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805 results for “nodulation”
Fig. 3 in Neanthes goodayi sp. nov. (Annelida, Nereididae), a remarkable new annelid species living inside deep-sea polymetallic nodules
Fig. 3. Neanthes goodayi sp. nov., holotype (NHM_739). A. Chaetiger 1, posterior view. B. Chaetiger 3, posterior view. C. Chaetiger 6, posterior view. D. Chaetiger 20, posterior view. E. Chaetiger 29, posterior view. F. Chaetiger 29, posterior view, detail of neuracicular postchaetal lobe. G. Chaetiger 40, posterior view. H. Chaetiger 46, posterior view. I. Notochaetae, detail of homogomph spinigers, chaetiger 20. J. Supraciular neurochaetae, detail of homogomph spiniger, chaetiger 3. K. Supracicular neurochaetae, detail of heterogomph falciger, chaetiger 10. L. Subacicular neurochaetae, detail of homogomph spiniger (left) and homogomph falciger (right), chaetiger 20. M. Subacicular neurochaetae, detail of heterogomph falcigers, chaetiger 20. Abbreviations: PtL = postchaetal lobe; VC = ventral cirrus. Postchaetal lobe in A–D, F outlined with a fine white line. Parapodia in C, E–H dissected from left side of specimen; parapodia in A–B, D dissected from right side of specimen, with images laterally inverted follow direction of other plates. Scale bars: A–E, G–H = 200 µm; F, I–M = 50 µm.
Fig. 1 in Neanthes goodayi sp. nov. (Annelida, Nereididae), a remarkable new annelid species living inside deep-sea polymetallic nodules
Fig. 1. Sampling sites, showing occurrences of Neanthes goodayi sp. nov. A. UK-1 Stratum-A study area within the UK Seabed Resources UK-1 exploration contract area. B. UK-1 Stratum-B study area within the UK Seabed Resources UK-1 exploration contract area. C. OMS Stratum-A study area, in the Ocean Mineral Singapore (OMS) polymetallic nodule exploration contract area. D. Area of Particular Environmental Interest APEI-6. Inset map showing location of Clarion-Clipperton Fracture Zone in the Central Eastern Pacific. Bathymetric survey data and sampling localities from the AB01 2013 RV Melville survey cruise (MV1313) and AB02 2015 RV Thomas G. Thompson survey cruise (TN319); data courtesy of Craig R. Smith (University of Hawaii), UK Seabed Resources Ltd. and Seafloor Investigations, LLC.
Text-fig. 4. Taphonomic features of the studied localities of ammonoids. a: Sandstone slab with fragmentary remains of productid and spiriferid brachiopods, orthocerids, coiled nautiloids and ammonoids (stratigraphic level No. 3). b: Shell debris cluster and fragment of crushed ammonoid conch (stratigraphic level No. 1). c: Epibionts on the surface of an ammonoid conch (stratigraphic level No. 5). d: Cluster of bivalves, gastropods and cephalopods remains in a siderite nodule (stratigraphic level No. 5). e: Fragment of an ammonoid conch (stratigraphic level No. 3). f: Fragment of an ammonoid conch (?) with terminal aperture and brachiopod valve (stratigraphic level No. 3). g: Specimen of?Anthracoceratites sp. with conch injuries (shown by arrows) (stratigraphic level No. 8). h, i: Bioerosion trace fossils Cyclopuncta girtyi ELIAS, 1958 on the fragments of cephalopod conchs (stratigraphic level No. 5). j: Limonitized conchs of the ammonoid (stratigraphic level No. 7). k: Fragment of an ammonoid conch (stratigraphic level No. 5). Scale bars 10 mm. in Late Bashkirian Ammonoids From The Mospyne Formation Of The Donets Basin, Ukraine
Text-fig. 4. Taphonomic features of the studied localities of ammonoids. a: Sandstone slab with fragmentary remains of productid and spiriferid brachiopods, orthocerids, coiled nautiloids and ammonoids (stratigraphic level No. 3). b: Shell debris cluster and fragment of crushed ammonoid conch (stratigraphic level No. 1). c: Epibionts on the surface of an ammonoid conch (stratigraphic level No. 5). d: Cluster of bivalves, gastropods and cephalopods remains in a siderite nodule (stratigraphic level No. 5). e: Fragment of an ammonoid conch (stratigraphic level No. 3). f: Fragment of an ammonoid conch (?) with terminal aperture and brachiopod valve (stratigraphic level No. 3). g: Specimen of?Anthracoceratites sp. with conch injuries (shown by arrows) (stratigraphic level No. 8). h, i: Bioerosion trace fossils Cyclopuncta girtyi ELIAS, 1958 on the fragments of cephalopod conchs (stratigraphic level No. 5). j: Limonitized conchs of the ammonoid (stratigraphic level No. 7). k: Fragment of an ammonoid conch (stratigraphic level No. 5). Scale bars 10 mm.
Synthetic Nodules for Evaluation of 3D Deep Learning Segmentation Attribution
<p>Both the algorithm used to generate this dataset as well as the comprehensive evaluation metric for visual explanations are detailed in the paper "Attribution of 3D Deep Learning Segmentation in Medical Imaging".</p> <p>This is a synthetic dataset developed to enable the comprehensive evaluation of visual explanation methods applied to deep learning segmentation predictions. The data provided here include 100 training and 100 testing volumes, binary segmentation labels for model training, and explanation segmentation labels for explanation evaluation.</p> <p>The intended workflow for this dataset is: 1) Train a deep learning segmentation model using the 100 training volumes and binary segmentation labels. 2) Use a method of visual explanation to explain the trained model's segmentation decisions on the 100 testing volumes. 3) Use the explanation labels to evaluate the generated explanations.</p> <p> </p> <p>The folders <em>imagesTr</em> and <em>imagesTs</em> contain the training and testing image volumes, respectively. A <em>dataset.json</em> file has also been generated for the images to enable training using the nnUNet pipeline.</p> <p>The folders <em>labelsTr</em> and <em>labelsTs</em> contain the training and testing binary segmentation labels. In both cases, 1 indicates foreground voxels (spiculated nodule) and 0 indicates background voxels.</p> <p>The folders <em>labelsTr_full</em> and <em>labelsTs_full</em> contain the training and testing explanation labels. In both cases, 1 indicates non-spiculated nodule, 2 indicates spiculation structure (discriminating background), 3 indicates spiculated nodule body (segmentation foreground), and 0 indicates background.</p>
Lung nodule CT false positive reduction
<p>This data set is part of the public development data for the <a href="http://auc23.grand-challenge.org/">2023 Automated Universal Classification Challenge</a> (AUC23). The data set concerns the classification of lung nodules on screening thoracic computed tomography (CT) scans and was derived from the <a href="https://luna16.grand-challenge.org/Data/">2016 Lung Nodule Analysis (LUNA) challenge</a>. The data set was previously introduced and described by <a href="https://www.sciencedirect.com/science/article/pii/S1361841517301020?via%3Dihub">Setio et al. (2017)</a> and no images or patient information were added. Only the "false positive reduction" track was considered, where a provided set of nodule candidates should be classified. Data was restructured in compliance with the <a href="https://auc23.grand-challenge.org/">AUC23</a> challenge format. The data set was collected from the largest publicly available reference database for lung nodules: <a href="https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=1966254">The Lung Image Database Consortium image collection</a>.</p> <p>Images are 3D tensors:</p> <ul> <li>0: 3D axial screening CT scan (cropped to candidate nodule's region of interest)</li> </ul> <p>Classification labels:</p> <ul> <li>0: Is a nodule</li> <li>1: Is not a nodule</li> </ul> <p>Folder structure:</p> <p>imagesTr (root folder with all patients and studies)<br> ├── LUNA16_0000_0000.mha (axial CT imaging for nodule 0000)<br> ├── LUNA16_0000_0002.mha (axial CT imaging for nodule 0002)<br> ├── ...<br> </p> <p>Please cite the following article if you are using the <a href="https://luna16.grand-challenge.org/Data/">2016 Lung Nodule Analysis (LUNA) challenge</a> false positive reduction track data set:</p> <pre><code>Setio AAA, Traverso A, de Bel T, Berens MSN, Bogaard CVD, Cerello P, Chen H, Dou Q, Fantacci ME, Geurts B, Gugten RV, Heng PA, Jansen B, de Kaste MMJ, Kotov V, Lin JY, Manders JTMC, Sóñora-Mengana A, García-Naranjo JC, Papavasileiou E, Prokop M, Saletta M, Schaefer-Prokop CM, Scholten ET, Scholten L, Snoeren MM, Torres EL, Vandemeulebroucke J, Walasek N, Zuidhof GCA, Ginneken BV, Jacobs C. Validation, comparison, and combination of algorithms for automatic detection of pulmonary nodules in computed tomography images: The LUNA16 challenge. Med Image Anal. 2017 Dec;42:1-13. doi: 10.1016/j.media.2017.06.015. Epub 2017 Jul 13. PMID: 28732268.</code></pre> <p> </p>
Data from: Mesophotic Foraminiferal-Algal Nodules play a role in the Red Sea carbonate budget
<p>Free-living mesophotic Foraminiferal-Algal Nodules (FANs) have been discovered along the coast of the northern Saudi Arabian Red Sea (NEOM region) where they form a novel benthic ecosystem in mesophotic water depths on the continental shelf. Being mostly spheroidal, the nodules are transported <em>en masse</em> down slope, into the deep water of the basin, where they stop accreting. Radiometric dating informs that FANs can be more than two thousand years old and that they collectively contribute up to 66 g m<sup>-2</sup> year<sup>-1</sup> to the mesophotic benthic carbonate budget and account for at least 980 megatons of CaCO<sub>3</sub>, a substantial contribution considering the depauperate production of carbonate by other means in this light-limited environment. Our findings advance the knowledge of mesophotic biodiversity and carbonate production, and provide data that will inform conservation policies in the Saudi Arabian Red Sea.</p>
CBCT-Guided Navigational Bronchoscopy For Lung Nodules
ClinicalTrials.gov study NCT04758403. IPD Sharing: YES. Countries: 1. Publications: 24.
Data from: Mesophotic Foraminiferal-Algal Nodules play a role in the Red Sea carbonate budget
Open the record for dataset details and reuse information.
A select-and-resequence approach reveals strain-specific effects of Medicago nodule-specific PLAT-domain genes
Open the record for dataset details and reuse information.
Data from: Managing friends and foes: Sanctioning mutualists in mixed‐infection nodules trades off with defense against antagonists
Open the record for dataset details and reuse information.
Effects of stem canker disease on N fixation inputs by Alnus tenuifolia to early-successional floodplains in interior and south-central Alaska. II. Nodule biomass and incidence of canker for individual genets.
This dataset contains nodule biomass and incidence of canker infection for individual genets of Alnus tenuifolia as part of a project studying disease-mediated declines in N-fixation inputs by Alnus tenuifolia to early-successional floodplains in interior and south-central Alaska
Nitrogen fixation, nodule respiration, and nodule Frankia identiy in alder growing in control, N-fertilized, and P-fertilized stands.
This data file includes data of simultaneous measurements of nitrogen fixation and nodule respiration in nodule clusters where Frankia identities were determined using molecular techniques from Alnus tenuifolia growing in replicate control, N-fertilized, and P-fertilized mid-successional stands along the Tanana River.
Data from: Nitrogen fertilization differentially enhances nodulation and host growth of two invasive legume species in an urban environment
Invasive plants negatively impact native communities by altering ecosystem processes and reducing species diversity. Plants in the legume family are overrepresented among invasive taxa and establish in disturbed environments common in urban ecosystems. Mutualisms with rhizobia and anthropogenic activities, such as nitrogen fertilization, may be key mechanisms driving legume invasions of urban habitats. Moreover, legume species and genetic lineages within species may vary in their responses to nitrogen fertilization, making some more likely to invade than others. Despite this threat, it remains unclear whether nitrogen fertilization impacts mutualism and plant growth traits of invasive legumes in urban environments, and whether these effects depend on the genetic origin of invaders. We conducted a common garden experiment using two widespread, invasive legume species, Medicago sativa and Trifolium pratense, to test the effects of species, genetic origin of lineages within species, and nitrogen fertilization on the mutualism. Soil nitrogen was manipulated and effects on traits associated with the mutualism (nodule traits) and plant growth were quantified. Nitrogen fertilization improved nodule traits and host growth for both species, but M. sativa and certain genetic lineages of this species benefited more from fertilization than any of the tested T. pratense lineages. This work reveals how anthropogenic activities alter mutualism traits and plant growth in urban environments, potentially facilitating invasions by leguminous taxa. Because species and lineages varied in the strength of their responses to fertilization, over time some invading legumes may outcompete other plant species or lineages, leading to differential impacts on native communities in urban environments.
Data from: Symbioses with nitrogen-fixing bacteria: nodulation and phylogenetic data across legume genera
How species interactions shape global biodiversity and influence diversification is a central – but also data-hungry – question in evolutionary ecology. Microbially-based mutualisms are widespread and could cause diversification by ameliorating stress and thus allowing organisms to colonize and adapt to otherwise unsuitable habitats. Yet the role of these interactions in generating species diversity has received limited attention, especially across large taxonomic groups. In the massive angiosperm family Leguminosae, plants often associate with root-nodulating bacteria that ameliorate nutrient stress by fixing atmospheric nitrogen. These symbioses are ecologically-important interactions, influencing community assembly, diversity, and succession, contributing ~100-290 million tons of N annually to natural ecosystems, and enhancing growth of agronomically-important forage and crop plants worldwide. In recent work attempting to determine whether mutualism with N-fixing bacteria led to increased diversification across legumes, we were unable to definitively resolve the relationship between diversification and nodulation. We did, however, succeed in compiling a very large searchable, analysis-ready database of nodulation data for 749 legume genera (98% of Leguminosae genera; LPWG 2017), which, along with associated phylogenetic information, will provide a valuable resource for future work addressing this question and others. For each legume genus, we provide information about the species richness, frequency of nodulation, subfamily association, and topological correspondence with an additional data set of 100 phylogenetic trees curated for database compatibility. We found 386 legume genera were confirmed nodulators (i.e., all species examined for nodulation nodulated), 116 were non-nodulating, 4 were variable (i.e., containing both confirmed nodulators and confirmed non-nodulators), and 243 had not been examined for nodulation in published studies. Interestingly, data exploration revealed that nodulating legume genera are ~3× more species-rich than non-nodulating genera, but we did not find evidence that this difference in diversity was due to differences in net diversification rate. Our metadata file describes in more detail the structure of these data that provide a foundational resource for future work as more nodulation data become available, and as greater phylogenetic resolution of this ca. 19,500-species family comes into focus.
Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach
<p>There is interest in understanding the factors behind the biogeography of root-associated bacteria due to the joint effects that plant host, climate, and soil conditions can have on bacterial diversity. For legume crops with remaining wild populations, this is of even more importance, because the effects of cropping on undisturbed root-associated bacterial communities can be addressed. Here, we used a community prediction approach to describe the diversity of the root nodule bacterial communities of rooibos (<i>Aspalathus linearis</i>), an endemic legume crop from South Africa. The goal was to reveal whether patterns of root nodule community composition in paired cultivated and wild rooibos populations could be related to geographical distance, plant traits, and plant population type (i.e. cultivated or uncultivated). We identified a core of dominant and widespread <i>Mesorhizobium</i> ZOTUs that each defined one of 4 different root nodule community classes. Rooibos cultivation impacted root nodule bacterial diversity at regional and local scales, while the geographical origin of the root nodule communities was the strongest predictor of root nodule community structure. Beyond impacts of cultivation on root nodule bacterial diversity, this study suggests a mixture of dispersal limitation and ecological drift regionally, and selection by different plant populations locally, define the biogeography of rooibos root nodule bacterial communities. </p>
Neve David - Flint Nodule I
The artifact is included in this paper: https://www.sciencedirect.com/science/article/pii/S1040618217302185 Neve David is an Early Epipaleolithic site located at the foot of the western slope of the Mount Carmel hills in northern Israel. It was inhabited in the later part of the Early Epipaleolithic, about 15,000–13,000 BC. https://en.wikipedia.org/wiki/Neve_David Photography and photogrammetry - Eli Crater Gershtein Source: Objaverse 1.0 / Sketchfab
Text-fig. 2 Section in proglacial sands and gravels in the abandoned sand pit near Fukov. in Fossils In Late Cretaceous To Early Palaeocene Flint Nodules Embedded In Pleistocene Glaciofluvial Sediments Near Fukov (Děčín District, Northern Bohemia)
Text-fig. 2 Section in proglacial sands and gravels in the abandoned sand pit near Fukov.
Convergent evolution of NFP-facilitated root nodule symbiosis
<p># NFP</p> <p>Scripts and data associated with the manuscript "Convergent evolution of NFP-facilitated root nodule symbiosis."</p> <p>## 00_sequences<br>This directory contains NFP/LYR homologs and annotations.</p> <p>## 02_alignments<br>This directory contains NFP alignments</p> <p>## 03_trees<br>This directory contains gene trees and species tree guides for the analyses.</p> <p>## 04_reconciliation<br>This directory contains notung files and figures for the gene tree reconciliation analysis</p> <p>## 05_synteny<br>This directory contains files for the synteny analyses. The base directory contains circos plots and a subdirectory `Synteny.2.2020` containing scripts and summary output as well as the following:<br>### Results_Apr01.zip<br>Summary of synteny results<br>### csvs.zip<br>An archive containing all csvs in the analysis.<br>### fastas.zip<br>synteny analysis - chr 5 v 8.zip<br>### tsvs.zip<br>An archive containing all csvs in the analysis.<br>### blasts.zip<br>An archive containing blast results.<br>### coords.zip<br>An archive containing genome coordinate files.<br>### gffs.zip<br>An archive containing GFF annotations.<br>### gff3s.zip<br>An archive containing GFF annotations.<br>### imgs.zip<br>An archive containing figure files used for preparing the manuscript.<br> <br>## figs<br>This directory contains figure files used for preparing the manuscript.</p> <p>## Scripts_used_CF<br>This directory contains submission and shell scripts used to conduct the analyses.</p>
A 4.7-myr record of geochemical scanning of a ferromanganese nodule
<p>The geochemical study of a ferromanganese nodule provides a 4.7-myr record of abyssal oxygenation in the Eastern Pacific.</p>
Nitrate and dissolved trace metal data from Mn nodule reduction experiments under anoxic conditions
<p>The uploaded dataset includes nitrate and dissolved trace metal (Mn, Cd, Co, Cu, Fe, Mn, Ni, Pb, Sc, and Zn) data from laboratory incubation experiments using crushed Mn nodules under anoxic conditions. Please refer to our submitted paper for more details about data interpretations.</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.