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914 results for “filter”
Occurrence filtered by invasive species list: occurrence-filtered-by-invasive-species v2
<p>Data snapshot, invasive species</p> <p>From [DATA-1682](https://eol-jira.bibalex.org/browse/DATA-1682)</p> <p>Total rows = 10,826</p>
COCO dataset and neural network weights for micro-FTIR particle detection on filters.
<h3>The IMPTOX project has received funding from the EU's H2020 framework programme for research and innovation under grant agreement n. 965173. Imptox is part of the European MNP cluster on human health.</h3> <p>More information about the project <a href="https://www.imptox.eu/en/">here</a>.</p> <p><strong>Description:</strong> This repository includes the trained weights and a custom COCO-formatted dataset used for developing and testing a Faster R-CNN R_50_FPN_3x object detector, specifically designed to identify particles in micro-FTIR filter images.</p> <p><strong>Contents:</strong></p> <ol> <li> <p><strong>Weights File (<code>neuralNetWeights_V3.pth</code>):</strong></p> <ul> <li>Format: .pth</li> <li>Description: This file contains the trained weights for a Faster R-CNN model with a ResNet-50 backbone and a Feature Pyramid Network (FPN), trained for 3x schedule. These weights are specifically tuned for detecting particles in micro-FTIR filter images.</li> </ul> </li> <li> <p><strong>Custom COCO Dataset (<code>uFTIR_curated_square.v5-uftir_curated_square_2024-03-14.coco-segmentation.zip</code>):</strong></p> <ul> <li>Format: .zip</li> <li>Description: This zip archive contains a custom COCO-formatted dataset, including JPEG images and their corresponding annotation file. The dataset consists of images of micro-FTIR filters with annotated particles.</li> <li>Contents: <ul> <li><strong>Images:</strong> JPEG format images of micro-FTIR filters.</li> <li><strong>Annotations:</strong> A JSON file in COCO format providing detailed annotations of the particles in the images.</li> </ul> </li> <li>Management: The dataset can be managed and manipulated using the <a href="https://pypi.org/project/pycocotools/">Pycocotools</a> library, facilitating easy integration with existing COCO tools and workflows.</li> </ul> </li> </ol> <p><strong>Applications:</strong> The provided weights and dataset are intended for researchers and practitioners in the field of microscopy and particle detection. The dataset and model can be used for further training, validation, and fine-tuning of object detection models in similar domains.</p> <p><strong>Usage Notes:</strong></p> <ul> <li>The <code>neuralNetWeights_V3.pth</code> file should be loaded into a PyTorch model compatible with the Faster R-CNN architecture, such as Detectron2.</li> <li>The contents of <code>uFTIR_curated_square.v5-uftir_curated_square_2024-03-14.coco-segmentation.zip</code> should be extracted and can be used with any COCO-compatible object detection framework for training and evaluation purposes.</li> <li>Code can be found on the related <a href="https://github.com/ThibaultSchowing/IMPTOX" target="_blank" rel="noopener">Github repository.</a></li> </ul> <p> </p>
Filtered GNPS dataset for MSBERT and retrain Spec2Vec model
<p>Embedding Tandem Mass Spectra into Chemically Rational Space by Mask Learning and Contrastive Learning</p>
Applications of Fast Iterative Filtering in NMR spectroscopy [NMR DATASETS]
<p>Employed NMR spectra for the application of denoising and baseline correction method described in the manuscript.</p>
quaqc: Efficient and quick ATAC-seq quality control and filtering at any scale
<p>This repository contains data and code necessary to replicate the analyses for the associated manuscript. Copies of the quaqc and quaqcr programs are also included.</p>
Table S1: Processed, filtered, and supplemented data
<p>Cleaned and processed data used for analysis in "β-Lactamase Diversity in <em>Acinetobacter Baumannii</em>" by Andrew R. Mack, Andrea M. Hujer, Maria F. Mojica, Magdalena A. Taracila, Michael Feldgarden, Daniel H. Haft, William Klimke, Arjun B. Prasad, and Robert A. Bonomo. Derived from National Center for Biotechnology Information databases on September 9th, 2024.</p>
Table S1: Processed, filtered, and supplemented data
<div> <p>Cleaned and processed data used for analysis in "β-Lactamase Diversity in <em>Pseudomonas aeruginosa</em>" by Andrew R. Mack, Andrea M. Hujer, Maria F. Mojica, Magdalena A. Taracila, Michael Feldgarden, Daniel H. Haft, William Klimke, Arjun B. Prasad, and Robert A. Bonomo. Derived from National Center for Biotechnology Information databases on September 9th, 2024.</p> </div>
Catalysts in gasoline particulate filters
<p>Galaxy RO Crate object containing the workflow and data with the reproduction of the results published in: Panchal, Monik, Callison, June, Skukauskas, Vainius, Gianolio, Diego, Cibin, Giannantonio, York, Andrew P E, Schuster, Manfred E, Hyde, Timothy I, Collier, Paul, Catlow, C Richard A, Gibson, Emma K (2021) <em>Operando XAFS investigation on the effect of ash deposition on three-way catalyst used in gasoline particulate filters and the effect of the manufacturing process on the catalytic activity</em> DOI: 10.1088/1361-648x/abfe16.</p> <p>This RO is published as part of the research data submitted for the paper <strong>Facilitating Reproducibility in Catalysis Research with Managed Workflows and RO-Crates: A Galaxy Case Study</strong>, ChemCatChem, DOI: 10.1002/cctc.202401676.</p>
Agreement of multiple night- and daytime filtering approaches of eddy covariance-derived net ecosystem CO2 exchange over a mountain forest. Reproducible workflow.
<p>Datasets and python scripts to reproduce results from the publication <em>Agreement of multiple night- and daytime filtering approaches of eddy covariance-derived net ecosystem CO2 exchange over a mountain forest.</em></p> <p>See README.txt for a description of the single files.</p>
Potential growth more than functional traits explain successional habitat filtering of rainforest trees
<ol> <li>Species along successional gradients differ in functional traits, which may function as environmental filters and also explain differences in growth rates. Alternatively, species might be filtered by growth rates and these are explained by differences in other traits. We explored the relationships between leaf and wood traits, growth and successional habitat, and asked if growth is related to habitat because both are driven by a similar set of traits or if growth is the main trait explaining habitat and relationships with other traits are indirect.</li> <li>Tropical trees are often classified as second-growth (SG) or old-growth (OG) specialists, and generalists. Since succession is a continuous process and lumping species into three groups may not do justice to gradual differences, we tested if a continuous variable based on relative tree abundance in OG and SG forests might be a better predictor than classifying trees' habitat preferences into categories.</li> <li>We measured height growth of 47 trees species planted in a reforestation trial in Costa Rica and evaluated size-standardized potential growth during the first years when there was little shading among trees. Growth and habitat were related to wood density (WD), theoretical hydraulic conductivity (Kh), specific leaf area (SLA), leaf dry matter content (LDMC) and leaf nitrogen content (N).</li> <li>Potential growth rates and Kh were significantly correlated with habitat measured on a continuous scale, while growth and LDMC differed among the three groups of habitat specialization. Growth was also correlated with WD and Kh.</li> <li>Habitat specialization was correlated with the first principal component of the functional traits space. However, structural equation models suggest that the relationship with leaf and wood traits is mostly indirect and potential growth is the most important trait directly related to environmental filtering along a successional gradient. In our dataset, classifiying the successional status of species using the proportion of records from OG forests explains traits about as well as a classification into three groups, but provides more information about the species' position along the successional gradient.</li> </ol>
Wavelet filters for automated recognition of birdsong in long-time field recordings
<p>1. Ecoacoustics has the potential to provide a large amount of information about the abundance of many animal species at a relatively low cost. Acoustic recording units are widely used in field data collection, but the facilities to reliably process the data recorded -- recognising calls that are relatively infrequent, and often significantly degraded by noise and distance to the microphone -- are not well developed yet. 2. We propose a call detection method for continuous field recordings that can be trained quickly and easily on new species, and degrades gracefully with increased noise or distance from the microphone. The method is based on the reconstruction of the sound from a subset of the wavelet nodes (elements in the wavelet packet decomposition tree). It is intended as a preprocessing filter, therefore we aim to minimise false negatives: false positives can be removed in subsequent processing, but missed calls will not be looked at again. 3. We compare our method to standard call detection methods, and also to machine learning methods (using as input features either wavelet energies or Mel-Frequency Cepstral Coefficients (MFCC)) on real-world noisy field recordings of six bird species. The results show that our method has higher recall (proportion detected) than the alternative methods: 87% with 85% specificity on >53 hrs of test data, resulting in an 80% reduction in the amount of data that needed further verification. It detected >60% of calls that were extremely faint (far away), even with high background noise. 4. This preprocessing method is available in our AviaNZ bioacoustic analysis program and enables the user to significantly reduce the amount of subsequent processing required (whether manual or automatic) to analyse continuous field recordings collected by spatially and temporally large-scale monitoring of animal species. It can be trained to recognise new species without difficulty, and if several species are sought simultaneously, filters can be run in parallel.</p>
Agricultural intensification erodes taxonomic and functional diversity in Mediterranean olive groves by filtering out rare species
<p><span>1. Agri-Environmental Schemes (AES) have been proposed to mitigate the impact of agriculture on both taxonomic and functional biodiversity. However, a better knowledge of the mechanisms involved in the loss of agrobiodiversity is needed to implement efficient AES. An unbalanced effort on research towards arable lands compared to permanent crops, and on fauna relative to plants, is patent, which limits the generalization of AES effectiveness. </span></p> <p><span>2. We evaluated the effects of agricultural management and landscape simplification on taxonomic and functional diversity of the ground herb cover of 40 olive groves. We use a recently developed approach based on Hill numbers (rare, common and dominant species based) to analyze taxonomic and functional dissimilarity between farms with contrasting agricultural practices, and its potential attenuation by landscape complexity. We further explore the filtering effect of agricultural intensification on functional traits, and the relationship between functional and species richness across landscapes.</span></p> <p><span>3. We found that taxonomic and functional dissimilarity of herb assemblages between intensively and low-intensively managed fields was mainly due to rare species. Dissimilarity decreased as landscape complexity increased, evidencing that complex landscapes attenuate the impact of agriculture intensification on herb assemblage composition. Agricultural intensification favoured more functionally homogeneous assemblages and disfavoured the herbs pollinated by insects, while it did not seem to affect wind-pollinated species. </span></p> <p><span>4. Overall, functional richness increased exponentially with species richness across landscapes, but the latter was insufficient to drive any clear enhancement in functional richness in simple landscapes. In contrast, high species richness accelerated the enhancement in functional richness in intermediate and complex landscapes. These results highlight the functional filtering that intensive agriculture has generated for decades in homogeneous olive-dominated landscapes. </span></p> <p><span>5. Herb cover is essential to support the fauna of permanent croplands and their sustainable production. Hence, AES in these croplands should promote management practices favouring the diversity and functionality of herb assemblages. Such AES should be particularly prioritized in homogeneous landscapes, where ground herb cover composition and function has long been homogenized to a great extent. </span></p>
Implementation of an adaptive bias-aware extended Kalman filter for sea-ice data assimilation in the HARMONIE-AROME numerical weather prediction system: numerical experiments
<p>This data set provides the post-processed output of the numerical experiments performed to assess the possible effects of applying sea ice data assimilation within the surface analysis procedure of the HARMONIE-AROME NWP system. Results of five numerical experiments are provided:</p> <ul> <li>HA-REF – reference experiment <em>without</em> sea ice data assimilation applied, and with blending for upper-air initialization</li> <li>HA-EKF – sensitivity experiment with sea ice data assimilation applied, and with blending for upper-air initialization</li> <li>3DVAR-REF – reference experiment <em>without</em> sea ice data assimilation applied, and with 3DVAR for the upper-air analysis</li> <li>3DVAR-EKF – sensitivity experiment with sea ice data assimilation applied, and with 3DVAR for the upper-air analysis</li> <li>3DVAR-EKF-TS – sensitivity experiment with sea ice data assimilation, and with 3DVAR for the upper-air analysis using coupled surface and atmospheric data assimilation procedures</li> </ul> <p>For the HA-REF and HA-EKF experiments a subset of the gridded model output is provided; for the 3DVAR-REF, 3DVAR-EKF and 3DVAR-EKF-TS experiments a subset of the gridded model output and model data extracted at the positions of the SYNOP and TEMP stations within the model domain are provided. Additionally, in-situ observations, covering the same time period as the 3DVAR-REF, 3DVAR-EKF, 3DVAR-EKF-TS experiments, are provided.</p>
Data from: The importance of biotic filtering on boreal conifer recruitment at alpine treeline
<p>Treeline, the ecotone where forest transitions to alpine or tundra ecosystems, is considered the thermal limit to tree growth and survival. Despite temperature increases across mountainous areas and high latitudes globally, there has been no ubiquitous change in treeline position. The process of range expansion must initially depend on increased recruitment at, or beyond current range limits and recruitment limitations have been hypothesized as a mechanism for the variable response of treeline position to climate warming.<b> </b>We conducted a unique series of observational and experimental studies to quantify early-life stage constraints, from seed production to seedling establishment, on black spruce (<i>Picea mariana</i>) and tamarack (<i>Larix laricina</i>) recruitment at a model alpine treeline in Newfoundland, Canada.<b> </b>We found recruitment at treeline to be simultaneously seed and establishment limited. The treeline population produced fewer seeds than the forest population and black spruce seeds produced at treeline were less viable. Tamarack was more seed limited than black spruce where seed viability was low regardless of altitudinal position.<b> </b>Post-dispersal seed predation greatly constrained recruitment across the altitudinal gradient; however, black spruce seeds experienced the lowest levels of invertebrate seed predation on the lichen mat at treeline. If seeds were not consumed, individuals at treeline were establishment limited where germination and seedling establishment was both less abundant and delayed on lichen substrate. Our study highlights the need for multiple factors to align temporally for significant recruitment at treeline to occur.</p>
Dataset for "A graph-theoretic approach for spatial filtering and its impact on mixed-type spatial pattern recognition in wafer bin maps"
<p>This is the dataset used in the paper, Ezzat, Liu, Hochbaum, and Ding, 2021, “A graph-theoretic approach for spatial filtering and its impact on mixed-type spatial pattern recognition in wafer bin maps,” <em>IEEE Transactions on Semiconductor Manufacturing</em>, Vol. 34, pp. 194-206.</p>
Chembl Filtered Dataset for TorchDrug
<p>A preprocessed ChEMBL dataset containing 456K molecules with 1310 kinds of diverse and extensive biochemical assays from paper "Strategies for Pre-training Graph Neural Networks" used by TorchDrug library.</p>
Royer & Pastres, Kalman Filter applied to Oxygen estimation in Land-based Aquaculture
<p>These two csv files contains the data relative to the paper "<strong>Data assimilation as a key step towards the implementation of an efficient management of dissolved oxygen in land-based aquaculture</strong>" submitted to Aquaculture International.</p>
Can short-term data accurately model long-term environmental exposures? Investigating the multigenerational adaptation potential of Daphnia magna to environmental concentrations of organic ultraviolet filters
<p>Organic ultraviolet filters (UVFs) are contaminants of concern, ubiquitously found in many aquatic environments due to their use in personal care products to protect against ultraviolet radiation. Research regarding the toxicity of UVFs such as avobenzone, octocrylene and oxybenzone indicates that these chemicals may pose a threat to invertebrate species; however, minimal long-term studies have been conducted to determine how these UVFs may affect continuously exposed populations. The present study modeled the effects of a 5-generation exposure of <em>Daphnia</em> <em>magna</em> to these UVFs at environmental concentrations. Avobenzone and octocrylene resulted in minor, transient decreases in reproduction and wet mass. Oxybenzone exposure resulted in > 40% mortality, 46% decreased reproduction and 4-fold greater reproductive failure over the F0 and F1 generations; however, normal function was largely regained by the F2 generation. These results indicate that <em>Daphnia</em> are able to acclimate over long-term exposures to concentrations of 6.59 μg/L avobenzone, ~0.6 μg/L octocrylene or 16.5 μg/L oxybenzone. This suggests that short-term studies indicating high toxicity may not accurately represent long-term outcomes in wild populations, adding additional complexity to risk assessment practices at a time when many regions are considering or implementing UVF bans in order to protect these most sensitive invertebrate species.</p>
aKmerBroom ancient Bloom filter
<p>Bloom filter built on set of trusted oral k-mers as described in the manuscript "aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets"</p> <p>See GitHub repo <a href="https://github.com/CamilaDuitama/aKmerBroom">https://github.com/CamilaDuitama/aKmerBroom</a> for instructions on how to use it </p>
Tabula sapiens filtered data
<p>This folder contains pre-filtered files of Tabula sapiens per tissue used to generate scvi models stored in scvi-hub. Due to inconsistencies in the cell-type resolution across donors data was filtered. Please refer to pre-processed files as adata object for the trained scvi models which contains gene filtered and minified data for the models.</p> <p>Data is preprocessed data downloaded from <a href="https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5">https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5</a>. Please refer to their data usage guide before reusing the data.</p>
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.