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Primeira versão do site dadosatmosfericos.org
<p>Screenshot of our first portal showing the results of the supervisor software of the telemetric tests with a meteorological measurements tower.</p>
FIGURES 21 – 22. Pneuminion distribution maps. — 21. All Pneuminion collecting sites. — 22. P in A revision of the South African endemic water beetle genus Pneuminion Perkins (Coleoptera: Hydraenidae)
FIGURES 21 – 22. Pneuminion distribution maps. — 21. All Pneuminion collecting sites. — 22. P. endroedyi.
T-DNAreader: fast and precise identification of T-DNA insertion sites using RNA-seq data
<p><em><span>Agrobacterium</span></em><span>-mediated plant transformation, which enables the delivery of DNA using transfer DNA (T-DNA) binary vectors, is an essential technique in plant research. T-DNAs randomly integrate into the host genome and multiple T-DNAs can integrate in a single transformation event, necessitating the development of efficient, reliable tools to identify the T-DNA insertion sites (TISs). Here, we developed T-DNAreader to identify TISs from RNA-sequencing (RNA-seq) data with high precision, sensitivity, and speed, outperforming existing tools. T-DNAreader detected previously unknown TISs in characterized mutant plants. Overall, T-DNAreader enables the simple identification of TISs within transcribed regions and standardizes the characterization of T-DNA-containing transgenic plants.</span></p>
sea-surface temperature proxy data (TEX86 and UK'37) from Ocean Drilling Program Site 1168
<p>These 2 data files contain the TEX86 and UK'37 sea surface temperature proxy data from Ocean Drilling Program Site 1168, covering the Eocene to recent (35–0 Ma). These were updated compared to previous versions, wherein some alkenone data was omitted.</p>
Supplementary material for "Playback experiments highlight the importance of nearest-neighbor distance and social information for nest site selection in the House Martin (Delichon urbicum)"
<p><strong>Abstract</strong></p> <p>Understanding nest site selection is crucial for species conservation. Bird conservation often involves installing nesting aids to increase nest site availability and induce colonization of unoccupied sites. However, prospecting individuals must find nesting aids, which may be facilitated by social information. Here, we investigated the effectiveness of artificial nests and playback in the declining, migratory House Martin <em>Delichon urbicum</em>. We selected unoccupied sites with artificial nests along a distance gradient to occupied sites and broadcasted conspecific vocalizations during prospection times of House Martins in both the post- and the following pre-breeding periods. Visitation and colonization rates increased considerably in proximity to occupied sites. Playback during the post-breeding and pre-breeding periods enhanced visitation rates, while pre-breeding-only and post-breeding-only playback had smaller positive effects. Colonization rate increased exclusively with pre-breeding-only playback. Colonized playback and non-playback sites had similar breeding success, indicating that playback did not create ecological traps by attracting House Martins to suboptimal sites. Hence, broadcasting conspecific vocalizations informs prospecting birds of nest site availability, thereby increasing visitation, and to some degree, colonization of unoccupied House Martin sites. To boost colonization, we recommend installing artificial House Martin nests within approximately 500 meters of occupied sites and using playback of conspecific vocalizations.</p>
Catalyst sites and active species in the early stages of MTO conversion over cobalt AlPO-18 followed by IR spectroscopy
<p>Supplementary material: Ex-situ DR-UV-visible spectroscopy, Ex-situ FT-IR Spectroscopy. In-situ FT-IR Spectroscopy, In continuo FT-IR Spectroscopy, Brønsted acidity of SAPO-18 </p>
Cropped News Article from University of Potsdam News Site
<p>This data was cropped from the <a href="https://www.uni-potsdam.de/de/nachrichten">University of Potsdam news website</a>. The annotated labels are made by the writers of the articles.</p>
Victorian Coastal Monitoring Program: (1) VCMP Sites; (2) VCMP Coastal Erosion Indicators
<p>This dataset was produced by the Victorian Coastal Monitoring Program (VCMP), Department of Energy, Environment and Climate Action, Victoria State Government, Australia.</p><p><a href="https://www.marineandcoasts.vic.gov.au/marine-and-coastal-knowledge/victorian-coastal-monitoring-program">https://www.marineandcoasts.vic.gov.au/marine-and-coastal-knowledge/victorian-coastal-monitoring-program</a> </p><p><a href="https://www.marineandcoasts.vic.gov.au/__data/assets/pdf_file/0023/625352/VCMP_Erosion-Indicators_April_2023.pdf">https://www.marineandcoasts.vic.gov.au/__data/assets/pdf_file/0023/625352/VCMP_Erosion-Indicators_April_2023.pdf</a></p><p>[ADD LINK TO VCMP SITES METADATA REPORT - ONCE PUBLISHED TO VCMP WEBSITE]</p><p>Products include: </p><p>(1) Complete processed shorelines dataset ('VCMP Sites'), including drone and satellite data, with transects, shorelines, time series, and cross-sections for drone surveys</p><p>(2) Summary outputs ('VCMP Coastal Erosion Indicators'), including the Erosion Warning Indicator (<i>EWI</i>) summary statistics and Erosion Hotspot Detector (<i>EHD</i>) outputs. </p><p>Survey data in this repository were updated to the start of 2023. </p><p>Regularly updated outputs for all VCMP products, including pre-processed VCMP drone data (digital surface models and orthomosaics) can be accessed through the Victorian government (contact <a href="mailto:vcmp@delwp.vic.gov.au">vcmp@delwp.vic.gov.au</a>; <a href="https://www.marineandcoasts.vic.gov.au/marine-and-coastal-knowledge/victorian-coastal-monitoring-program">https://www.marineandcoasts.vic.gov.au/marine-and-coastal-knowledge/victorian-coastal-monitoring-program</a>). </p><p>'VCMP Sites' and 'VCMP Coastal Erosion Indicator' outputs and a wide array of marine and coastal data are viewable through the decision support portal CoastKit (<a href="https://mapshare.vic.gov.au/coastkit/">https://mapshare.vic.gov.au/coastkit/</a>). </p><p>Select outputs are also downloadable in spatial file format through DataShare Victoria (<a href="https://datashare.maps.vic.gov.au/search?q=vcmp">https://datashare.maps.vic.gov.au/search?q=vcmp</a>).</p>
Fig.ç1.C ollection sites of pelagic caligids including 3 stations in Japanese waters (St. 2–4, 2010) and 1 station in the Gulf of ffiailand (St. 1, 2006). in Occurrence of Caligid Copepods (Crustacea) in Plankton Samples Collected from Japan and Ŋailand, with the Description of a New Species
Fig.ç1.C ollection sites of pelagic caligids including 3 stations in Japanese waters (St. 2–4, 2010) and 1 station in the Gulf of ffiailand (St. 1, 2006).
Smoke designations for eastern Kansas monitoring sites during March-May 2022
<p class="Abstract">Prescribed fires (fires intentionally set for mitigation purposes) produce pollutants, which have negative effects on human and animal health. One of the pollutants produced from fires is fine particulate matter (PM<sub>2.5</sub>). PM<sub>2.5</sub> can penetrate deep into the lungs and harm cardiovascular and respiratory systems. The Flint Hills region of Kansas experiences extensive prescribed burning each spring (March - May). Smoke from prescribed fires is often understudied due to a lack of monitoring in the rural regions where prescribed burning occurs, as well as the short duration and small size of the fires. Our goal was to attribute PM<sub>2.5</sub> concentrations to the prescribed burning in the Flint Hills. To determine PM<sub>2.5</sub> increases from local burning, we used low-cost PM<sub>2.5</sub> sensors (PurpleAir) and satellite observations. The Flint Hills were also affected by smoke transported from fires in other regions during 2022. We separated the transported smoke from smoke from fires in eastern Kansas. Based on data from the PurpleAir sensors, we found the 24-hour median PM<sub>2.5</sub> increased by 5.2 µg m<sup>-3</sup> on days impacted by smoke from fires in the eastern Kansas region compared to days unimpacted by smoke. We found the Flint Hills to be the most smoke PM<sub>2.5</sub> impacted region compared to the surrounding area across satellite products and in-situ measurements. </p>
Text-fig. 1. Situation of Early Miocene plant localities. a: Central Europe with Brno area and other fossil sites mentioned in text (1 – Znojmo and Přímětice, 2 – Oberdorf, 3 – Modrý Kameň Basin, 4 – Lipovany, 5 – Ipolytarnóc; CZ – the Czech Republic, PL – Poland, SK – Slovakia, H – Hungary, A – Austria, D – Germany). b: Brno area with Líšeň municipal district indicated. c: Líšeň municipal district with fossil sites indicated by asterisk. in A New Early Miocene (Ottnangian) Flora Of The "Rzehakia Beds" From Brno-Líšeň
Text-fig. 1. Situation of Early Miocene plant localities. a: Central Europe with Brno area and other fossil sites mentioned in text (1 – Znojmo and Přímětice, 2 – Oberdorf, 3 – Modrý Kameň Basin, 4 – Lipovany, 5 – Ipolytarnóc; CZ – the Czech Republic, PL – Poland, SK – Slovakia, H – Hungary, A – Austria, D – Germany). b: Brno area with Líšeň municipal district indicated. c: Líšeň municipal district with fossil sites indicated by asterisk.
Interactions of netrin-1 through its glycosylation sites immobilize DCC receptors by favoring its constitutive clustering
Open the record for dataset details and reuse information.
AERPAW helikite spectrum measurements at Lake Wheeler site in May 2022
<p>The AERPAW helikite flew up to 500 feet altitude, at increments of 10 meters, while waiting for 5 minutes in between altitude changes at the Lake Wheeler site on May 2022. The USRP B205mini continuously sweeps the spectrum up to 6 GHz while the helikite is at a fixed altitude, and power measurements at each frequency band are logged. The results are post-processed in Matlab to observe the spectrum occupancy at different bands and the effect of spectrum sensing altitude on the occupancy results.</p> <p>Similar datasets for August 2022 and August 2023 are in separate Dryad deposits. </p>
Dataset for the paper "A framework for robotic excavation and dry stone construction using on-site materials"
<p>Stone data from the <i>Science Robotics</i> paper "A framework for robotic excavation and dry stone construction using on-site materials" containing:</p><ul><li>Mesh files of 1,100 stones (quarried boulders, erratics, and concrete debris) that were digitized by the autonomous excavator HEAP<ul><li><a href="https://zenodo.org/api/records/10038881/draft/files/1100%20Unprocessed%20Stone%20Meshes.zip/content">1100 Unprocessed Stone Meshes.zip: </a>Raw mesh files directly from the poisson reconstruction of accumulated LiDAR points, containing some artifacts and floating geometries</li><li><a href="https://zenodo.org/api/records/10038881/draft/files/1100%20Closed%20Stone%20Meshes.zip/content">1100 Closed Stone Meshes.zip: </a>Clean, closed, downsampled meshes</li><li><a href="https://zenodo.org/api/records/10038881/draft/files/Stone_Shape_Properties.csv/content">Stone_Shape_Properties.csv: </a>Properties file with a list of the stone IDs (IDs in the 1xxx and 3xxx range typically correspond to concrete elements) and select shape properties</li></ul></li><li>A dataset of candidate placements from automatically generated stone walls. The candidate placement data zip files contain:<ul><li><a href="https://zenodo.org/api/records/10038881/draft/files/Candidate_Placement_Data-npy.zip/content">Candidate_Placement_Data-npy.zip: </a>SDF (.npy) representation of each candidate, with three channels of 32x32x32 for distances to the stone, the already-placed stones, and the target wall</li><li><a href="https://zenodo.org/api/records/10038881/draft/files/Candidate_Placement_Data-pcd.zip/content">Candidate_Placement_Data-pcd.zip: </a>Point cloud (.pcd) representations of each candidate, with separate files for the placed stone, target wall (search volume), and already-placed stones (where they exist)</li></ul></li><li><a href="https://zenodo.org/api/records/10038881/draft/files/sdf_classifier.zip/content">sdf_classifier.zip: </a>Python examples:<ul><li>Rendering the three channel SDF data to mesh geometry using marching cubes and libigl</li><li>Candidate SDF classification using the pretrained model</li></ul></li><li>Candidate attributes and labels<ul><li><a href="https://zenodo.org/api/records/10038881/draft/files/candidate_attributes_labels.csv/content">candidate_attributes_labels.csv: </a>CSV file containing a list of UUID's corresponding to each candidate placement in the dataset. For each candidate, additional information is included about the dimensions and location of the solution, together with the (subjectively) hand-labelled binary value for placement viability. </li></ul></li><li><a href="https://zenodo.org/api/records/10038881/draft/files/README.md/content">README.md: </a>An additional readme with some details on the attributes file</li></ul><p>If you use this data in your research, please cite the <a href="https://www.science.org/doi/10.1126/scirobotics.abp9758">journal article</a>.</p><p> </p>
Figs 1–2. Collection sites. 1 in Coccolithophorids in Polar Waters: Calciarcus spp. Revisited
Figs 1–2. Collection sites. 1 – map of the Antarctic region indicating sampling sites; 2 – map of the Arctic showing the location of sampling sites.
Ecosystem fluxes and ground temperatures - Abisko tundra site
<p>Observational data from a tundra site near Abisko in Northern Sweden (68°21’N, 18°49′E) consisting of NEE, daily GPP, ER, and ground temperature (5 cm depth), for the growing seasons 2011 to 2012.</p> <p>Finderup Nielsen T., Ravn N. R., Michelsen A. (2019) Increased CO2 efflux due to long-term experimental summer warming and litter input in subarctic tundra – CO2 fluxes at snowmelt, in growing season, fall and winter. Plant and Soil 444:365-382 https://doi.org/10.1007/s11104-019-04282-9</p> <p> </p>
Costa Rica mosquito community species occurrence and site environmental data, July - August 2017
<p>Land use change is an important driver of both biodiversity loss and zoonotic disease transmission in tropical countryside landscapes. Developing solutions for protecting biodiversity, public health, and livelihoods in working landscapes requires understanding the spatial scales at which habitat characteristics such as land cover shape biodiversity, especially for arthropods that transmit pathogens. A growing body of evidence shows that species richness for many taxa correlates with tree cover at small spatial scales of <100 m, indicating that local tree cover management is a promising conservation tool. To investigate whether mosquito species richness, community composition, and presence of specific disease vector species respond to tree cover—and if so, whether at spatial scales similar to other taxa—we surveyed mosquito communities along a tree cover gradient and across agricultural, residential, and forested land uses in rural southern Costa Rica. We found that tree cover was both positively correlated with mosquito species richness and negatively correlated with the presence of the common invasive dengue vector <em>Aedes albopictus</em>, particularly at small spatial scales of 80 – 200m<em>. </em>Beyond tree cover, land use type predicted community composition and <em>Ae. albopictus </em>presence, but not species richness. The results suggest that preservation and expansion of tree cover at local scales can protect biodiversity for a wide range of taxa and also confer protection against disease vector occurrence.</p>
Supplemental Movie 2: Clustered Ca2+ transients (CTCs) in gastric ICC-MY occur from multiple firing sites.
<p><strong><span>Supplemental Movie 2: Clustered Ca<sup>2+</sup> transients (CTCs) in gastric </span><span>ICC-MY occur from multiple firing sites</span></strong><span>.<span> </span>ICC-MY in the gastric antrum firing of CTCs and imaged at high resolution with a spinning disk confocal microscope using a 60x objective. </span><span>Ca</span><sup><span>2+</span></sup><span><span> </span></span><span>signals were monitored in a gastric muscle from a mouse with the genetically encoded </span><span>Ca</span><sup><span>2+</span></sup><span><span> </span></span><span>indicator, GCaMP6f, expressed exclusively in ICC. The left panel shows typical stellate-shaped ICC-MY with multiple interconnecting processes. The middle panel shows the </span><span>Ca</span><sup><span>2+</span></sup><span><span> </span></span><span>particle (PTCL) activity, color coded in blue for raw PTCLs, and the centroids of particles are indicated in purple and green indicates </span><span>Ca</span><sup><span>2+</span></sup><span><span> </span></span><span>firing sites. There are multiple sites firing </span><span>Ca</span><sup><span>2+</span></sup><span><span> </span></span><span>transients during the CTCs.<span> </span>The right panel shows an occurrence map of color-coded initiation/firing sites. The pattern of firing sites </span><span>Ca</span><sup><span>2+</span></sup><span><span> </span></span><span>activity was temporally clustered as activation of </span><span>Ca</span><sup><span>2+</span></sup><span><span> transients </span></span><span>swept through the network of ICC-MY.<span> </span>The onset of the CTCs was explosive, and then asynchronous firing of occurred at multiple sites and was sustained for more than 2 sec.<span> </span>Note also the complete quiescence of firing immediately upon conclusion of a CTC (absolute refractory period) and then sporadic initiation of firing with time.<span> </span>It is the re-initiation of firing that sets off the next CTC by activating ANO1 channels, depolarization and activation of voltage-dependent Ca<sup>2+</sup> current (see text for details).<span> </span>Reformatted with permission from reference </span><span><span>(106)</span></span><span>.<span> </span></span></p>
Manual active layer and and water table depth measurements from the autochamber sites at Stordalen Mire, northern Sweden (2003-2017)
<p>Files:</p> <ul> <li><strong>Active_Layer_Water_Table_03-17.xlsx</strong> - Data file, with main data in the "DATA" tab.</li> <li><strong>IsoGenieSite_AL_WTD_MapsVisualNotes_200310.pdf</strong> - Visual notes on the measurement locations.</li> </ul> <p>The following site labels (with chamber numbers in parentheses) correspond to the main autochamber sites:</p> <ul> <li>Dry (1,3,5) = Palsa Autochamber Site</li> <li>Mesic (2,4,6) = Sphagnum Autochamber Site</li> <li>Wet (7,8) = Eriophorum Autochamber Site</li> </ul> <p>Water table depth (W D) was measured in wells.</p> <p>Active layer depth (A L) was measured by inserting a metal rod into the surface. The original instruction page is included in page 3 of the pdf.</p> <p>All depths are in centimeters (cm) below peat surface (i.e. peat or <em>Sphagnum</em> spp. vegetation surface = 0), with negative values indicating depth below the surface and positive values (for water table) indicating height of standing water above the surface. Blank data in the Palsa or water table column means no water table observed.</p> <p>Staff gauge was added July 2006 at the edge of a small pond in the fen visible from the shack, with measurements reported in meters. All other measures are in cm.</p> <p> </p> <p>FUNDING:</p> <p>We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164.</p> <p>This research is a contribution of the EMERGE Biology Integration Institute, funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070. The IsoGenie Project (which funded much of the work at these sites during the measurement period) was funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research, grant #s DE-SC0004632, DE-SC0010580, and DE-SC0016440.</p>
DoubleChEC program to identify transcription factor binding sites from mapped ChEC-seq data
<p>ChIP-seq (chromatin immunoprecipitation followed by sequencing) is commonly used to identify genome-wide protein-DNA interactions. However, ChIP-seq often gives a low yield, which is not ideal for quantitative outcomes. An alternative method to ChIP-seq is ChEC-seq (Chromatin endogenous cleavage with high-throughput sequencing). In this method, the endogenous TF (transcription factor) of interest is fused with MNase (micrococcal nuclease) that non-specifically cleaves DNA near binding sites. Compared to the <a href="https://www.nature.com/articles/ncomms9733" rel="nofollow">original ChEC-seq method</a>, the <a href="https://sites.northwestern.edu/bricknerlab/" rel="nofollow">modified version</a> requires far less amplification. Since <a href="https://github.com/macs3-project/MACS/tree/master#introduction">MACS3</a> failed to identify peaks in data generated from the modified ChEC-seq method, a new peak finder has been developed specifically for it.</p> <p>There are three functions in the <em><code>peak_finder/</code></em>. <code>callpeaks()</code> is used to identify peaks from BAM files. <code>goanalysis()</code> is used to make GO (Gene Ontology) term plots from peaks. <code>bedtomeme()</code> is a wrapper function to perform <a href="https://meme-suite.org/meme/tools/meme" rel="nofollow">MEME analysis</a> in R <strong>after <a href="https://meme-suite.org/meme/doc/download.html" rel="nofollow">MEME Suite</a> is installed locally</strong>.</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.