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7,503 results for “methods”
Pelagic, epilimnetic production estimates in Sparkling, Trout (Wisconsin), Acton (Ohio), and Castle (California) Lakes (USA) calculated using 14C and free-water O2 metabolism methods, 2007 - 2017
Concurrent daily estimates of pelagic, eplilimnetic production (mmol C m3 d) generated from 14C incubations and diel changes in high frequency dissolved oxygen data (free-water). Original data derived from the North Temperate Lakes Long Term Ecological Research program (Sparkling [2007-2013], Trout [2007-2012] Lakes), Castle Lake Research Station (Castle Lake [2014-2017]), and Center for Aquatic and Watershed Sciences (Acton Lake [2010-2014]). 14C production estimates were generated as part of each research programs core data collection. Free-water production estimates generated using high frequency sensor data provided by research programs and Phillips (2020) time-varying, Bayesian metabolism model.
Creating multi-themed ecological regions for macroscale ecology: Testing a flexible, repeatable, and accessible clustering method
This dataset was created for the following publication: Cheruvelil, K.S., S. Yuan, K.E. Webster, P.-N. Tan, J.-F. Lapierre, S.M. Collins, C.E. Fergus, C.E. Scott, E.N. Henry, P.A. Soranno, C.T. Filstrup, T. Wagner. Under review. Creating multi-themed ecological regions for macrosystems ecology: Testing a flexible, repeatable, and accessible clustering method. Submitted to Ecology and Evolution July 2016. This dataset includes lake total phosphorus (TP) and Secchi data from summer, epilimnetic water samples, as well as 52 geographic variables at the HU-12 scale; it is a subset of the larger LAGOS-NE database (Lake multi-scaled geospatial and temporal database, described in Soranno et al. 2015). LAGOS-NE compiles multiple, individual lake water chemistry datasets into an integrated database. We accessed LAGOSLIMNO version 1.054.1 for lake water chemistry data and LAGOSGEO version 1.03 for geographic data. In the LAGOSLIMNO database, lake water chemistry data were collected from individual state agency sampling and volunteer programs designed to monitor lake water quality. Water chemistry analyses follow standard lab methods. In the LAGOSGEO database geographic data were collected from national scale geographic information systems (GIS) data layers. The dataset is a subset of the following integrated databases: LAGOSLIMNO v.1.054.1 and LAGOSGEO v.1.03. For full documentation of these databases, please see the publication below: Soranno, P.A., E.G. Bissell, K.S. Cheruvelil, S.T. Christel, S.M. Collins, C.E. Fergus, C.T. Filstrup, J.F. Lapierre, N.R. Lottig, S.K. Oliver, C.E. Scott, N.J. Smith, S. Stopyak, S. Yuan, M.T. Bremigan, J.A. Downing, C. Gries, E.N. Henry, N.K. Skaff, E.H. Stanley, C.A. Stow, P.-N. Tan, T. Wagner, K.E. Webster. 2015. Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science and data reuse. GigaScience 4:28 doi:10.1186/s13742-015-0067-4 .
Database of measurements for damage detection of steel beam splice connection by Coaxial Correlation Method in 6-D space
<p>This database includes series of measurements of the structure's response taken in six-dimensional space using two 6D sensors, coaxially positioned on either side of the investigated splice connection between two steel beams. The data set consists of two parts. The first part of the data set is measurements for six different specimens with wave type impact – short sweep signal with duration 0.05 s. The second part is the measurements during splice connection degradation of one of the specimens with short impulse. The degradation of a connection is presented by four different states of joints. In the "<strong>Read_me_first.pdf</strong>" is described the experiment, the format of .csv files names and files' structure.</p><p>Used materials, methods and results for the second part of the data set is described in Buka-Vaivade, K.; Kurtenoks, V.; Serdjuks, D. Non-Destructive Damage Detection of Structural Joint by Coaxial Correlation Method in 6D Space. <i>Buildings</i> <strong>2023</strong>, <i>13</i>, 1151. https://doi.org/10.3390/buildings13051151</p>
Database of measurements for damage detection of steel beam splice connections by Coaxial Correlation Method in 6-D space
<p>This database includes series of measurements of the structure's response taken in six-dimensional space using two 6D sensors, coaxially positioned on either side of the investigated splice connection between two steel beams. The data set consists of measurements for six different specimens with two types of impact – sweep signal with duration 0.5 s and short impulse, during degradation of the splice connections realised by unbolting the bolts in the connections. In the "<strong>Read_me_first.pdf</strong>" is described the experiment, the format of .csv files names and files' structure.</p><p>This database is a continuation of the database Kurtenoks, V., Buka-Vaivade, K., Serdjuks, D., Lapkovskis, V., Mironovs, V., & Podkoritovs, A. (2023). Database of measurements for damage detection of steel beam splice connection by Coaxial Correlation Method in 6-D space (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10077332<br>Suggested by authors data post-processing is described in Buka-Vaivade, K.; Kurtenoks, V.; Serdjuks, D. Non-Destructive Damage Detection of Structural Joint by Coaxial Correlation Method in 6D Space. <i>Buildings</i> <strong>2023</strong>, <i>13</i>, 1151. https://doi.org/10.3390/buildings13051151</p>
Perry et al. (2025) Data Package: Effects of diluted bitumen and remediation methods on lower trophic levels within boreal lake enclosures. Data were collected during 2019 at the IISD Experimental Lakes Area in Northwestern Ontario.
This data package corresponds to a research study by Perry et al. (2025) titled "The effects of diluted bitumen, the shoreline cleaner Corexit EC9580A, and bio-stimulation on the lower food web of a boreal lake, with a focus on natural phytoplankton communities." The study examines the effect of controlled spills of diluted bitumen and two remediation methods on lower trophic levels (phytoplankton, periphyton, zooplankton). The study was undertaken within shoreline enclosures within Lake 260 at the IISD Experimental Lakes Area during 2019. In addition to primary oil recovery using sorbent pads, the two secondary remediation methods: 1) enhanced monitoring natural recovery (eMNR) that included the biostimulation of microbial communities via a slow release nutrient fertilizer, and 2) a shoreline washing agent (SWA or SCA; Corexit 9580) used to increase oil removal from affected shorelines. This data package includes the response of perphyton and zooplankton.
Data to 'The updated and improved method for water scarcity impact assessment in LCA, AWARE2.0'
<p>This dataset includes the AWARE2.0 characterization factors as documented in the article "The updated and improved method for water scarcity impact assessment in LCA, AWARE2.0" (<a href="https://www.doi.org/10.1111/jiec.70023" target="_blank" rel="noopener">DOI: 10.1111/jiec.70023</a>). When using the dataset in your own work, please cite the article and provide reference to this zenodo repository.</p> <p>For importing the country-level characterization factors into LCA software, please see the AWARE2.0 implementations (openLCA, SimaPro, brightway2) in IMPACT World+, version 2.1: <a title="IMPACT World+ version 2.1" href="https://doi.org/10.5281/zenodo.14041258">https://doi.org/10.5281/zenodo.14041258</a></p> <h3>Content</h3> <p><strong>- native resolution (monthly, watershed scale):</strong></p> <ul> <li><strong>AWARE20_Native_CFs_geospatial.gpkg</strong>: Geospatial file containing the AWARE2.0 basins as polygons with associated monthly and annual CFs</li> <li><strong>AWARE20_Native_CFs_geospatial.kmz</strong>: Version of <em>AWARE20_Native_CFs_geospatial.gpkg </em>for GoogleEarth</li> <li><strong>AWARE20_Native_CFs.xlsx</strong>: AWARE2.0 CFs on basin level (monthly and annual) and associated water consumption used for weighting</li> <li><strong>AWARE20_Intermediate_Variables.xlsx</strong>: Intermediate Variables from the calculation of the AWARE2.0 CFs, such as the longterm average natural and actual water availability, the AMDs, the EFRs, etc.</li> <li><strong>figures_AWARE_AWARE20_comparison_all_basins.zip</strong>: Figures comparing CFs, AMDs, Natural and Actual Availability, EWRs, and EFR coefficients between AWARE and AWARE2.0, for each of the 8149 basins individually. Consult these figures for a visual impression of how and why CFs might have changed between AWARE and AWARE2.0.</li> </ul> <p><strong>- spatiotemporal aggregations:</strong></p> <ul> <li><strong>AWARE20_Countries_and_Regions.xlsx</strong>: AWARE2.0 CFs aggregated according to geography definitions of GLAM and ecoinvent <a href="https://geography.ecoinvent.org/#version-2-5-ecoinvent-3-10" target="_blank" rel="noopener">(version 2.5, applicable to ecoinvent 3.10) </a></li> <li><strong>AWARE20_Subnational_Resolution.xlsx</strong>: AWARE2.0 CFs aggregated to subnational resolution, using the GADM dataset version 4.1 (<a href="https://gadm.org/old_versions.html" target="_blank" rel="noopener">https://gadm.org/old_versions.html</a>)</li> <li><strong>AWARE20_Crop_Specific.xlsx</strong>: AWARE2.0 CFs aggregated according to geography definitions of ecoinvent <a href="https://geography.ecoinvent.org/#version-2-5-ecoinvent-3-10" target="_blank" rel="noopener">(version 2.5, applicable to ecoinvent 3.10)</a>, using crop-specific irrigation water consumption for 27 crop classes as spatiotemporal weights. See readme sheet in Excel file for more information.</li> </ul> <p> </p> <h3><strong>Changes:</strong></h3> <ul> <li>v1.0.1: <ul> <li>addition of crop-specific spatiotemporal aggregations (AWARE20_Crop_Specific.xlsx)</li> </ul> </li> <li>v1.0.0 (corresponding to published article): <ul> <li>update of readme sheets with appropriate references to corresponding article</li> <li>update of reference "Müller Schmied et al. (2024)"</li> <li>added file: AWARE20_Subnational_Resolution.xlsx</li> </ul> </li> <li> v0.0.3: <ul> <li>use bug-fixed WaterGAP2.2e data from Sept 2023</li> <li>added country and subnational aggregations</li> <li>changed "NoData" to "NotDefined" in the tables</li> <li>added gridcell pHWC to intermediate variables</li> <li>corrected table of water consumption data without post-processing in "Intermediate_Variables"</li> </ul> </li> </ul> <p> </p> <h3><strong>Caveats:</strong></h3> <ul> <li>Spatial CF aggregations for treaties: <ul> <li>Due to the creation date of the data set, the <strong>BRICS aggregations </strong>in<strong> </strong><em>AWARE20_Countries_and_Regions.xlsx</em> do not include the states that joined after 2023. In <em>AWARE20_Crop_Specific.xlsx</em>, the 10-member BRICS is labeled BRICS+.</li> </ul> </li> </ul>
Database of measurements for damage detection of T-type timber structural joint by Coaxial Correlation Method in 6-D space
<p>This database includes series of measurements of the structure's response taken in six-dimensional space using two 6D sensors, coaxially positioned on either side of the investigated joint between two timber beams connected at an angle of 90⁰. Presented data related to seven different states of joints, five load levels, and two type of input signal (short impulse and sweep signal with duration 0.5 seconds). In the "<strong>Read_me_first.pdf</strong>" is described the experiment, the format of .csv files names and files' structure.</p>
Database of measurements for damage detection of panel-to-panel moment joints in timber structures by Coaxial Correlation Method
<p>This database includes series of measurements of the structure's response taken in six-dimensional space using two 6D sensors, coaxially positioned in two different ways on either side of the investigated panel-to-panel connection. Presented data related to ten different states of joints, two load levels, and two type of input signal (short impulse and sweep signal with duration 0.5 seconds with frequency range from 10 Hz to 2000 Hz). In the "<strong>Read_me_first.pdf</strong>" is described the experiment, the format of .csv files names and files' structure.</p><p>Used materials, methods and results for the case of static load equal to 151.8 kg with sweep-type input signal, and T2 scheme of sensors placement is described in Kurtenoks, V.; Kurajevs, A.; Buka-Vaivade, K.; Serdjuks, D.; Lapkovskis, V.; Mironovs, V.; Podkoritovs, A.; Vilnitis, M. The Quality Assessment of Timber Structural Joints Using the Coaxial Correlation Method. <i>Buildings</i> <strong>2023</strong>, <i>13</i>, 1929. https://doi.org/10.3390/buildings13081929</p>
WILLOW - Norther: data set for the full-scale validation of model-based virtual sensing methods for an operational offshore wind turbine
<h1><em><strong>1. General description </strong></em></h1> <p>This data set contains as-build design information, as well as full-scale vibration response measurements from an operational offshore wind-turbine. The turbine is part of the Norther wind farm which is located in the Belgian North Sea<em> </em>and includes a total of 44 Vestas V164 (8.4MW) wind turbines on monopile foundations, see <a href="../api/records/11093262/draft/files/Fig1_Norther_locaction.png/content" target="_blank" rel="noopener noreferrer">Fig1_Norther_locaction.png</a>. This data set is intended to verify and validate model-based virtual sensing algorithms, using data as well as modeling information from a real turbine. </p> <h2><em><strong>1.1 Summary of the shared structural information</strong></em></h2> <p>The included information entails a detailed description of the geometric properties of the monopile and transition piece, distributed and lumped structural masses . All information shared in this record is conform the as-designed documentation. An example of the lumped masses considered in the model input files is presented in "<a href="../api/records/11093262/draft/files/Fig2_Sensor_Network.png/content" target="_blank" rel="noopener">Fig2_Sensor_Network.png"</a></p> <h2><em><strong>1.2 Summary of the shared geotechnical information</strong></em></h2> <p>Monopiles are distinguished by the significant role of soil-structure interaction. Ground reaction is most typically included in the structural model as non-linear p-y curves. Different p-y curves are available for a certain number of soils in the standards applicable to offshore structures (API RP 2GEO, 2011, and ISO 19901-4:2016(E), 2016).</p> <p>The required soil properties to define p-y curves according to the API framework are given in the soil profile provided in a separate Excel. Rather than symbols, the name of the soil properties is generally used as column header (e.g., <em>Undrained shear strength</em>). Therefore, it is straightforward to identify each soil parameter. The only soil parameter that might lead to confusion is:</p> <ul> <li><em>"epsilon50 [-]" </em>represents the vertical strain at half the maximum principal stress difference in a static undrained triaxial compression test on an undisturbed soil sample.</li> </ul> <p>It's worthy to note that estimates for the small shear strain stiffness, referred to as Gmax, are also included. Despite not being required as an input to define the API p-y curves, this parameter remains a key input for other soil reaction frameworks than the API (e.g., PISA). </p> <h2><em><strong>1.3 Summary of the shared measurement data</strong></em></h2> <p>Two sets of measurement data have been curated for validation purposes; the first interval has been collected during parked conditions, whereas the second interval has been collected during rated operational conditions. Both records have a length of 2 hours, and are subdivided into 10-minute data sets. Furthermore 1Hz SCADA data has been made available for the selected intervals. All different data sources are time synchronized and have been subjected to several internal quality checks. </p> <p>The sensor network on NRT-WTG is illustrated in in <strong>Fig. 2, </strong>whereas a description of the sensor types is presented in <strong>Tab.1.</strong> The acceleration sensors are installed in the horizontal plane, and measure tangential (Y) and orthogonal (X) to the wall, where the positive Y direction is pointing clockwise and the positive X direction is pointing inwards. All strain sensors are installed vertically and are located on the inside of the wall.</p> <table> <tbody> <tr> <td><strong>Data type </strong></td> <td><strong>Sensor type</strong></td> <td><strong>Fs (Hz)</strong></td> <td> <p><strong>Level mLAT (m)</strong></p> </td> <td><strong>Description </strong></td> </tr> <tr> <td>Acceleration (g) </td> <td>Piezo-electric acc. sensor (<strong>ACC</strong>)</td> <td>30</td> <td>15, 69, 97 </td> <td>3 Bi-directional accelerometers at different levels. LAT 15 installed at 240 degree heading; LAT 69 and 97 at 60 degree.</td> </tr> <tr> <td>Strain (micro strain)</td> <td>Resistive strain gauge (<strong>SG</strong>)</td> <td>30</td> <td>14</td> <td>6 SGs: equally spaced around the inner circumference of the can. Headings: 50, 110, 170, 230, 290, 350 degree.</td> </tr> <tr> <td>Strain (micro strain)</td> <td>Fiber-Bragg Grating strain gauge (<strong>FBG</strong>)</td> <td>100</td> <td>-17, -19</td> <td>2 FBGs per level at 165 and 255 degree respectively.</td> </tr> </tbody> </table> <p><strong>Table 1. Description of sensor types.</strong></p> <p>The FBG strain time series have been synchronized with the SG time series using using a cross-correlation based approach. Therefore the SG data has been used to genereate refrence strain time series at the headings of the FBG sensors; the FBG data is subsequently synchronized with regard to this reference time series. No synchronization of the acceleration data was needed, since these are collected using the same data aquisition system as the SG data. </p> <p>The SG strain time series have been calibrated and temperature compensated, whereas this is not the case for the FBG strain time series. The latter have a yet to be determined calibration offset. </p> <p>In conjunction to the sensor channels presented in <strong>Tab. 1</strong>, 1 Hz SCADA data is provided. A summary of the provided SCADA parameters, all sampled at 1Hz, is presented in <strong>Tab 2.</strong></p> <table> <tbody> <tr> <td><strong>Parameter</strong></td> <td><strong>Unit</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>Wind speed</td> <td>m/s</td> <td>Wind speed as recorded in the turbine SCADA</td> </tr> <tr> <td>Wind direction</td> <td>°</td> <td>Wind direction relative to North (0°) as recorded in the turbine SCADA</td> </tr> <tr> <td>Yaw angle</td> <td>°</td> <td>Yaw orientation of the nacelle relative to North (0°) as recorded in the turbine SCADA</td> </tr> <tr> <td>Pitch angle</td> <td>°</td> <td>Rotor blade pitch as recorded in the turbine SCADA</td> </tr> <tr> <td>Rotor speed</td> <td>rpm</td> <td>Rotor speed in rotations per minute as recorded in the turbine SCADA</td> </tr> <tr> <td>Power</td> <td>kW</td> <td>Active power of the turbine as recorded in the turbine SCADA</td> </tr> </tbody> </table> <p><strong>Table 2. </strong>List of provided SCADA parameters</p> <p> </p> <p>A summary of the selected intervals and relevant corresponding scada parameters is given in <strong>Tab 3</strong>.</p> <table> <tbody> <tr> <td><strong>Scenario </strong></td> <td><strong>T1 (UTC)</strong></td> <td><strong>T2 (UTC) </strong></td> <td><strong>Windspeed</strong></td> <td><strong>RPM </strong></td> <td><strong>Pitch </strong></td> </tr> <tr> <td>Parked</td> <td> <p>03/07 01:30</p> </td> <td> <p>03/07 03:30</p> </td> <td>< 4.5 m/s</td> <td>~1</td> <td>~18 °</td> </tr> <tr> <td>Rated</td> <td> <p>05/07 22:30</p> </td> <td> <p>06/07 00:30 </p> </td> <td>~15 m/s</td> <td>10.5</td> <td>8.1°</td> </tr> </tbody> </table> <p><strong>Table 3. </strong>Selected data intervals and relevant scada parameters</p> <p> </p> <h1><em><strong>2. Included in this version </strong></em></h1> <h2><em><strong>2.1 Version - 0.1.0</strong></em></h2> <ul> <li>Relevant Design information can be found in: <ul> <li>Geometry data for NRT-WTG: "WILLOW-Geometry_v4.xlsx"</li> <li>Best estimate soil profile: "WILLOW-BE_soil_profile.xlsx"</li> </ul> </li> <li>Acceleration, strain and scada data can be found in the following parquet files: <ul> <li>Measurement data for the parked case: "NRT-WTG_Parked.parquet.gz"</li> <li>Measurement data for the rated case: "NRT-WTG_Rated.parquet.gz"</li> </ul> </li> </ul> <p> </p> <h1><em><strong>3. Importing parquet files </strong></em></h1> <p>To import the measurement data into Python it is recommended to use pandas:</p> <pre>import pandas as pd<br># Read Parquet file with Pandas: relative_file_path = '<a href="../api/records/11093262/draft/files/NRT-WTG_Parked.parquet.gz/content" target="_blank" rel="noopener noreferrer">NRT-WTG_Parked.parquet.gz</a>' data = pd.read_parquet(relative_file_path ) <br><br>Once the dataframe has been imported, the users can process/re-arrange the raw data according the their needs; it should be noted that the imported dataframe contains NAN values - these are caused by the different sampling rates of the provided signals. </pre>
Datasets to "Compressible test-field method and its application to shear dynamos"
<pre>This directory contains an index.html file with links to the run directories and idl plotting routines with secondary data for the other figures for the paper "Compressible test-field method and its application to shear dynamos" by M. J. Kapyla, M. Rheinhardt, & A. Brandenburg (Astrophys. J., in press, arXiv:2106.01107). If anything turns out to be incomplete, please email maarit.kapyla@aalto.fi or brandenb@nordita.org. </pre>
Experimental data for "Deep Learning Methods for Colloidal Silver Nanoparticle Concentration and Size Distribution Determination from UV-Vis Extinction Spectra"
<p>Testing data (experimental data) for neural networks published in preprint https://doi.org/10.48550/arXiv.2404.10891</p> <p>The UV-VIS-NIR spectral data was also used in the dissertation of Nadzeya Khinevch, titled "Two-dimensional structures of nanoparticles for elements of surface-enhanced Raman scattering substrates".</p> <p>Emails of the corresponding authors:</p> <p>Tomas Klinavičius tomas.klinavicius@ktu.lt</p> <p>Tomas Tamulevičius tomas.tamulevicius@ktu.lt</p>
FixMe: An Incremental Lightweight Method for Vulnerability Data Collection for Security Patch Prediction
<div> <div>This repository has the FixMe dataset and the source code for extracting the new dataset. is a lightweight approach for collecting code patches based on analyzing the commits of various version control systems. The practical framework is designed to generate patches across a wide array of programming languages. This open-source tool streamlines the process of gathering vulnerability records from the Common Vulnerabilities and Exposures (CVE) database through an incremental approach. By embracing an incremental methodology, we expedite the acquisition of data, ensuring the inclusion of newly identified vulnerabilities and their corresponding patch pairs. Our methodology involves extracting security issues, obtaining vulnerability-fixing commits, and retrieving relevant source code from various projects. The extracted dataset by the FixMe tool supports for the automated patch prediction, automated program repair, commit classification, vulnerability prediction and more.</div> </div>
GPR data used to test the efficient deconvolution method of Schmelzbach and Huber (2015)
<p>GPR data recorded with Pulse Ekko Pro from Sensors & Software on the river bed of the Tagliamento River (NE Italy).</p> <p>This data was used to test the efficient deconvolution scheme of Schmelzbar and Huber (2015):</p> <p>C. Schmelzbach, E. Huber (2015) Efficient Deconvolution of Ground-Penetrating Radar Data. IEEE Transactions on Geoscience and Remote Sensing, 53(9): 5209 - 5217<br> doi: <a href="http://dx.doi.org/10.1109/TGRS.2015.2419235">10.1109/TGRS.2015.2419235</a></p>
Mappings for "Developing a Scalable Annotation Method for Large Datasets That Enhances Alarms With Actionability Data to Increase Informativeness: Mixed Methods Approach"
<p>Studies identified false and non-actionnable alarms as a factor for alarm fatigue in intensive care units.</p> <p>To annotate patient alarms, and analyse the alarm situation in intensive care units, we conceptualized and performed data mappings related to airway management and medication interventions. The mappings were based on information retrieved from the patient data management system (PDMS) and clinical expertise. For the airway management mappings, we used additional resources such as ISO 19223:2019 or ventilator instruction manuals. The mappings do not include patient data.</p> <p>As the mappings are generic, they could be used in other contexts than alarm annotation and research.</p> <p><strong>1. Respiratory Management Mappings:</strong></p> <ul> <li>General tables summarizing the 1) categories based on ISO 19223:2019 to describe respiratory support therapies (RSTs), 2) defining the invasiveness level of a RST and 3) listing the abbreviations used in the mappings</li> <li> <p>Tables including PDMS entries for airway devices (ADs), ventilation devices (VDs), and ventilation modes (VMs)</p> </li> <li> <p>Mapping of AD entries (from the PDMS) to defined categories</p> </li> <li> <p>Mapping of VDs, VMs, and ADs to defined RSTs, including information on invasiveness</p> </li> <li> <p>Table specifying suitable ventilation parameters in the context of each RST</p> </li> </ul> <p><strong>2. Medication Mappings:</strong></p> <ul> <li> <p>General tables providing information on physiological alarm conditions (PACs), interventions, routes, and techniques of administration of interest</p> </li> <li> <p>Mapping of routes of administration to techniques of administration including PDMS entries</p> </li> <li> <p>Mapping of active ingredients (including SNOMED CT Fully Specified Names and Identifiers), related PDMS information, and routes and techniques of administration to defined PAC and interventions</p> </li> </ul>
Extended data for the paper: "SentemQC - A novel and cost-efficient method for quality assurance and quality control of high-resolution frequency sensor data in fresh waters"
<p>Extended data 1 to 4 for the software article:<br>SentemQC - A novel and cost-efficient method for quality assurance and quality control of high-resolution frequency sensor data in fresh waters. </p> <p>The extended data is tables and a Figure output and input from/to SentemQC runs relevant for the SentemQC paper.</p>
LDEO pCO2-Residual Method
<p>The ocean reduces human impacts on global climate by absorbing and sequestering CO<sub>2</sub> from the atmosphere. To quantify global, time-resolved air-sea CO<sub>2</sub> fluxes, surface ocean pCO<sub>2</sub> is needed. A common approach for estimating full-coverage pCO<sub>2</sub> is to train a machine learning algorithm on sparse in situ pCO<sub>2</sub> data and associated physical and biogeochemical observations. Though these associated variables have understood relationships to pCO<sub>2</sub>, it is often unclear how they drive pCO<sub>2</sub> outputs. Here, we make two advances that enhance connections between physical understanding and reconstructed pCO<sub>2</sub>. First, we apply pre-processing to the pCO<sub>2</sub> data to remove the direct effect of temperature. This enhances the biogeochemical/physical component of pCO<sub>2</sub> in the target variable and reduces the complexity that the machine learning must disentangle. Second, we demonstrate that the resulting algorithm has physically understandable connections between input data and the output biogeochemical/physical component of pCO<sub>2</sub>. The final pCO<sub>2</sub> reconstruction agrees modestly better with independent data than most other approaches. Uncertainties in the reconstructed pCO<sub>2</sub> and impacts on the estimated CO<sub>2</sub> fluxes are quantified. Uncertainty in piston velocity drives substantial flux uncertainties in some regions, but does not increase globally integrated estimates of uncertainty in CO<sub>2</sub> fluxes from observation-based products. Our reconstructed CO<sub>2</sub> fluxes show larger interannual variability than smoother neural network approaches, but a lesser trend since 2005. </p>
Dataset for: Stereorandomization as a Method to Probe Peptide Bioactivity
<p>The upload contains additional primary data associated with the publication, including raw data in the original file format whenever possible.</p> <p>Data content: HRMS, HPLC-MS, CD, MD, TEM, Serum stability, Vesicle leakage assay, Cytotoxicity, Hemolysis.</p>
Finite element method (FEM) models for translational research in non-invasive brain stimulation
<p>Finite element method (FEM) models for non-invasive brain stimulation modeling using SimNIBS or other compatible software.<br> The mouse and monkey models are described in detail in Alekseichuk et al., Comparative modeling of transcranial magnetic and electric stimulation in mouse, monkey, and human, NeuroImage 2019.<br> The Petri dish model follows a typical experimental setup for in-vitro TMS, similar to what is described in Lenz et al. Repetitive magnetic stimulation induces plasticity of inhibitory synapses, Nature Communications 2016.<br> <br> The following files are included:<br> 1. Brain tissue slice in a Petri dish.<br> 2. Normal adult male nude mouse "Digimouse" (brain volume of 0.38 cm3).<br> 3. Normal adult male capuchin monkey "S" (brain volume of 68.31 cm3).<br> <br> The models include the following tissues (coded with numbers):<br> 1. White matter volume<br> 2. Grey matter volume<br> 3. CSF volume<br> 4. Skull volume<br> 5. Soft tissues volume<br> 8. Eyeballs volume<br> 1001. White matter outer surfaces<br> 1002. Grey matter outer surfaces<br> 1003. CSF outer surfaces<br> 1004. Skull outer surfaces<br> 1005. Soft tissues outer surfaces<br> 1008. Eyeballs outer surfaces<br> <br> With any questions, please, contact the corresponding authors of the relevant papers or <a href="mailto:aopitz@umn.edu">aopitz@umn.edu</a> (Alexander Opitz).</p>
Iterative Bleaching Extends multi-pleXity (IBEX) imaging method, mouse spleen
<p>This dataset was acquired using the Iterative Bleaching Extends multi-pleXity (IBEX) imaging method described in: “IBEX: A versatile multi-plex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues“, A. Radtke et al., 2020, <a href="https://doi.org/10.1073/pnas.2018488117">doi:10.1073/pnas.2018488117</a>.</p> <p>It is comprised of a three cycle IBEX experiment performed on mouse spleen sections labeled with the nuclear marker JOJO-1 and membrane label CD4 AF594. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 mm), y (0.284 mm), and z (1 mm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p> </p> <p>Markers per channel in each of the three cycles:</p> <ol> <li>spleen_panel1.nrrd (6 channels): B220 PE, CD8 BV421, IgD AF700, CD4 AF594, JOJO, Foxp3 eF660</li> <li> <p>spleen_panel2.nrrd (7 channels): CD169 PE, F480 BV421, MHCII AF700, CollIV AF488, JOJO, CD11c AF647, CD4 AF594</p> </li> <li> <p>spleen_panel3.nrrd (7 channels): CD31 PE, CD68 BV421, Ki67 AF700, CD45 AF488, CD4 AF594, JOJO, CD3 AF647</p> </li> </ol> <p>The panels can be registered using the code available on github: <a href="https://github.com/niaid/sitk-ibex">https://github.com/niaid/sitk-ibex</a></p> <p>To view these multi-channel images, in <a href="http://teem.sourceforge.net/nrrd/format.html">nrrd format</a>, use the <a href="https://imagej.net/Fiji">Fiji viewer</a>. The data is stored in XYZC order.</p>
Supplementary Data for MOCCASIN: A method for correcting known and unknown confounders in RNA-Seq-based splicing analysis
<p>Contents</p> <ol> <li><strong>moccasin_paper_env.yaml</strong>: conda environment file with R and Python packages and modules needed to reproduce analyses.</li> <li><strong>FigureReproduction.zip</strong>: data and code to reproduce main and supplemental figures.</li> <li><strong>MOCCASIN_ExampleDataset.zip</strong>: A small subset of the simulated data with example code to run MOCCASIN.</li> <li><strong>encode_corrected.zip</strong>: Folder with batch-corrected ENCODE differential splicing quantifications (dPSI).</li> </ol> <p> </p> <p> </p> <p>(1) <strong>moccasin_paper_env.yaml</strong></p> <p>Use the moccasin_paper_env.yaml file to create a conda environment from which all analyses for the paper can be reproduced.</p> <pre><code class="language-bash"># need to first install conda. See here: # https://docs.conda.io/en/latest/miniconda.html # Next, create a conda environment: conda env create --name moccasin_paper_env --file moccasin_paper_env.yaml --force # Activate the environment: conda activate moccasin_paper_env</code></pre> <p><br> The only Python packages not included in this environment are MAJIQ & VOILA. Please see majiq.biocipers.org for installation instructions.</p> <p> </p> <p> </p> <p>(2) <strong>FigureReproduction.zip</strong></p> <p>Within FigureReproduction are folders with code and data to reproduce the main and supplemental figures of the publication. Each folder contains data, script(s) and a README.txt with instructions on how to reproduce figures.</p> <p> </p> <p> </p> <p>(3) <strong>MOCCASIN_ExampleDataset.zip</strong></p> <p>Within this folder is an example dataset to test MOCCASIN. The README.txt file contains detailed line-by-line instructions for how to run MOCCASIN and do post-MOCCASIN analyses. In this example, we show how to run MOCCASIN on a group of .majiq samples with one known confounding effect. Also demonstrated is how to run an "explore unknown residuals" analysis as described in the detailed methods in the supplemental of the paper. </p> <p> </p> <p> </p> <p>(4) <strong>encode_corrected.zip</strong></p> <p>Includes a file called ENCODE_BeforeAndAfterMOCCASIN.voila.tsv.zip which includes LSV quantifications before and after MOCCASIN. Each row in the file represents a junction from an LSV. Each column header starts with the prefix "BeforeMOCCASIN" or "AfterMOCCASIN" and headers ending in dPSI corresponds to the dPSI of an ENCODE knockdown vs control experiment. </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.