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Persistent gene flow suggests an absence of reproductive isolation in an African antelope speciation model
<p>African antelope diversity is a globally unique vestige of a much richer world-wide Pleistocene megafauna. Despite this, the evolutionary processes leading to the prolific radiation of African antelopes are not well understood. Here, we sequenced 145 whole genomes from both subspecies of the waterbuck, an African antelope believed to be in the process of speciation. We investigated genetic structure and population divergence and found evidence of a mid-Pleistocene separation on either side of the eastern Great Rift Valley, consistent with vicariance caused by a rain shadow along the so-called 'Kingdon's Line'. However, we also found pervasive evidence of not only isolated and recent, but also widespread historical gene flow across the Rift Valley barrier. By inferring the genome-wide landscape of variation among subspecies, we found 14 genomic regions of elevated differentiation, including a locus that may be related to each subspecies' distinctive coat pigmentation pattern. We investigated these regions as candidate speciation islands. However, we observed no significant reduction in gene flow in these regions, nor any indications of selection against hybrids. Altogether, these results suggest a pattern whereby climatically driven vicariance is the most important process driving the African antelope radiation, and suggest that reproductive isolation may not set in until very late in the divergence process.</p>
Data from: Isolation of diverse simian arteriviruses causing hemorrhagic disease
<p>Genetically diverse simian arteriviruses (simarteriviruses) naturally infect geographically and phylogenetically diverse monkeys, and cross-species transmission and emergence are of considerable concern. Characterization of most simarteriviruses beyond sequence analysis has not been possible because the viruses fail to propagate in the laboratory. We attempted to isolate 4 simarteriviruses, Kibale red colobus virus 1, Pebjah virus, simian hemorrhagic fever virus, and Southwest baboon virus 1, by inoculating an immortalized grivet cell line (known to replicate simian hemorrhagic fever virus), primary macaque cells, macrophages derived from macaque induced pluripotent stem cells, and mice engrafted with macaque CD34+-enriched hematopoietic stem cells. The combined effort resulted in successful virus isolation; however, no single approach was successful for all 4 simarteriviruses. We describe several approaches that might be used to isolate additional simarteriviruses for phenotypic characterization. Our results will expedite laboratory studies of simarteriviruses to elucidate virus-host interactions, assess zoonotic risk, and develop medical countermeasures.</p>
Figure 3 in Cytotoxicity of extracts and compounds isolated from Croton echioides in animal tumor cell (HTC)
Figure 3. Clerodan diterpenes tested.
Figure 2 in Phenolic compound and fatty acid properties of some microalgae species isolated from Erbil City
Figure 2. Total phenolic content (mg/g) extracted from algal isolates.
Figure 4 in Phenolic compound and fatty acid properties of some microalgae species isolated from Erbil City
Figure 4. Chemical composition of fatty acid in algae obtained by HPLC.
Figure 3 in Characterization of a Coliphage AS1 isolated from sewage effluent in Pakistan
Figure 3. PH stability determination range 3-13. No lytic activity seen below PH 4 and above PH 11.
Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies
<p>Range contraction and expansion from glaciation has led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (<em>Geomys bursarius</em>) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found <em>G. b. wisconsinensis </em>was monophyletic with recent divergence. Further assessment is needed for <em>G. b. major </em>because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified <em>G. b. illinoensis </em>as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because <em>G. b. illinoensis </em>faces continued pressures from niche reduction and habitat loss, we recommend that <em>G. b. illinoensis </em>be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units.</p>
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>
Strain diversity of human-residential Lactiplantibacillus plantarum across children cohorts of two ethnic groups geographically isolated
<p>This file includes seven genes, groEL-ileS-murC-murE-pheS-pyrG-recA, and has been used for multi-site sequence typing (MLST) studies.</p>
Data from a field plot experiment with the canola pathogen Leptosphaeria maculans including disease severity at the leaf spot and canker stages of the epidemic, and population composition as isolates infectivity pathotypes.
<p><strong>Data set</strong></p> <p>Data are from an experiment simulating how differences in <em>Brassica napus</em> resistance deployment strategies and landscape connectivity influence epidemic severity and pathogen population composition of the fungus <em>Leptosphaeria maculans</em> on field plots inoculated with combinations of stubble in 2016 at CSIRO Canberra, ACT, Australia. Disease severity was assessed on the 60 field plots [Data_severity.csv] and 1490 isolates were sampled and assessed for infectivity [Data_infectivity.csv]. This dataset is described and analyzed in Bousset et al. (2018).</p> <p>Treatments were factorial combination of Resistance, Genetic Connectivity and Spatial Connectivity, replicated in 4 blocks (B1 to B4). Resistance has 3 categories (Rlm4, Rlm6 LepR1) differing by the resistance genes in oilseed rape varieties. Genetic Connectivity has 2 levels (HighGC, LowGC) differing by the pre-adaptation of the stubble populations to the host variety. Spatial Connectivity has two levels (HighSC, LowSC) differing by the stubble load. Control plots had NoStubble.</p> <p><strong>Data files</strong></p> <p>[Data_severity.csv] Disease severity was assessed on the 60 field plots at leaf spot and canker stages of the epidemic. Leaf spots data are counts. Canker data are numbers of stems in 12 categories defined by the cankered area on cross section (0 = no canker to 100 = fully cankered).</p> <p>[Data_infectivity.csv] Two types of isolates (122 from 3 stubble sources with contrasting preadaptation and 1368 from leaves sampled on 50 field plots) were tested for infectivity response (V = infective; A = non-infective) on the three host varieties (Rlm4, Rlm6 LepR1), at the seedling stage in greenhouse.</p> <p><strong>Associated publication</strong></p> <p>Bousset L, Sprague S, Thrall PH, Barrett LG (2018). Spatio-temporal connectivity and host resistance influence evolutionary and epidemiological dynamics of the canola pathogen <em>Leptosphaeria maculans. Evolutionary Applications</em> [ DOI: 10.1111/eva.12630 ].</p> <p><strong>Funding information</strong></p> <p>This work benefited from the financial support of INRA – the French National Institute for Agronomical Research, a CSIRO Sir Frederick McMaster fellowship to L. Bousset (Impact of inoculum carry-over on landscape dynamics of the blackleg canola pathogen) and the Grains Research & Development Corporation (GRDC Grant CSP00192)</p>
Characterization of NAD(P)H and FAD autofluorescence signatures in an isolated-perfused rat heart model
<p>Raw data concerning publication titled "Characterization of NAD(P)H and FAD autofluorescence signatures in an isolated-perfused rat heart model"</p> <p>Abstract</p> <p>Autofluorescence spectroscopy is a promising label-free approach to characterize biological samples with demonstrated potential to report structural and biochemical alterations in tissues in a number of clinical applications. We report a characterization of the ex vivo autofluorescence fingerprint of cardiac tissue, exploiting a Langendorff-perfused isolated rat heart model to induce physiological insults to the heart, with a view to understanding how metabolic alterations affect the autofluorescence signals. Changes in the autofluorescence intensity and lifetime signatures associated with reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD) were characterized during oxygen- or glucose-depletion protocols. Results suggest that both NAD(P)H and FAD autofluorescence intensity and lifetime parameters are sensitive to changes in the metabolic state of the heart owing to oxygen deprivation. We also observed changes in NAD(P)H fluorescence intensity and FAD lifetime parameter on reperfusion of oxygen, which might provide information on reperfusion injury, and permanent tissue damage or changes to the tissue during recovery from oxygen deprivation. We found that changes in the autofluorescence signature following glucose-depletion are, in general, less pronounced, and most clearly visible in NAD(P)H related parameters. Overall, the results reported in this investigation can serve as baseline for future investigations of cardiac tissue involving autofluorescence measurements.</p>
Raw data for "Radii of Rydberg states of isolated silicon donors" by Juerong Li et al, Phys Rev B 2018
<p>This upload contains raw data for the field dependent spectra, as in the example of Figure 1a of the manuscript. </p> <p>The data consists of interferograms in columns. Each interferogram has been averaged 30 times. The first row of each data matrix refers to the magnetic field value in the units of Tesla, while the first column indicates the step number in units of wavenumber, which is in power-of-two multiples of the HeNe laser wavelength i.e. 16x632.8 nm. A tab is used to separate data within the rows. The length of the interferogram determines the resolution, which is different for each figure/file.</p> <p>The samples (and field resolution) used for each figure are different. All samples are FZ grown with the growth direction of <100>, all were polished to 1 degree wedge. The sample details are as follows:</p> <p>Name, Doping species, Doping concentration (10^14 cm-3), data file name. <br> Corretto (reference sample), P, 8, Supplementary Data 1.txt<br> Black, Bi, 1.28, Supplementary Data 2.txt<br> 85-3, Li and Mg, 2.3 for Li and 5 x for Mag, Supplementary Data 3.txt<br> V496, P and Sb, 18 for P and 12 for Sb, Supplementary Data 4.txt<br> 72-8a, Se, 26, Supplementary Data 5.txt<br> 66.7, S, 13, Supplementary Data 6.txt </p> <p> </p>
Airborne microbial transport limitation to isolated Antarctic soil habitats
<p>Supplementary Figures 2-4 and 4-6 for Manuscript "Airborne microbial transport limitation to isolated Antarctic soil habitats".</p> <p> </p> <p> </p>
Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/#abs/2018MNRAS.475..772S/abstract">Smith et al. (2018)</a>. MESA version 8118.</p> <p>Publication DOI: <a href="https://doi.org/10.1093/mnras/stx3181">10.1093/mnras/stx3181</a></p>
Persistent effects of fragmentation on tropical rainforest canopy structure after 20 years of isolation
<p>Data of Ecological Application paper "Persistent effects of fragmentation on tropical rainforest canopy structure after 20 years of isolation"</p>
Experimentally Measuring an Isolated Branch of Nonlinear Normal Modes
<p>Dataset for "Experimentally Measuring an Isolated Branch of Nonlinear Normal Modes", Journal of Sound and Vibration.</p> <p>See "readme.txt" for details</p>
Dataset - Improved Isolation of Microbiologically Produced (2R,3S)-Isocitric Acid by Adsorption on Activated Carbon and Recovery with Methanol
<p>This dataset in form of an Excel-format contains the data of the journal article “Improved Isolation of Microbiologically Produced Isocitric Acid by Adsorption on Activated Carbon and Recovery with Methanol”. The dataset shows the values of different experiments, calculations carried out for this publication.</p>
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