patterns for 109 species and provide data sources. We also now consider that the African forest elephant (<em>Loxodonta cyclotis</em>) is a separate species to the African savannah elephant (<em>Loxodonta africana</em>).</p> <p>(2) README.md file describing Data S1</p> <p>(3) Supplementary information in the form of appendixes, figures and tables</p> <p> </p> <p> </p>
Dataset of redundantly rigid graphs
<p>This data set collectes all redundantly rigid graphs for dimension d<=25 with at most d+k vertices, where k might be different.<br> The graphs are collected in a zip file with respect to the dimension. Graphs are stored in graph6 data format.</p>
Supporting Information: Measuring Functional Redundancy Using Generalized Hill Numbers
<p>A number of metrics for quantifying the amount of functional redundancy in a community have been proposed over the years. Two of the most popular metrics are based on comparing a taxonomic diversity measure with a generalized form of the same measure that accounts for functional dissimilarities between taxa. These two metrics express redundancy as either an absolute or relative difference between the taxonomic diversity measure and its generalized form. Because they express the amount of redundancy in a community in terms of raw diversity values, both redundancy metrics are susceptible to the same issues that complicate the interpretation of most commonly used diversity indices.</p> <p>It is possible to overcome these issues by restating these two indices using a Hill numbers framework. As a growing number of authors have noted, these modified metrics provide a more intuitive quantitative definition of functional redundancy when used to rank communities. Beyond this intuitive definition, measuring redundancy in terms of Hill numbers allows researchers to control the influence of rare taxa on the output value, enabling ecologists to better predict how a community is expected to respond when exposed to an external perturbation that selectively eliminates rare or common taxa.</p> <p>Here I show that, of the two possible Hill number-based redundancy metrics, the form based on a popular absolute redundancy metric is extremely sensitive to differences in taxonomic diversity and can provide a misleading picture of how much redundancy is present in a community. For this reason, I argue that Hill number-based functional redundancy should be quantified using a relative metric that explicitly accounts for differences in effective taxonomic diversity. The proposed Hill number-based relative redundancy measure is shown to provide a much more complete picture of the distribution of redundant taxa within a community, highlighting subtle patterns that are completely missed by the Hill number-based absolute redundancy metric.</p>
Simulation Data for "GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway"
<p>Molecular dynamics simulation data for "GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway"</p>
Subset of non-redundant, high resolution multi-pass membrane protein PDB structure files from OPM
<p>A subset of OPM PDB structure files with membrane predictions curated for the MSc thesis project '<strong>Structural characterization of triplets of transmembrane α-helical segments consecutive in sequence in integral membrane proteins: a fragment-based computational pipeline'. </strong>The dataset contains PDB files downloaded from OPM on 22/02/2023. The files are alpha-helical integral membrane proteins with at least three transmembrane regions at better than 2.7 Angtrom resolution. They are non-redundant, with a sequence identity of less than 40% based on clustering with the cd-hit algorithm. </p>
Data for Non-Redundant Image Clustering of Early Medieval Glass Beads (DSAA 2023)
<p>Archeological glass beads images with measurements (width, height, weight), pretrained models, resampled data (with less color bias) and clustering results from the paper Non-Redundant Image Clustering of Early Medieval Glass Beads (Accepted at DSAA 2023)</p>
Supporting Information: Measuring Functional Redundancy Using Generalized Hill Numbers
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Data from: Multi-modal defenses in aphids offer redundant protection and increased costs likely impeding a protective mutualism
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Land-use change erodes trophic redundancy in tropical forest streams: Evidence from amino acid stable isotope analysis
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Mapping trait versus species turnover reveals spatiotemporal variation in functional redundancy and network robustness in a plant‐pollinator community
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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.