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12,346 results for “derivatives”
Resistance web archive collection derivatives
<p>Web archive derivatives of the <a href="https://archive-it.org/collections/8752">Resistance</a> collection from <a href="https://archive-it.org/home/Columbia">Columbia University Libraries</a>. The derivatives were created with the <a href="https://github.com/archivesunleashed/aut/">Archives Unleashed Toolkit</a> and <a href="https://cloud.archivesunleashed.org/">Archives Unleashed Cloud</a>.</p> <p>The <strong>cul-8752-parquet.tar.gz</strong> derivatives are in the <a href="https://parquet.apache.org/">Apache Parquet format</a>, which is a <a href="http://en.wikipedia.org/wiki/Column-oriented_DBMS">columnar storage</a> format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See <a href="https://github.com/archivesunleashed/notebooks/blob/master/datathon-nyc/parquet_pandas_stonewall.ipynb">this</a> notebook for examples.</p> <p><strong>Domains</strong></p> <pre><code class="language-java">.webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc)</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>domain</li> <li>count</li> </ul> <p><strong>Web Pages</strong></p> <pre><code class="language-java">.webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content"))</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>url</li> <li>mime_type_web_server</li> <li>mime_type_tika</li> <li>content</li> </ul> <p><strong>Web Graph</strong></p> <pre><code class="language-java">.webgraph()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>src</li> <li>dest</li> <li>anchor</li> </ul> <p><strong>Image Links</strong></p> <pre><code class="language-java">.imageLinks()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>src</li> <li>image_url</li> </ul> <p><a href="https://github.com/archivesunleashed/aut-docs/blob/master/current/binary-analysis.md#binary-analysis"><strong>Binary Analysis</strong></a></p> <ul> <li>PDFs</li> <li>Spreadsheets</li> <li>Text files</li> <li>Word processor files<br> </li> </ul> <p>The <strong>cul-8752-auk.tar.gz </strong>derivatives<strong> </strong>are the <a href="https://cloud.archivesunleashed.org/derivatives">standard set of web archive derivatives</a> produced by the Archives Unleashed Cloud.</p> <ul> <li><strong>Gephi </strong>file, which can be loaded into <a href="https://gephi.org/">Gephi</a>. It will have basic characteristics already computed and a basic layout.</li> <li><strong>Raw Network</strong> file, which can also be loaded into <a href="https://gephi.org/">Gephi</a>. You will have to use that network program to lay it out yourself.</li> <li><strong>Full text</strong> file. In it, each website within the web archive collection will have its full text presented on one line, along with information around when it was crawled, the name of the domain, and the full URL of the content.</li> <li><strong>Domains count</strong> file. A text file containing the frequency count of domains captured within your web archive.</li> </ul>
Geologic Field Trip Guidebooks Web Archive collection derivatives
<p>Web archive derivatives of the collection <a href="https://archive-it.org/collections/12576">Geologic Field Trip Guidebooks Web Archive</a> from the <a href="https://archive-it.org/home/IvyPlus">Ivy Plus Libraries Confederation</a>. The derivatives were created with the <a href="https://github.com/archivesunleashed/aut/">Archives Unleashed Toolkit</a> and <a href="https://cloud.archivesunleashed.org/">Archives Unleashed Cloud</a>.</p> <p>The <strong>ivy-12576-parquet.tar.gz</strong> derivatives are in the <a href="https://parquet.apache.org/">Apache Parquet format</a>, which is a <a href="http://en.wikipedia.org/wiki/Column-oriented_DBMS">columnar storage</a> format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See <a href="https://github.com/archivesunleashed/notebooks/blob/master/datathon-nyc/parquet_pandas_stonewall.ipynb">this</a> notebook for examples.</p> <p><strong>Domains</strong></p> <pre><code class="language-java">.webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc)</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>domain</li> <li>count</li> </ul> <p><strong>Web Pages</strong></p> <pre><code class="language-java">.webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content"))</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>url</li> <li>mime_type_web_server</li> <li>mime_type_tika</li> <li>content</li> </ul> <p><strong>Web Graph</strong></p> <pre><code class="language-java">.webgraph()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>src</li> <li>dest</li> <li>anchor</li> </ul> <p><strong>Image Links</strong></p> <pre><code class="language-java">.imageLinks()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>src</li> <li>image_url</li> </ul> <p><a href="https://github.com/archivesunleashed/aut-docs/blob/master/current/binary-analysis.md#binary-analysis"><strong>Binary Analysis</strong></a></p> <ul> <li>Audio</li> <li>Images</li> <li>PDFs</li> <li>Presentation program files</li> <li>Spreadsheets</li> <li>Text files</li> <li>Word processor files<br> </li> </ul> <p>The <strong>ivy-12576-auk.tar.gz </strong>derivatives<strong> </strong>are the <a href="https://cloud.archivesunleashed.org/derivatives">standard set of web archive derivatives</a> produced by the Archives Unleashed Cloud.</p> <ul> <li><strong>Gephi </strong>file, which can be loaded into <a href="https://gephi.org/">Gephi</a>. It will have basic characteristics already computed and a basic layout.</li> <li><strong>Raw Network</strong> file, which can also be loaded into <a href="https://gephi.org/">Gephi</a>. You will have to use that network program to lay it out yourself.</li> <li><strong>Full text</strong> file. In it, each website within the web archive collection will have its full text presented on one line, along with information around when it was crawled, the name of the domain, and the full URL of the content.</li> <li><strong>Domains count</strong> file. A text file containing the frequency count of domains captured within your web archive.</li> </ul>
Coalition Avenir Québec (CAQ) web archive collection derivatives
<p>Web archive derivatives of the Coalition Avenir Québec (CAQ) collection from the <a href="https://www.banq.qc.ca/accueil/">Bibliothèque et Archives nationales du Québec</a>. The derivatives were created with the <a href="https://github.com/archivesunleashed/aut/">Archives Unleashed Toolkit</a>. Merci beaucoup BAnQ!</p> <p>These derivatives are in the <a href="https://parquet.apache.org/">Apache Parquet format</a>, which is a <a href="http://en.wikipedia.org/wiki/Column-oriented_DBMS">columnar storage</a> format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See <a href="https://github.com/archivesunleashed/notebooks/blob/master/parquet_pandas_example.ipynb">this</a> notebook for examples.</p> <p><strong>Domains</strong></p> <pre><code class="language-java">.webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc)</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>domain</li> <li>count</li> </ul> <p><strong>Web Pages</strong></p> <pre><code class="language-java">.webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content"))</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>url</li> <li>mime_type_web_server</li> <li>mime_type_tika</li> <li>content</li> </ul> <p><strong>Web Graph</strong></p> <pre><code class="language-java">.webgraph()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>src</li> <li>dest</li> <li>anchor</li> </ul> <p><strong>Image Links</strong></p> <pre><code class="language-java">.imageLinks()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>src</li> <li>image_url</li> </ul> <p><a href="https://github.com/archivesunleashed/aut-docs/blob/master/current/binary-analysis.md#binary-analysis"><strong>Binary Analysis</strong></a></p> <ul> <li>Audio</li> <li>Images</li> <li>PDFs</li> <li>Presentation program files</li> <li>Spreadsheets</li> <li>Text files</li> <li>Videos</li> <li>Word processor files</li> </ul>
Harvest Quebec Government Websites from December 2006 web archive collection derivatives
<p>Web archive derivatives of the Sites of the Harvest Quebec Government Websites from December 2006 collection from the <a href="https://www.banq.qc.ca/accueil/">Bibliothèque et Archives nationales du Québec</a>. The derivatives were created with the <a href="https://github.com/archivesunleashed/aut/">Archives Unleashed Toolkit</a>. Merci beaucoup BAnQ!</p> <p>These derivatives are in the <a href="https://parquet.apache.org/">Apache Parquet format</a>, which is a <a href="http://en.wikipedia.org/wiki/Column-oriented_DBMS">columnar storage</a> format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See <a href="https://github.com/archivesunleashed/notebooks/blob/master/parquet_pandas_example.ipynb">this</a> notebook for examples.</p> <p><strong>Domains</strong></p> <pre><code class="language-java">.webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc)</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>domain</li> <li>count</li> </ul> <p><strong>Web Pages</strong></p> <pre><code class="language-java">.webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content"))</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>url</li> <li>mime_type_web_server</li> <li>mime_type_tika</li> <li>content</li> </ul> <p><strong>Web Graph</strong></p> <pre><code class="language-java">.webgraph()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>src</li> <li>dest</li> <li>anchor</li> </ul> <p><strong>Image Links</strong></p> <pre><code class="language-java">.imageLinks()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>src</li> <li>image_url</li> </ul> <p><a href="https://github.com/archivesunleashed/aut-docs/blob/master/current/binary-analysis.md#binary-analysis"><strong>Binary Analysis</strong></a></p> <ul> <li>Audio</li> <li>Images</li> <li>PDFs</li> <li>Presentation program files</li> <li>Spreadsheets</li> <li>Text files</li> <li>Videos</li> <li>Word processor files</li> </ul>
Quebec International Relation and Economy web archive collection derivatives
<p>Web archive derivatives of the Sites of the Quebec International Relation and Economy collection from the <a href="https://www.banq.qc.ca/accueil/">Bibliothèque et Archives nationales du Québec</a>. The derivatives were created with the <a href="https://github.com/archivesunleashed/aut/">Archives Unleashed Toolkit</a>. Merci beaucoup BAnQ!</p> <p>These derivatives are in the <a href="https://parquet.apache.org/">Apache Parquet format</a>, which is a <a href="http://en.wikipedia.org/wiki/Column-oriented_DBMS">columnar storage</a> format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See <a href="https://github.com/archivesunleashed/notebooks/blob/master/parquet_pandas_example.ipynb">this</a> notebook for examples.</p> <p><strong>Domains</strong></p> <pre><code class="language-java">.webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc)</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>domain</li> <li>count</li> </ul> <p><strong>Web Pages</strong></p> <pre><code class="language-java">.webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content"))</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>url</li> <li>mime_type_web_server</li> <li>mime_type_tika</li> <li>content</li> </ul> <p><strong>Web Graph</strong></p> <pre><code class="language-java">.webgraph()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>src</li> <li>dest</li> <li>anchor</li> </ul> <p><strong>Image Links</strong></p> <pre><code class="language-java">.imageLinks()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>src</li> <li>image_url</li> </ul> <p><a href="https://github.com/archivesunleashed/aut-docs/blob/master/current/binary-analysis.md#binary-analysis"><strong>Binary Analysis</strong></a></p> <ul> <li>Audio</li> <li>Images</li> <li>PDFs</li> <li>Presentation program files</li> <li>Spreadsheets</li> <li>Text files</li> <li>Videos</li> <li>Word processor files</li> </ul>
Example computer vision classification training data derived from British Library 19th Century Books Image collection
<p>Example computer vision classification training data derived from British Library 19th Century Books Image collection</p> <p>This dataset provides training data for image classification for use in a computer vision workshop. The images are derived from '<a href="https://doi.org/10.21250/db17">Digitised Books - Images identified as Embellishments. c. 1510 - c. 1900. JPG'</a> from the year '1839'.</p> <p>Currently, included are four folders containing a variety of images derived from the BL books corpus.</p> <ul> <li>'cv_workshop_exercise_data' include images of: 'building', 'people', 'coat of arms'</li> <li>'humancats' contains images of humans and images of cats</li> </ul> <p>The 'fashion' and 'portraits' folders both contain images of people organised into 'female' and 'male'. These labels were annotated by a single annotator and these categories may themselves not be meaningful. They are included in the workshop data as a point of discussion about how we should label data both in general and when working with historical data. </p> <p>This data is intended primarily as an educational resource.</p>
Quebec Ministry of Tourism (2012 to 2017) web archive collection derivatives
<p>Web archive derivatives of the Quebec Ministry of Tourism (2012 to 2017) collection from the <a href="https://www.banq.qc.ca/accueil/">Bibliothèque et Archives nationales du Québec</a>. The derivatives were created with the <a href="https://github.com/archivesunleashed/aut/">Archives Unleashed Toolkit</a>. Merci beaucoup BAnQ!</p> <p>These derivatives are in the <a href="https://parquet.apache.org/">Apache Parquet format</a>, which is a <a href="http://en.wikipedia.org/wiki/Column-oriented_DBMS">columnar storage</a> format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See <a href="https://github.com/archivesunleashed/notebooks/blob/master/parquet_pandas_example.ipynb">this</a> notebook for examples.</p> <p><strong>Domains</strong></p> <pre><code class="language-java">.webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc)</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>domain</li> <li>count</li> </ul> <p><strong>Web Pages</strong></p> <pre><code class="language-java">.webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content"))</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>url</li> <li>mime_type_web_server</li> <li>mime_type_tika</li> <li>content</li> </ul> <p><strong>Web Graph</strong></p> <pre><code class="language-java">.webgraph()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>src</li> <li>dest</li> <li>anchor</li> </ul> <p><strong>Image Links</strong></p> <pre><code class="language-java">.imageLinks()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>src</li> <li>image_url</li> </ul> <p><a href="https://github.com/archivesunleashed/aut-docs/blob/master/current/binary-analysis.md#binary-analysis"><strong>Binary Analysis</strong></a></p> <ul> <li>Audio</li> <li>Images</li> <li>PDFs</li> <li>Presentation program files</li> <li>Spreadsheets</li> <li>Text files</li> <li>Videos</li> <li>Word processor files</li> </ul>
Quebec Health Ministry (2013-2018) web archive collection derivatives
<p>Web archive derivatives of the Quebec Health Ministry (2013-2018) collection from the <a href="https://www.banq.qc.ca/accueil/">Bibliothèque et Archives nationales du Québec</a>. The derivatives were created with the <a href="https://github.com/archivesunleashed/aut/">Archives Unleashed Toolkit</a>. Merci beaucoup BAnQ!</p> <p>These derivatives are in the <a href="https://parquet.apache.org/">Apache Parquet format</a>, which is a <a href="http://en.wikipedia.org/wiki/Column-oriented_DBMS">columnar storage</a> format. These derivatives are generally small enough to work with on your local machine, and can be easily converted to Pandas DataFrames. See <a href="https://github.com/archivesunleashed/notebooks/blob/master/parquet_pandas_example.ipynb">this</a> notebook for examples.</p> <p><strong>Domains</strong></p> <pre><code class="language-java">.webpages().groupBy(ExtractDomainDF($"url").alias("url")).count().sort($"count".desc)</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>domain</li> <li>count</li> </ul> <p><strong>Web Pages</strong></p> <pre><code class="language-java">.webpages().select($"crawl_date", $"url", $"mime_type_web_server", $"mime_type_tika", RemoveHTMLDF(RemoveHTTPHeaderDF(($"content"))).alias("content"))</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>url</li> <li>mime_type_web_server</li> <li>mime_type_tika</li> <li>content</li> </ul> <p><strong>Web Graph</strong></p> <pre><code class="language-java">.webgraph()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>crawl_date</li> <li>src</li> <li>dest</li> <li>anchor</li> </ul> <p><strong>Image Links</strong></p> <pre><code class="language-java">.imageLinks()</code></pre> <p>Produces a DataFrame with the following columns:</p> <ul> <li>src</li> <li>image_url</li> </ul> <p><a href="https://github.com/archivesunleashed/aut-docs/blob/master/current/binary-analysis.md#binary-analysis"><strong>Binary Analysis</strong></a></p> <ul> <li>Audio</li> <li>Images</li> <li>PDFs</li> <li>Presentation program files</li> <li>Spreadsheets</li> <li>Text files</li> <li>Word processor files</li> </ul>
Dataset related to article "Nicotinamide Phosphoribosyltransferase Acts as a Metabolic Gate for Mobilization of Myeloid-Derived Suppressor Cells"
<p>Cancer induces alteration of hematopoiesis to fuel disease progression. We report that in tumor-bearing mice the macrophage colony-stimulating factor elevates the myeloid cell levels of nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in the NAD salvage pathway, which acts as negative regulator of the CXCR4 retention axis of hematopoietic cells in the bone marrow. NAMPT inhibits CXCR4 through a NAD/Sirtuin 1-mediated inactivation of HIF1α-driven <em>CXCR4</em> gene transcription, leading to mobilization of immature myeloid-derived suppressor cells (MDSC) and enhancing their production of suppressive nitric oxide. Pharmacologic inhibition or myeloid-specific ablation of NAMPT prevented MDSC mobilization, reactivated specific antitumor immunity, and enhanced the antitumor activity of immune checkpoint inhibitors. Our findings identify NAMPT as a metabolic gate of MDSC precursor function, providing new opportunities to reverse tumor immunosuppression and to restore clinical efficacy of immunotherapy in patients with cancer. SIGNIFICANCE: These findings identify NAMPT as a metabolic gate of MDSC precursor function, providing new opportunities to reverse tumor immunosuppression and to restore clinical efficacy of immunotherapy in cancer patients.</p>
Locations and derived diameters of RMDSs as per Fig. 6 and all the 8281 RMDSs identified so far across the global Moon by March, 2020
<p>F. Zhang, J. W. Head, C. Wöhler, R. Bugiolacchi, L. Wilson, A. T. Basilevsky, A. Grumpe, Y. L. Zou.</p> <p>Ring-Moat Dome Structures (RMDSs) in the Lunar Maria: Statistical, Compositional, and Morphological Characterization and Assessment of Theories of Origin.</p> <p>Journal of Geophysical Research: Planets, 125, e2019JE005967. https://doi.org/10.1029/2019JE005967</p> <p> </p> <p>1. <strong>Point_Location_Figure_6</strong>: The table of locations and derived diameters of all the RMDSs shown in Figure 6 of point density map of 870 RMDSs (black dots) in central Mare Tranquillitatis on the Moon. </p> <p>2. <strong>All_RMDSs_8281_By_March_2020</strong>: The table of locations and derived diameters of all the 8281 RMDSs identified so far across the global Moon by 15 March, 2020.</p>
Partitioning of Catechol Derivatives in Lipid Membranes: Implications for Substrate Specificity to Catechol-O-methyltransferase
<p>The data used for publication "Partitioning of Catechol Derivatives in Lipid Membranes: Implications for Substrate Specificity to Catechol-<em>O</em>-methyltransferase" in ACS Chemical Neuroscience (2020), 11(6), 969-978.</p>
Time series data of rotational angular velocity of Typhoon Lan (2017) derived by Tsukada and Horinouchi (2020)
<p>Time series data of rotational angular velocity in the eye of Typhoon Lan (2017) on October 21, 2017, derived by Tsukada and Horinouchi (2020) using the data observed by Himawari-8 satellite. More information is also available at <a href="http://wwwoa.ees.hokudai.ac.jp/people/horinouchi-lab/TC/data_en.html">http://wwwoa.ees.hokudai.ac.jp/people/horinouchi-lab/TC/data_en.html</a>.</p>
A dataset of long-term consistency values of resting-state fMRI connectivity maps in a single individual derived at multiple sites and vendors using the Canadian Dementia Imaging Protocol
<p>This dataset contains preprocessed resting state fMRI data (.nii.gz) with accompanying confound files (.tsv) from the Single Individual volunteer for Multiple Observations across Networks (SIMON; http://fcon_1000.projects.nitrc.org/indi/retro/SIMON.html) dataset that has been minimally preprocessed using the NeuroImaging Analysis Kit (NIAK; http://niak.simexp-lab.org/build/html/PREPROCESSING.html). Preprocessing steps included: (1) Slice timing correction; (2) Estimation of rigid-body motion in fMRI runs, both within- and between sessions; (3) Linear or non-linear coregistration of the structural scan in stereotaxic space; (4) Individual coregistration between structural and functional scans; (5) Resampling of functional scans in stereotaxic space. Confound files (.tsv) have been included for purposes of scrubbing and regression of confounds using NIAK or other analysis software, allowing for further processing without conflicts.</p>
Chemical characteristics of the assigned elemental formulas from the FT-ICR MS data of aerosol-derived organic matter simultaneously collected in Beijing, China and Gwangju, Korea in January 2018
<p>In this study, ambient fine particles (PM2.5) were simultaneously collected in two urban cities in China and Korea (Beijing and Gwangju, respectively) in January 2018. Comprehensive compositional analysis of the organic matter (OM) samples, extracted using dichloromethane, was performed on a 15 Tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an atmospheric pressure photoionization (APPI) interface in positive ion mode. Analysis of the nonpolar and semipolar OM using APPI FT-ICR MS revealed that CHO and CHON accounted for more than 90% of the total intensity of the OM peaks. Higher proportions of CHON compounds were observed during PM2.5 events (i.e., days with abnormally high PM2.5 levels) at both sites than on regular or non-event days. </p>
The code and mathematical derivation associated with "The role of random vorticity stretching in an idealized tropical depression genesis problem"
<p>1. The "SWE.rar" is the shallow water model (SWE).</p> <p>2. The "postprocess.rar" is the postprocessing code, include plottings and parameter estimation.</p> <p>3. The hand-written mathematical derivation of this paper is made with ONENOTE. It can be found at:</p> <p>https://office365stanford-my.sharepoint.com/:o:/g/personal/haofu_stanford_edu/El0w-3bEQABDnEVScJH6CK8BYVtxF33RzjmeZTbgaPyU-g?e=wae0Ra</p> <p>4. If there is any question or difficulty in downloading, please contact Hao Fu: haofu@stanford.edu</p>
PDX1-/NKX6.1+ progenitors derived from human pluripotent stem cells as a novel source of insulin-secreting cells
<p>PDX1-/NKX6.1+ progenitors derived from hESCs were differentiated to pancreatic beta cell stage where they generated glucose-responsive, insulin-secreting cells. The transcriptome profile of hESC- derived PDX1-/NKX6.1+ progenitors were compared with hPSC-derived PDX1+/NKX6.1+ pancreatic progenitors as described in the article entitled "<strong>PDX1<sup>-</sup>/NKX6.1<sup>+</sup>progenitors derived from human pluripotent stem cells as a novel source of insulin-secreting cells</strong>" by Memon et al. 2020. Furthermore, beta cells derived from PDX1-/NKX6.1+ progenitors (3D-beta) were compared with their own endocrine progenitors at an earlier stage (stage 5, 3D-S5) to map their development. </p> <p>The file name is : Sample name_replicate_sample ID_read direction_001 where:</p> <p>-3D-beta: insulin-expressing cells derived from self-detached, 3D, PDX1-/NKX6.1+ progenitors</p> <p>-3D-S5: endocrine progenitors from stage 5, derived from self-detached, 3D, PDX1-/NKX6.1+ progenitors</p> <p>- RNA-seq data were generated from two biological replicates in most cases.</p> <p>- Read direction: R1 (Forward), R2 (Reverse).</p>
Single cell transcriptomes of of primary tumors and normal endometrial derived organoids treated with DBZ
<p>Endometrial carcinoma, the most common gynecologic cancer, develops from endometrial epithelium which is composed of secretory and ciliated cells. Pathologic classification is unreliable and there is a need for prognostic tools. We used single cell sequencing to study organoid model systems derived from normal endometrial endometrium to discover novel markers specific for endometrial ciliated or secretory cells. We performed 10X based single cell sequencing on both normal and DBZ treated organoids, and on endometrial and ovarian tumours.</p>
Evaluating the inhibition of ALK2 phosphorylation of SMAD1/5 by M4K lead compounds in DIPG patient-derived cells (SU-DIPG-IV, HSJD-DIPG-007, HSJD-DIPG-018 and SU-DIPG-XXI)
<p>The binding potency of M4K compounds to ALK2 has been assayed in biochemical assay and cellular assays in HEK293 or C2C12 myoblast cell lines. However, the potency of ALK2 inhibition by M4K compounds has not determined directly in DIPG patient-derived cell lines. While no major deviation from existing assay data is expected, direct experimental evidence is essential.</p> <p>DIPG cells will be trypsinized and resuspended in TSM-base medium without any growth factor for one-hour starvation. Subsequently, equal volume of TSM-base with 2X Activin A (200ng/mL) and M4K compounds or DMSO vehicle control will be added. After one-hour treatment, the cells will be pelleted and lysed in buffer with protease and phosphatase inhibitors for Western Blot analysis.</p> <p>For other related studies, please refer to my opennotebook blog.</p> <p><a href="https://openlabnotebooks.org/evaluating-the-inhibition-of-alk2-phosphorylation-of-smad1-5-by-m4k-lead-compounds-in-dipg-patient-derived-cells-su-dipg-iv-hsjd-dipg-007-hsjd-dipg-018-and-su-dipg-xxi/">https://openlabnotebooks.org/evaluating-the-inhibition-of-alk2-phosphorylation-of-smad1-5-by-m4k-lead-compounds-in-dipg-patient-derived-cells-su-dipg-iv-hsjd-dipg-007-hsjd-dipg-018-and-su-dipg-xxi/</a></p>
Lidar-derived snow depth maps along the Chilean Extratropical Andes, winter 2018
<p>All the files included here contain the data produced for the manuscript "<strong>Spatial distribution and scaling properties of lidar-derived snow depth in the extratropical Andes</strong>", submitted for possible publication in Water Resources Research. Lidar measurements for snow-covered conditions were conducted on September 4th, August 9th, and October 25th 2018 in Tascadero, Las Bayas and Valle Hermoso, respectively. Each data acquisition was conducted using a Riegl VZ6000 long range scanner on dates with and without snow, using an angular resolution of 0.01°.</p> <p>Lidar-derived maps are contained in the following files:</p> <p>SiteName_SD_TPI.txt (SiteName: Tascadero, Las Bayas, VH East or VH West).</p> <p>Where the file structure is as follows:</p> <p>X,Y,Z,SD,SLP,NOR,TPI04,TPI07,TPI15,TPI20,TPI30,TPI40,TPI50</p> <p>where Z is bare earth elevation (m a.s.l.), SD is snow depth, SLP is slope (°), NOR is northness (°) whereby 180 = north facing and 0 = south facing, TPIXX is the Topographic Position Index (TPI) computed for a search distance of XX m, whereby positive differences are convex landforms, and negative is concave. The magnitude of TPI indicates the scale of the relative concavity/convexity.</p> <p>Variogram results are contained in files .rsav with the following nomenclature:</p> <p>SiteName_X_TypeOfVariogram.rsav</p> <p>Where X can be SD (snow depth) or Z (bare earth topography), and the type of variogram can be omnidirectional or directional.</p>
Reactive extraction of fructose for efficient separation of sucrose-derived glucosides produced by enzymatic glycosylation
<p>We provide here the underlying data of the scientific publication "Reactive extraction of fructose for efficient separation of sucrose-derived glucosides produced by enzymatic glycosylation". Please find the abstract below:</p> <p>The disaccharide sucrose (α-D-glucopyranosyl-1,2-β-D-fructofuranoside) is a highly efficient donor substrate for enzymatic glucosylation reactions. A large number of commercially relevant glucosides are produced via this general route. Every sucrose-based glucosylation involves co-production of D-fructose in amounts corresponding to the target glucoside. A separation technology for selective removal, and efficient recovery, of the D-fructose co-product would be highly desirable as a generic platform for downstream process development. Here, we demonstrate organoboronate-complex reactive extraction of D-fructose into an 1-octanol/hexane (4/1, v/v) solvent using methyltrioctyl ammonium chloride as phase transfer catalyst and extractant. We show separation of the D-fructose co-product (100 mM) from equimolar mixture with 2-α-D-glucosyl-glycerol, a cosmetic ingredient that is manufactured industrially from sucrose and glycerol using sucrose phosphorylase. With the main parameters of extraction, stripping and organic phase recycling identified and their effect on product/co-product yield and purity characterized, we developed a three-step extraction process with alternating extraction and stripping stages that removed the D-fructose efficiently at 50 ml operating scale. 2-α-D-glucosyl-glycerol and D-fructose were cleanly separated and obtained in excellent purity (≥90%) at a recovery of 90% and 83%, respectively. Reactive extraction appears to be faster and more selective and resource-efficient than applicable alternatives for separation, including chromatography and membrane nanofiltration. Thus, the established extraction process is promising for industrial application. It could be generically useful to separate D-fructose from glucosides</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.