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Ochrobactrum pituitosum BH3
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Ochrobactrum pituitosum BH3, a\(n\) Alphaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Dataset: Focus Impact BH3 Acquisition Company (BHACU) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Dataset: Focus Impact BH3 Acquisition Company (BHACW) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Dataset: Focus Impact BH3 Acquisition Company (BHAC) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Dataset from the paper "The boring history of GAIA BH3 from isolated binary evolution": IIC - simulation outcomes, fiducial 1E8
<p>This repository contains (a part) of the population synthesis outputs analysed in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. In particular, it contains the results of the subsets that compose the model fiducial2E8 (see <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>). The complete model includes also the results from the fiducial model stored in the repository <a href="https://doi.org/10.5281/zenodo.11992265" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.11992265</a></p> <h2>Content</h2> <p>Each tar file contains the outputs of a given simulation set from <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The name of the files corresponds to the name of the set as reported in Table 1 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The details of the sets can be found in Section 2.2 and Section 2.3 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The outputs stored in this repository contain only the systems that satisfy the following conditions:</p> <ul> <li>The two objects are in a binary system</li> <li>An object is a black hole and the other one is a star in any evolutionary phase prior to the ignition of the helium burning in the core</li> <li>The two objects are not currently interacting except for wind mass transfer (no ongoing Roche-Lobe overflow, common envelope or merger).</li> </ul> <p>The tar files contain three different files in gunzipped parquet format (<a href="https://parquet.apache.org">https://parquet.apache.org</a>):</p> <h3><strong>Python scripts</strong></h3> <ul> <li><em>analyse_sample.py</em>: python script we used to produce the file BHMS.pq.gz and BHMS_ic.pq.gz analysing the SEVN outputs</li> <li><em>create_aux.py</em>: python script we used to produce the file BHMS_VSNCE.pq.gz by combining the SEVN log outputs with the BHMS_ic.pq.gz file</li> </ul> <h3> </h3> <h3>BHMS.pq.gz</h3> <p><strong> </strong>File containing all the systems satisfying the above condition.</p> <p><strong>Columns:</strong></p> <ul> <li>ID: unique id of the binary (Long integer)</li> <li>name: unique name of the binary (Long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminosity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Euclidean distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p> <strong>Notice-1: </strong>in this file each system (identified by ID and name) can appear more than once. Indeed this file contains all the outputs in which a system satisfy the condition BH-star condition discussed above.</p> <p> <strong>Notice-2: </strong><em>the dataframe is sorted based on the bh3dist column,</em> so the first rows contains the objects that are closer to the properties of Gaia BH3 based on the bh3dist statistic.</p> <p> <strong>Notice-3: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_ic.pq.gz</h3> <p>File containing the initial conditions of all the systems included in the file BHMS.pq.gz</p> <p><strong>Columns:</strong></p> <p><em>Info from BHMS.pq.gz</em>:</p> <p>these columns report the same information as in the BHMS.pq.gz file, but each system (identified by ID and name) appears just once (the occurrence from the BHMS.pq.gz with the minimum bh3dist)</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminoisity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Eucledian distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p><em>Initial properties</em>:</p> <ul> <li>mzams_0: Initial (ZAMS) mass of the black hole in Msun</li> <li>mzams_1: Initial (ZAMS) mass of the star in Msun</li> <li>Semimajor_ini: Initial semimajor axis of the binary in Rsun </li> <li>Eccentricity_ini: Initial eccentricity axis of the binary </li> <li>seed: Random seed used in the SEVN simulation</li> <li>P_ini: Intial period of the binary in days </li> </ul> <p><strong> Notice: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_VSNCE.pq.gz</h3> <p>A file containing additional information about the evolutionary events of the systems stored in BHMS.pq.gz</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>time_SN: formation time of the black hole (BH) in Myr (all the simulations start from time=0)</li> <li>Vcom: Velocity magnitude of the center of mass after the formation of the BH (before the formation Vcom=0 is assumed)</li> <li>time_CE_preSN: time of the last CE before the BH formation (if empty no CE before BH formation)</li> <li>time_CE_postSN: time of the first CE after the BH formation (if empty no CE after BH formation)</li> <li>time_RL_preSN: time of the last Roche-Lobe overflow before the BH formation (if empty no RLO before BH formation)</li> <li>time_RL_postSN: time of the first Roche-Lobe overflow after the BH formation (if empty no RLO before BH formation)</li> </ul> <p><strong>Note: </strong>The file has been created by combining the file BHMS_ic.pq.gz with the main SEVN outputs using the script <em>create_aux.py </em>included in this repository</p> <h3>How to read the files</h3> <p>The parquet files can be easily read in Python by using the <a href="https://pandas.pydata.org/docs/reference/api/pandas.read_parquet.html">Pandas module</a>:</p> <pre><code>import pandas as pd df_bhms=pd.read_parquet("BHMS.pq.gz") df_bhms_ic=pd.read_parquet("BHMS_ic.pq.gz") df_bhms_vsnce=pd.read_parquet("BHMS_VSNCE.pq.gz")</code></pre> <p> </p> <h2>Notes</h2> <p>The code used in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> is SEVN (<a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio et al., 2023</a>) version 2.10.1 (commit <a href="https://gitlab.com/sevncodes/sevn/-/tree/a4753f1177aab076da2641afc497a06006b30267">a4753f11</a>). </p>
Dataset from the paper "The boring history of GAIA BH3 from isolated binary evolution": I - initial conditions & run scripts
<p>This repository contains the initial condition files and the run scripts to reproduce the results in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>.</p> <h2>Content</h2> <h3>Files XXX.ic</h3> <p>Ascii files containing the initial conditions of 2e7 binary systems. The files do not contain a header, and the columns report (from left to right):</p> <ol> <li>Mass of the primary [Msun]</li> <li>Absolute metallicity of the primary </li> <li>Initial spin (angular velocity over critical angular velocity)</li> <li>Supernova model for the primary</li> <li>Initial age of the star (Myr or special keywords)</li> <li>Mass of the secondary [Msun]</li> <li>Absolute metallicity of the secondary</li> <li>Initial spin (angular velocity over critical angular velocity)</li> <li>Supernova model for the secondary</li> <li>Initial age of the star (Myr or special keywords)</li> <li>Initial semimajor axis [Rsun]</li> <li>Initial Eccentricity </li> <li>Ending time or condition of the simulation [Myr or special keyword]</li> <li>Output frequency [Myr or special]</li> <li>Random seed</li> </ol> <p>Some columns contains the special placeorder keyword XXX. In this case, the values are undefined and they are set at runtime using the value on the runscripts. For additional information see the SEVN <a href="https://gitlab.com/sevncodes/sevn/-/blob/a4753f1177aab076da2641afc497a06006b30267/resources/SEVN_userguide.pdf">Userguide</a>.</p> <p>The initial conditions are:</p> <ul> <li><a href="../api/records/11617742/draft/files/SEVNIC20M_qmin0005.in/content" target="_blank" rel="noopener noreferrer">SEVNIC20M_qmin0005.in,</a> initial conditions used in all the simuations of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> except for the model fiducial_ICthermal (see Table 1) e partially for the model fiducial2E8 (see below).</li> <li><a href="../api/records/11617742/draft/files/SEVNIC20M_qmin0005_ethermal.in/content" target="_blank" rel="noopener noreferrer">SEVNIC20M_qmin0005_ethermal.in</a>, initial conditions for the simulation set fiducial_ICthermal</li> <li>SEVNIC20M_X.in (where X ranges from 1 to 9), initial conditions (split in different chuncks) used for the simulation set fiducial2e8. This set is also complemetned by the <a href="../api/records/11617742/draft/files/SEVNIC20M_qmin0005.in/content" target="_blank" rel="noopener noreferrer">SEVNIC20M_qmin0005.in</a> initial conditions. </li> </ul> <h3>Runscripts</h3> <p>The runscripts are contained in the archive runscripts.zip. See the README in the archive for additional information. </p> <h2>Notes</h2> <p>The code used in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> is SEVN (<a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio et al., 2023</a>) version 2.10.1 (commit <a href="https://gitlab.com/sevncodes/sevn/-/tree/a4753f1177aab076da2641afc497a06006b30267">a4753f11</a>). </p>
Dataset from the paper "The boring history of GAIA BH3 from isolated binary evolution": IIA - simulation outcomes
<p>This repository contains (a part) of the population synthesis outputs analysed in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. In particular, it contains the results of our fiducial model and of the models in which we change stellar (e.g. kicks) and binary evolutions parameters (e.g. common envelope parameters).</p> <h2>Content</h2> <p>Each tar file contains the outputs of a given simulation set from <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The name of the files corresponds to the name of the set as reported in Table 1 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The details of the sets can be found in Section 2.2 and Section 2.3 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The outputs stored in this repository contain only the systems that satisfy the following conditions:</p> <ul> <li>The two objects are in a binary system</li> <li>An object is a black hole and the other one is a star in any evolutionary phase prior to the ignition of the helium burning in the core</li> <li>The two objects are not currently interacting except for wind mass transfer (no ongoing Roche-Lobe overflow, common envelope or merger).</li> </ul> <p>The tar files contain three different files in gunzipped parquet format (<a href="https://parquet.apache.org">https://parquet.apache.org</a>):</p> <h3><strong>Python scripts</strong></h3> <ul> <li><em>analyse_sample.py</em>: python script we used to produce the file BHMS.pq.gz and BHMS_ic.pq.gz analysing the SEVN outputs</li> <li><em>create_aux.py</em>: python script we used to produce the file BHMS_VSNCE.pq.gz by combining the SEVN log outputs with the BHMS_ic.pq.gz file</li> </ul> <h3> </h3> <h3>BHMS.pq.gz</h3> <p><strong> </strong>File containing all the systems satisfying the above condition.</p> <p><strong>Columns:</strong></p> <ul> <li>ID: unique id of the binary (Long integer)</li> <li>name: unique name of the binary (Long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminosity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Euclidean distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p> <strong>Notice-1: </strong>in this file each system (identified by ID and name) can appear more than once. Indeed this file contains all the outputs in which a system satisfy the condition BH-star condition discussed above.</p> <p> <strong>Notice-2: </strong><em>the dataframe is sorted based on the bh3dist column,</em> so the first rows contains the objects that are closer to the properties of Gaia BH3 based on the bh3dist statistic.</p> <p> <strong>Notice-3: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_ic.pq.gz</h3> <p>File containing the initial conditions of all the systems included in the file BHMS.pq.gz</p> <p><strong>Columns:</strong></p> <p><em>Info from BHMS.pq.gz</em>:</p> <p>these columns report the same information as in the BHMS.pq.gz file, but each system (identified by ID and name) appears just once (the occurrence from the BHMS.pq.gz with the minimum bh3dist)</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminoisity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Eucledian distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p><em>Initial properties</em>:</p> <ul> <li>mzams_0: Initial (ZAMS) mass of the black hole in Msun</li> <li>mzams_1: Initial (ZAMS) mass of the star in Msun</li> <li>Semimajor_ini: Initial semimajor axis of the binary in Rsun </li> <li>Eccentricity_ini: Initial eccentricity axis of the binary </li> <li>seed: Random seed used in the SEVN simulation</li> <li>P_ini: Intial period of the binary in days </li> </ul> <p><strong> Notice: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_VSNCE.pq.gz</h3> <p>A file containing additional information about the evolutionary events of the systems stored in BHMS.pq.gz</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>time_SN: formation time of the black hole (BH) in Myr (all the simulations start from time=0)</li> <li>Vcom: Velocity magnitude of the center of mass after the formation of the BH (before the formation Vcom=0 is assumed)</li> <li>time_CE_preSN: time of the last CE before the BH formation (if empty no CE before BH formation)</li> <li>time_CE_postSN: time of the first CE after the BH formation (if empty no CE after BH formation)</li> <li>time_RL_preSN: time of the last Roche-Lobe overflow before the BH formation (if empty no RLO before BH formation)</li> <li>time_RL_postSN: time of the first Roche-Lobe overflow after the BH formation (if empty no RLO before BH formation)</li> </ul> <p><strong>Note: </strong>The file has been created by combining the file BHMS_ic.pq.gz with the main SEVN outputs using the script <em>create_aux.py </em>included in this repository</p> <h3>How to read the files</h3> <p>The parquet files can be easily read in Python by using the <a href="https://pandas.pydata.org/docs/reference/api/pandas.read_parquet.html">Pandas module</a>:</p> <pre><code>import pandas as pd df_bhms=pd.read_parquet("BHMS.pq.gz") df_bhms_ic=pd.read_parquet("BHMS_ic.pq.gz") df_bhms_vsnce=pd.read_parquet("BHMS_VSNCE.pq.gz")</code></pre> <p> </p> <h2>Notes</h2> <p>The code used in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> is SEVN (<a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio et al., 2023</a>) version 2.10.1 (commit <a href="https://gitlab.com/sevncodes/sevn/-/tree/a4753f1177aab076da2641afc497a06006b30267">a4753f11</a>). </p>
Dataset from the paper "The boring history of GAIA BH3 from isolated binary evolution": IIB - simulation outcomes, different metallicities
<p>This repository contains (a part) of the population synthesis outputs analysed in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. In particular, it contains the simulation sets with different metallicities.</p> <h2>Content</h2> <p>Each tar file contains the outputs of a given simulation set from <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The name of the files corresponds to the name of the set as reported in Table 1 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The details of the sets can be found in Section 2.2 and Section 2.3 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The outputs stored in this repository contain only the systems that satisfy the following conditions:</p> <ul> <li>The two objects are in a binary system</li> <li>An object is a black hole and the other one is a star in any evolutionary phase prior to the ignition of the helium burning in the core</li> <li>The two objects are not currently interacting except for wind mass transfer (no ongoing Roche-Lobe overflow, common envelope or merger).</li> </ul> <p>The tar files contain three different files in gunzipped parquet format (<a href="https://parquet.apache.org">https://parquet.apache.org</a>):</p> <h3><strong>Python scripts</strong></h3> <ul> <li><em>analyse_sample.py</em>: python script we used to produce the file BHMS.pq.gz and BHMS_ic.pq.gz analysing the SEVN outputs</li> <li><em>create_aux.py</em>: python script we used to produce the file BHMS_VSNCE.pq.gz by combining the SEVN log outputs with the BHMS_ic.pq.gz file</li> </ul> <h3> </h3> <h3>BHMS.pq.gz</h3> <p><strong> </strong>File containing all the systems satisfying the above condition.</p> <p><strong>Columns:</strong></p> <ul> <li>ID: unique id of the binary (Long integer)</li> <li>name: unique name of the binary (Long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminosity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Euclidean distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p> <strong>Notice-1: </strong>in this file each system (identified by ID and name) can appear more than once. Indeed this file contains all the outputs in which a system satisfy the condition BH-star condition discussed above.</p> <p> <strong>Notice-2: </strong><em>the dataframe is sorted based on the bh3dist column,</em> so the first rows contains the objects that are closer to the properties of Gaia BH3 based on the bh3dist statistic.</p> <p> <strong>Notice-3: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_ic.pq.gz</h3> <p>File containing the initial conditions of all the systems included in the file BHMS.pq.gz</p> <p><strong>Columns:</strong></p> <p><em>Info from BHMS.pq.gz</em>:</p> <p>these columns report the same information as in the BHMS.pq.gz file, but each system (identified by ID and name) appears just once (the occurrence from the BHMS.pq.gz with the minimum bh3dist)</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminoisity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Eucledian distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p><em>Initial properties</em>:</p> <ul> <li>mzams_0: Initial (ZAMS) mass of the black hole in Msun</li> <li>mzams_1: Initial (ZAMS) mass of the star in Msun</li> <li>Semimajor_ini: Initial semimajor axis of the binary in Rsun </li> <li>Eccentricity_ini: Initial eccentricity axis of the binary </li> <li>seed: Random seed used in the SEVN simulation</li> <li>P_ini: Intial period of the binary in days </li> </ul> <p><strong> Notice: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_VSNCE.pq.gz</h3> <p>A file containing additional information about the evolutionary events of the systems stored in BHMS.pq.gz</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>time_SN: formation time of the black hole (BH) in Myr (all the simulations start from time=0)</li> <li>Vcom: Velocity magnitude of the center of mass after the formation of the BH (before the formation Vcom=0 is assumed)</li> <li>time_CE_preSN: time of the last CE before the BH formation (if empty no CE before BH formation)</li> <li>time_CE_postSN: time of the first CE after the BH formation (if empty no CE after BH formation)</li> <li>time_RL_preSN: time of the last Roche-Lobe overflow before the BH formation (if empty no RLO before BH formation)</li> <li>time_RL_postSN: time of the first Roche-Lobe overflow after the BH formation (if empty no RLO before BH formation)</li> </ul> <p><strong>Note: </strong>The file has been created by combining the file BHMS_ic.pq.gz with the main SEVN outputs using the script <em>create_aux.py </em>included in this repository</p> <h3>How to read the files</h3> <p>The parquet files can be easily read in Python by using the <a href="https://pandas.pydata.org/docs/reference/api/pandas.read_parquet.html">Pandas module</a>:</p> <pre><code>import pandas as pd df_bhms=pd.read_parquet("BHMS.pq.gz") df_bhms_ic=pd.read_parquet("BHMS_ic.pq.gz") df_bhms_vsnce=pd.read_parquet("BHMS_VSNCE.pq.gz")</code></pre> <p> </p> <h2>Notes</h2> <p>The code used in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> is SEVN (<a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio et al., 2023</a>) version 2.10.1 (commit <a href="https://gitlab.com/sevncodes/sevn/-/tree/a4753f1177aab076da2641afc497a06006b30267">a4753f11</a>). </p>
Metabolomic and BH3 Profiling of Esophageal Cancers: Identification of Novel Assessment Methods of Treatment Response for Precision Therapy
ClinicalTrials.gov study NCT03223662. IPD Sharing: NO. Countries: 1. Publications: 4.
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
<p><span>Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of these BH3 mimetics, the packing interface between BH3 domain ligands and pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to identify the amino acid residues responsible for interaction affinity and specificity. A Knob-Socket analysis organizes all the residues in a binding interface into simple 4 residue units: 3-residue sockets defining surfaces on a protein that pack a 4th residue knob from the other protein. In this way, the position and composition of the knobs packing into sockets across the BH3/BCL-2 interface can be classified. A Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal multiple conserved binding patterns across protein paralogs. Conserved knob residues such as a Gly, Leu, Ala and Glu most likely define binding specificity in the BH3/BCL-2 interface, whereas other residues such as Asp, Asn, and Val are important for forming surface sockets that bind these knobs. These findings can be used to inform the design of BH3 mimetics that are specific to pro-survival BCL-2 proteins for cancer therapeutics.</span></p>
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
Open the record for dataset details and reuse information.
Mitophagy promotes resistance to BH3 mimetics in acute myeloid leukemia
GEO Series GSE182401. Homo sapiens. 7 samples. Type: Expression profiling by high throughput sequencing.
A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response
GEO Series GSE245163. Homo sapiens. 138 samples. Type: Expression profiling by high throughput sequencing.
RAS-mutant AML LSCs originate from GMPs and drive clinical resistance to BH3 mimetics [CMPs and GMPs scRNA-Seq]
GEO Series GSE254478. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
RAS-mutant AML stem cells acquire resistance to BH3 mimetics through altered BCL-2 family expression
GEO Series GSE235206. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
BH3 mimetics and azacitidine show synergistic effects on juvenile myelomonocytic leukemia
GEO Series GSE242432. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
RAS-mutant AML LSCs originate from GMPs and drive clinical resistance to BH3 mimetics [scRNA-Seq]
GEO Series GSE275501. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
RAS-mutant AML LSCs originate from GMPs and drive clinical resistance to BH3 mimetics [RNA-Seq]
GEO Series GSE253426. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
RAS-mutant AML LSCs originate from GMPs and drive clinical resistance to BH3 mimetics [scRNA-Seq]
GEO Series GSE253702. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response [1]
GEO Series GSE245049. Homo sapiens. 42 samples. Type: Expression profiling by high throughput sequencing.
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