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Data from Selectivity filter mutations shift ion permeation mechanism in potassium channels
<p>Example mdp, gro files, topologies, scripts, run input files and trajectories used in https://doi.org/10.1101/2023.04.17.537168</p>
Fig. 6 in New cranial material of the earliest filter feeding flamingo Harrisonavis croizeti (Aves, Phoenicopteridae) informs the evolution of the highly specialized filter feeding apparatus
Fig. 6 Cladogram showing the relationship of Harrisonavis croizeti to other members of Mirandornithes (flamingos and grebes; Sangster, 2005). H. croizeti is placed outside of the crown group based on apomorphic data presented in this study. The relationships of the crown clade are from Torres et al. (2014). The placement of Juncitarsus (Olson and Feduccia 1980) is uncertain (indicated by a dashed line); treatment here follows Mayr (2014a). Extinct taxa denoted by dagger symbols
Fig. 4 in New cranial material of the earliest filter feeding flamingo Harrisonavis croizeti (Aves, Phoenicopteridae) informs the evolution of the highly specialized filter feeding apparatus
Fig. 4 Material representing lower bills of Harrisonavis croizeti compared to extinct Leakeyornis aethiopicus and extant Phoenicopterus roseus and Phoenicoparrus minor. H. croizeti (NMB SG 18285a), middle part of the left side, in right lateral (a) and internal (medial; b) views. H. croizeti (NMB SG 18285b), tip of the right side, in lateral (c) and internal (medial; d) views. P. roseus in right lateral (e) view. P. minor in right lateral (f) view. H. croizeti (NMHUK A 2665) in right lateral (g) view. L. aethiopicus (NMHUK A 4384) in right lateral (h) view. Arrow indicates ridging characteristic of flamingo bills. Scale bars 1 cm
Fig. 3 in New cranial material of the earliest filter feeding flamingo Harrisonavis croizeti (Aves, Phoenicopteridae) informs the evolution of the highly specialized filter feeding apparatus
Fig. 3 Sub-adult and adult upper bills from Harrisonavis croizeti compared to extinct Leakeyornis aethiopicus and adult extant Phoenicopterus roseus and Phoenicoparrus minor. Sub-adult H. croizeti (NMB MA 9594) in dorsal (a), ventral (b), and right lateral (n) views. Adult H. croizeti (FSL 442292) in dorsal (c), ventral (d), and right lateral (o) views. Adult P. roseus in dorsal (e), ventral (f), and right lateral (l) views. Adult P. minor in dorsal (g), ventral (h), and right lateral (m) views. L. aethiopicus (NMHUK A 4382) in dorsal (i), ventral (j), and right lateral (k) views. ct crista tomialis, mk maxillary keel; nf nasal furrows. Arrows indicate reticulated surface unique to extant flamingos. Arrowhead indicates fibrous texture on dorsal surface of NMB MA 9594, suggesting the bill belonged to a subadult individual. Scale bars 1 cm
Fig. 2 in New cranial material of the earliest filter feeding flamingo Harrisonavis croizeti (Aves, Phoenicopteridae) informs the evolution of the highly specialized filter feeding apparatus
Fig. 2 Skull of Harrisonavis croizeti (Gervais 1852), from the Late Oligocene of the Auvergne region in central France, compared with the extinct Palaelodus ambiguus and extant Phoenicopterus roseus and Phoenicoparrus minor in dorsal, ventral, and occipital views. P. ambiguus (ML StG 60) in dorsal (a), ventral (b), and occipital (i) views. H. croizeti (ML StG 203bis) in dorsal (c), ventral (d), and occipital (j) views. P. roseus in dorsal (e), ventral (f), and occipital (k) views. P. minor in dorsal (g), ventral (h), and occipital (l) views. cl os palatina, crista lateralis; cm os palatine, crista medialis; cn crista nuchalis; ct crista tomialis; cv os palatine, crista ventralis; fgn fossa glandularis nasalis; fo fonticulus occipitalis; mk maxillary keel; ppa processus paroccipitalis; ppo processus postorbitalis. Scale bars 1 cm
Fig. 1 in New cranial material of the earliest filter feeding flamingo Harrisonavis croizeti (Aves, Phoenicopteridae) informs the evolution of the highly specialized filter feeding apparatus
Fig. 1 Skull of Harrisonavis croizeti (Gervais 1852), from the Late Oligocene of the Auvergne region in central France, compared with the extinct Palaelodus ambiguus and extant flamingos Phoenicopterus roseus and Phoenicoparrus minor in lateral views. P. ambiguus (ML StG 60) in right lateral (a) and left lateral (b) views. H. croizeti (ML StG 203bis) in right lateral (c) and left lateral (d) views. P. roseus in right lateral (e) and left lateral (f) views. P. minor in right lateral (g) and left lateral (h) views. aj arcus jugalis, cn crista nuchalis, fr frontal ridges, ft fossa temporalis, mk maxillary keel, n nares, nf nasal furrow, np nasal prominence, pc prominentia cerebellaris, pmp processus maxillopalatinus, ppo processus postorbitalis. Scale bars 1 cm
Towards Filtering Out Deficient Pull Requests Collected through the GitHub API
<p>This is a replication package for an APSEC 2024 ERA paper.</p>
Bacterial fertilizer and filtered sludge enhance soil quality and eucalyptus growth in a eucalyptus plantation
Open the record for dataset details and reuse information.
filtered_ARG_database
Open the record for dataset details and reuse information.
1D simulation of land subsidence with ensemble Kalman filter
<p>This folder contains:</p> <p>a) output files from 1D simulations of land subsidence with ensemble Kalman filter in heterogeneous and highly compressible aquitards, reported in Zapata-Norberto et al., 2024.</p> <p>b) R Scripts to reproduce all figures and supplementary material in the cited reference.</p>
Data from: Land-use type and intensity differentially filter traits in above- and belowground arthropod communities
1. Along with the global decline of species richness goes a loss of ecological traits. Associated biotic homogenization of animal communities and narrowing of trait diversity threaten ecosystem functioning and human well-being. High management intensity is regarded as an important ecological filter, eliminating species that lack suitable adaptations. Belowground arthropods are assumed to be less sensitive to such effects than aboveground arthropods. 2. Here, we compared the impact of management intensity between (grassland vs. forest) and within land-use types (local management intensity) on the trait diversity and composition in below- and aboveground arthropod communities. 3. We used data on 722 arthropod species living above ground (Auchenorrhyncha and Heteroptera), primarily in soil (Chilopoda and Oribatida) or at the interface (Araneae and Carabidae). 4. Our results show that trait diversity of arthropod communities is not primarily reduced by intense local land use, but is rather affected by differences between land-use types. Communities of Auchenorrhyncha and Chilopoda had significantly lower trait diversity in grassland habitats as compared to forests. Carabidae showed the opposite pattern with higher trait diversity in grasslands. Grasslands had a lower proportion of large Auchenorrhyncha and Carabidae individuals, whereas Chilopoda and Heteroptera individuals were larger in grasslands. Body size decreased with land-use intensity across taxa, but only in grasslands. The proportion of individuals with low mobility declined with land-use intensity in Araneae and Auchenorrhyncha, but increased in Chilopoda and grassland Heteroptera. The proportion of carnivorous individuals increased with land-use intensity in Heteroptera in forests and in Oribatida and Carabidae in grasslands. 5. Our results suggest that gradients in management intensity across land-use types will not generally reduce trait diversity in multiple taxa, but will exert strong trait filtering within individual taxa. The observed patterns for trait filtering in individual taxa are not related to major classifications into above- and belowground species. Instead, ecologically different taxa resembled each other in their trait diversity and compositional responses to land-use differences. These previously undescribed patterns offer an opportunity to develop management strategies for the conservation of trait diversity across taxonomic groups in permanent grassland and forest habitats.
Data from: Dispersal versus environmental filtering in a dynamic system: drivers of vegetation patterns and diversity along stream riparian gradients
1. Both environmental filtering and dispersal filtering are known to influence plant species distribution patterns and biodiversity. Particularly in dynamic habitats, however, it remains unclear whether environmental filtering (stimulated by stressful conditions) or dispersal filtering (during re-colonization events) dominates in community assembly, or how they interact. Such a fundamental understanding of community assembly is critical to the design of biodiversity conservation and restoration strategies. 2. Stream riparian zones are species-rich dynamic habitats. They are characterized by steep hydrological gradients likely to promote environmental filtering, and by spatiotemporal variation in the arrival of propagules likely to promote dispersal filtering. We quantified the contributions of both filters by monitoring natural seed arrival (dispersal filter) and experimentally assessing germination, seedling survival and growth of 17 riparian plant species (environmental filter) along riparian gradients of three lowland streams that were excavated to bare substrate for restoration. Subsequently, we related spatial patterns in each process to species distribution and diversity patterns after 1 and 2 years of succession. 3. Patterns in initial seed arrival were very clearly reflected in species distribution patterns in the developing vegetation and were more significant than environmental filtering. However, environmental filtering intensified towards the wet end of the riparian gradient, particularly through effects of flooding on survival and growth, which strongly affected community diversity and generated a gradient in the vegetation. Strikingly, patterns in seed arrival foreshadowed the gradient that developed in the vegetation; seeds of species with adult optima at wetter conditions dominated seed arrival at low elevations along the riparian gradient while seeds of species with drier optima arrived higher up. Despite previous assertions suggesting a dominance of environmental filtering, our results demonstrate that nonrandom dispersal may be an important driver of early successional riparian vegetation zonation and biodiversity patterns as well. 4. Synthesis: Our results demonstrate (and quantify) the strong roles of both environmental and dispersal filtering in determining plant community assemblies in early successional dynamic habitats. Furthermore, we demonstrate that dispersal filtering can already initiate vegetation gradients, a mechanism that may have been overlooked along many environmental gradients where interspecific interactions are (temporarily) reduced.
Data-Two-dimensional numerical study on particle motion trajectories and deposition in a channel of partial diesel particulate filter
<p>A numerical investigation on the soot laden flow of gas in a PDPF (Partial Diesel Particulate Filter) is presented based on solving the momentum equations for continuous phase in the Euler frame and the motion equations for dispersed phase in the Lagrangian frame. The interaction between the gas and particles is treated as one-way coupling for extremely dilute particle concentration, while the interaction between particles and porous wall is implemented through user-defined-subroutines. To accurately track the motion of nanoscale particles, the drag force, the Brownian excitation, and the partial slip are included in the particle motion equation. Two methods are used to verify the gas flow model and reasonable agreement for both comparisons is observed. The effects of upstream velocity, wall permeability and particle size on the filtration efficiency and deposition distribution of the particles along the wall surface of inlet channel are quantitatively studied. The results show that (1) the wall permeability plays the most primary role in determining the filtration efficiency of PDPF; (2) high upstream velocity improves filtration efficiency and drives the deposition position of particles to the rear of inlet channel; (3) the dependence of the particle deposition distribution on its own size is mainly reflected in the initial deposition position; (4) the filtration efficiency of PDPF is not proportional markedly to the gas flow into inlet channel at a low wall permeability, implying an intense separation of particles from gas streamline at the flow entrance.</p>
Biomarker responses of the blue mussels to organic UV filters
<p>This is the metadata for the publication: <strong>Falfushynska, H., Sokolov, E. P., Fisch, K., Gazie, H., Schulz-Bull, D. E. and Sokolova, I. M.</strong> (2021). Biomarker-based assessment of sublethal toxicity of organic UV filters (ensulizole and octocrylene) in a sentinel marine bivalve Mytilus edulis. <em>Science of The Total Environment</em> <strong>798</strong>, 149171. DOI: <a href="https://doi.org/10.1016/j.scitotenv.2021.149171">10.1016/j.scitotenv.2021.149171</a></p>
The contribution of environmental and dispersal filters on beta diversity patterns in Amazonian tree communities
<p>Environmental filters (e.g. climate, geomorphology and soils) and dispersal filters are key determinants of species distributions of Amazonian tree communities. However, a comprehensive analysis of the role of environmental and dispersal filters is needed to understand the ecological and evolutionary processes that drive phylogenetic and taxonomic turnover of Amazonian tree communities. We compare measures of taxonomic and phylogenetic beta diversity in 40 one-hectare plots to test the relative importance of climate, soils, geology, geomorphology, pure spatial variables and the spatial variation of environmental drivers of phylogenetic and taxonomic turnover in Ecuadorian Amazon tree communities. We found low phylogenetic and high taxonomic turnover with respect to environmental and dispersal filters. In addition, our results suggest that climate is a significantly better predictor of phylogenetic turnover and species turnover than geomorphology and soils at all spatial scales. The influence of climate as a predictor of phylogenetic turnover was stronger at broader spatial scales (50 km<sup>2</sup>) whereas geomorphology and soils appear to be better predictors of taxonomic turnover at mid (5 km<sup>2</sup>) and fine spatial scales (0.5 km<sup>2</sup>) but a weak predictor of phylogenetic turnover at broad spatial scales. We also found that the combined effect of geomorphology and soils was significantly higher for species turnover at all spatial scales but not for phylogenetic turnover at large spatial scales. Geographic distances as proxy of dispersal limitation was a better predictor of phylogenetic turnover at distances of 50<500 km. Our findings suggest that climatic variation at local and regional scales can better predict phylogenetic and taxonomic turnover than geomorphology and soils.</p>
Can Proposed Service Interface Metrics Effectively Evaluate the Quality of RESTful APIs? Dataset and Filter Criteria
<p>The csv datasets contains repositories with API metrics and software quality metrics.</p> <p>We use linear regression to predict a software quality metric with the API metrics.</p> <p> </p> <p>The .txt files contain the lists for the filter criteria to filter out unsuitable repositories.</p>
Filtering and imaging of frequency-degenerate spin waves using nanopositioning of a single-spin sensor
<p>Data corresponding to the figures of the main text of "Filtering and imaging of frequency-degenerate spin waves using nanopositioning of a single-spin sensor"</p> <p> </p>
photo all filter DIGITAL FORENSIC AND AUTOPSY
<p>photo all filter DIGITAL FORENSIC AND AUTOPSY</p>
photos all filter by analyzing filter digital forensic and autopsy
<p>photos all filter by analyzing filter digital forensic and autopsy</p>
Supplementary FIles for Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study
<p>This repository contains supplementary files for the initial submission of:</p> <p>Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study<br> Evan J. van Aalst, Corey J. McDonald, and Benjamin J. Wylie</p> <p>Files found in this repository include:<br> 1. Raw fids corresponding to the solid-state NMR spectra used in this work.<br> 2. The script, model structures, and predicted chemical shifts used in the COMPASS proof of concept.<br> 3. Input molecular dynamics files derived from CHARMM-GUI including all mdp files, initial model structure files, and the production script.<br> 4. Model structures per ns derived from MD trajectories with corresponding predicted chemical shift lists and associated experimental chemical shift lists.</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.