541 research outputs found
Chilipp/psyplot-conda v1.1.0
No full text<p>psyplot-conda v1.1.0 provides new installers for <a href="https://psyplot.readthedocs.io">psyplot</a>, <a href="https://psyplot.readthedocs.io/projects/psyplot-gui">psyplot-gui</a>, <a href="https://psyplot.readthedocs.io/projects/psy-simple">psy-simple</a>, <a href="https://psyplot.readthedocs.io/projects/psy-simple">psy-maps</a> and <a href="https://psyplot.readthedocs.io/projects/psy-reg">psy-reg</a> of the versions v1.1.0.</p>
<p>Besides others, these new versions especially provide new <a href="http://xarray.pydata.org/en/stable/internals.html#extending-xarray">xarray accessors</a> and better widgets for the GUI. For more details, look into the changelogs of the corresponding packages.</p>The author thanks the Swiss National Science Foundation (SNF) for their support. Funding for the author came from the HORNET grant (200021_169598)
Multiple sequence alignments of Treponema pallidum complete genomes using three different references for mapping NGS reads
No full textEach file corresponds to the multiple sequence alignment of 75 complete Treponema pallidum genome sequences using the genomes of strains Nichols, SS14, and CDC-2 as references for mapping. This is supplemental data to the manuscript "Evolutionary processes in the emergence and recent spread of Treponema pallidum, the causative agent of syphilis" by Marta Pla-Díaz, Leonor Sánchez-Busó, Lorenzo Giacani, David Šmajs, Philipp P. Bosshard, Homayoun C. Bagheri, Verena J. Schuenemann, Kay Nieselt, Natasha Arora and Fernando González-Candela
Prefazione all'edizione italiana di "Il bambino e la coppia"
No full textL'Autrice connette il lavoro di Fivaz Depeursinge e Philipp agli studi di P. Minuchin sull'evoluzione del bambino nell'ambito delle relazioni familiari. Viene inoltre proposta una riflessione sull'utilità del volume nell'ambito della terapia familiare che coinvolge i bambini. Il ruolo attivo del bambino nel triangolo primario viene connesso a specifici disturbi per i quali può essere richiesto un aiuto psicoterapeutico dai genitori.The author connects the work of Fivaz Depeursinge and Philipp to the studies of P. Minuchin about evolution of the child in the context of family relationships. It also proposed a reflection on the usefulness of the book in the context of family therapy involving children. The active role of the child in primary triangle is connected to specific conditions for which may be required psychotherapeutic help from parents
Usefulness of IgM-specific enzyme immunoassays for serodiagnosis of syphilis: comparative evaluation of three different assays
Get PDFOBJECTIVES: IgM antibodies are usually the first to be produced during treponemal infection. Three commercially available enzyme immunoassays (EIA) for detection of IgM antibodies against Treponema pallidum were evaluated. METHODS: Results of the Anti-Treponema-pallidum-ELISA (IgM; Euroimmun), Pathozyme Syphilis M Capture (Omega Diagnostics) and recomWell Treponema IgM (Mikrogen) were compared with those of the T. pallidum particle agglutination (TPPA) and the Venereal Disease Research Laboratory (VDRL) tests for 307 serum samples. RESULTS: The overall sensitivity (95% confidence interval [CI]) of the TPPA was 100% (97.7-100%) compared to 83.3% (76.5-88.8%) of the VDRL, 88.5% (82.4-93.0%) of the Pathozyme, 84.6% (78.0-89.9) of the Euroimmun, and 73.6% (66.1-80.4%) of a modified recomWell test procedure. Specificities were in the range of 91.4-100%. In primary syphilis, sensitivities of the Pathozyme (89.8%; 95% CI, 79.2-96.2%) and Euroimmun tests (81.4%; 95% CI, 69.1-90.3%) were significantly higher (p < 0.05) than the sensitivity of the VDRL test (61%; 95% CI, 47.4-73.5%). IgM EIAs even were positive in some cases of suspected very early infection where the VDRL was non-reactive and the TPPA was indeterminate. CONCLUSIONS: In cases of suspected early infection specific IgM EIAs should be used in addition to other screening tests. The VDRL is not recommended for screening
Author Correction: Auto-aggressive CXCR6+ CD8 T cells cause liver immune pathology in NASH
No full textIn this Article, the surname of Tobias Boettler was incorrectly shown as ‘Böttler’, and the surname of author Jan-Philipp Mallm was incorrectly shown as ‘Malm’. The original Article has been corrected online
Incubation of fungal cultures: how long is long enough?
No full textFungal cultures are traditionally incubated for 4 weeks or longer to maximise the recovery of slowly growing fungi. However, the data in support of this are scarce. The objectives of this study were to determine the optimum incubation time for specimens in which moulds or yeast are suspected and to review the literature. A total of 3036 fungal cultures of 2216 dermatological and 820 non-dermatological specimens were analysed. The day on which fungal growth was first noted, was recorded. Eleven of 820 non-dermatological specimens were positive after day 14; in 10 cases, the fungus was considered clinically non-relevant and in one case, the cerebrospinal fluid of a patient receiving therapy for cryptococcosis was positive with Cryptococcus neoformans. Fourteen and three of 2216 dermatological samples showed the growth of a dermatophyte in the third week and fourth week respectively. The results indicate that for specimens sent for the detection of yeast or moulds (except dermatophytes and systemic dimorphic fungi), an incubation period of 2 weeks is sufficient, whereas for dermatophytes, a 4-week incubation period is necessary. Based on these results and previous literature, an algorithm for the incubation time of fungal cultures is proposed
Chilipp/psyplot-conda: v1.0.1: Conda installers for psyplot - The interactive visualization framework
No full text<p>psyplot-conda provides standalone installers for the psyplot interactive visualization framework.</p>
<p><strong>psyplot</strong> is an open source python project that mainly combines the plotting utilities of matplotlib (Hunter, 2007) and the data management of the xarray package (Hoyer & Hamman, 2017). The main purpose is to have a framework that allows a fast, attractive, flexible, easily applicable, easily reproducible and especially an interactive visualization of your data.</p>
<p>The ultimate goal is to help scientists and especially climate model developers in their daily work by providing a flexible visualization tool that can be enhanced by their own visualization scripts. psyplot can be used through the python command line and through the psyplot-gui module which provides a graphical user interface for an easier interactive usage.</p>
<p>These installers contains all necessary dependencies for psyplot, psyplot-gui, psy-simple, psy-maps and psy-reg plus the conda package for managing virtual environments. The installers have been created using using the conda constructor package and the packages from the conda-forge channel.</p>
<p>Other ways to install psyplot can be found in the psyplot docs: http://psyplot.readthedocs.io</p>
<p><strong>Source files</strong></p>
<p>These files contain the source python code for the psyplot-conda repository (tag v1.0.1) and it's submodules psyplot (tag v1.0.0), psy-simple (tag v1.0.0), psy-maps (tag v1.0.0), psy-reg (tag v1.0.0) and psyplot-gui (tag v1.0.1).</p>
<ul>
<li><strong>psyplot-conda-1.0.1.zip</strong>: The zipped source files including reference figures for psy-simple and psy-maps</li>
<li><strong>psyplot-conda-1.0.1-no-refs.zip</strong>: The zipped source files without reference figures</li>
</ul>
<p><strong>Documentation files</strong></p>
<p>These files contain the documentation for psyplot, psy-maps, psy-reg, psy-simple and psyplot-gui from http://psyplot.readthedocs.io/en/latest/, downloaded on August, 21st, 2017.</p>
<ul>
<li><strong>docs-epub.zip</strong>: Documentation files in epub format</li>
<li><strong>docs-pdf.zip</strong>: Documentation files in pdf format</li>
<li><strong>docs-html.zip</strong>: Documentation files in html format</li>
</ul>
<p><strong>Standalone installers</strong></p>
<p>These installers have been created using the conda constructor package and can be used to install psyplot, psy-simple, psy-maps, psy-reg and psyplot-gui. Installation instructions can be found in the Additional Notes.</p>
<ul>
<li><strong>psyplot-conda-1.0.1-Linux-x86-64.sh</strong>: Bash installer for 64-bit Linux systems</li>
<li><strong>psyplot-conda-1.0.1-MacOSX-x86-64.sh</strong>: Bash installer for 64-bit Mac OS X systems</li>
<li><strong>psyplot-conda-1.0.1-MacOSX-x86-64.pkg</strong>: Package installer for 64-bit Mac OS X systems</li>
<li><strong>psyplot-conda-1.0.1-Windows-x86-64.exe</strong>: Windows installer for 64-bit systems</li>
<li><strong>psyplot-conda-1.0.1-Windows-x86.exe</strong>: Windows installer for 32-bit systems</li>
<li><strong>psyplot-conda-1.0.1-Windows-no-shortcut-x86-64.exe</strong>: Windows installer for 64-bit systems without menu shortcut</li>
<li><strong>psyplot-conda-1.0.1-Windows-no-shortcut-x86.exe</strong>: Windows installer for 32-bit systems without menu shortcut</li>
</ul>
<p><strong>Packages</strong></p>
<p>These files contain packages for psyplot (1.0.0.post1), psy-simple (1.0.0), psy-maps (1.0.0), psy-reg (1.0.0) and psyplot-gui (1.0.1).</p>
<ul>
<li><strong>python-packages.zip</strong>: Python packages from pipy.org</li>
<li><strong>conda-packages.zip</strong>: Conda packages from https://anaconda.org/conda-forge</li>
</ul>
<p> </p>
<p><strong>Installation instructions for standalone installers</strong></p>
<p><strong>Installation on Linux</strong></p>
<p>Download the bash script and open a terminal window.</p>
<p>Type:</p>
<p>bash '<path-to-the-downloaded-file.sh>'</p>
<p>and simply follow the instructions.</p>
<p>For more information on the command line options type:</p>
<p>bash '<Path-to-the-downloaded-file.sh>' --help</p>
<p>It will ask you, whether you want to add a psyplot alias to your .bashrc, such that you can easily start the terminal and type psyplot to start the GUI. You can avoid this by setting NO_PSYPLOT_ALIAS=1. Hence, to install psyplot-conda without any terminal interaction, run:</p>
<p>NO_PSYPLOT_ALIAS=1 bash '<Path-to-the-downloaded-file.sh>' -b -p <target-path></p>
<p><strong>Uninstallation on Linux</strong></p>
<p>Just delete the folder where you installed psyplot-conda. By default, this is HOME/psyplot-conda, so just type:</p>
<p>rm -rf HOME/psyplot-conda</p>
<p>If you added a psyplot alias to your .bashrc or chose to add the bin directory to your PATH variable during the installation, open your HOME/.bashrc in an editor of your choice and delete those parts.</p>
<p><strong>Installation on OS X</strong></p>
<p>You can either install it from the terminal using a bash-script (.sh file), or you can install a standalone app using an installer (.pkg file).</p>
<p>The bash script will install a conda installation in your desired location. Both will create a Psyplot.app (see below).</p>
<p><strong>Installation using the OS X package</strong></p>
<p>This should be straight-forward, however Apple does not provide free Developer IDs for open-source developers. Therefore our installers are not signed and you have to give the permissions to open the files manually. The 4 steps below describe the process.</p>
<ol>
<li>Just download the .pkg file</li>
<li>To open it, you have to</li>
</ol>
<p> Right-click on the file, then Open With, then Installer. In the appearing window, click the Open button.</p>
<ol>
<li>Follow the instructions. It will create a Psyplot.app in the specified location.</li>
<li>To open the app the first time, change to the chosen installation directory for the App (by default HOME/Applications), right-click the Psyplot app and click on Open. In the appearing window, again click on Open.</li>
</ol>
<p><strong>Installation using the bash script</strong></p>
<p>Download the bash script (file ending on '.sh' for MacOSX) and open a terminal window.</p>
<p>Type:</p>
<p>bash '<path-to-the-downloaded-file.sh>'</p>
<p>and simply follow the instructions.</p>
<p>For more informations on the command line options type:</p>
<p>bash '<Path-to-the-downloaded-file.sh>' --help</p>
<p>By default, the installer asks whether you want to install a Psyplot.app into your Applications directory. You can avoid this be setting NO_PSYPLOT_APP=1.</p>
<p>Furthermore it will ask you, whether you want to add a psyplot alias to your .bash_profile, such that you can easily start the terminal and type psyplot to start the GUI. You can avoid this by setting NO_PSYPLOT_ALIAS=1. Hence, to install psyplot-conda without any terminal interaction, run:</p>
<p>NO_PSYPLOT_APP=1 NO_PSYPLOT_ALIAS=1 bash '<Path-to-the-downloaded-file.sh>' -b -p <target-path></p>
<p><strong>Uninstallation on OSX</strong></p>
<p>The uninstallation depends on whether you have used the package installer or the bash script for the installation.</p>
<p><strong>Uninstall the App installed through the OS X package</strong></p>
<p>Just delete the app from your Applications folder. There have been no changes made to your PATH variable.</p>
<p><strong>Uninstall the App installed via bash script</strong></p>
<p>As for linux, just delete the folder where you installed psyplot-conda. By default, this is HOME/psyplot-conda. Open a terminal and just type:</p>
<p>rm -rf HOME/psyplot-conda</p>
<p>If you added a psyplot alias to your .bash_profile or chose to add the bin directory to your PATH variable during the installation, open your HOME/.bash_profile in an editor of your choice and delete those parts.</p>
<p>If you chose to add a Psyplot app, just delete the symbolic link in /Applications or HOME/Applications.</p>
<p><strong>Installation on Windows</strong></p>
<p>Just download the installer for 64-bit or 32-bit, double click the downloaded file and follow the instructions. The installation will create an item in the windows menu (Start -> Programs -> Psyplot) which you can use to open the GUI. You can, however, also download installers that create no shortcut from below.</p>
<p>In any case, if you chose to modify your PATH variable during the installation, you can open a command window (cmd) and type psyplot.</p>
<p><strong>Uninstallation on Windows</strong></p>
<p>Just double-click the Uninstall-Anaconda.exe file in the directory where you installed psyplot-conda and follow the instructions.</p>
<p>This will also revert the changes in your PATH variable.</p>
<p><strong>Acknowledgements</strong></p>
<p>The author thanks the Swiss National Science Foundation (SNF) for their support. Funding for the author came from the ACACIA grant (CR10I2_146314) and the HORNET grant (200021_169598).</p>
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