Neonate Human Remains: A Window of Opportunity to the Molecular Study of Ancient Syphilis

Ancient DNA (aDNA) analysis can be a useful tool in bacterial disease diagnosis in human remains. However, while the recovery of Mycobacterium spp. has been widely successful, several authors report unsuccessful results regarding ancient treponemal DNA, casting doubts on the usefulness of this technique for the diagnosis of ancient syphilis. Here, we present results from an analysis of four newborn specimens recovered from the crypt of “La Ermita de la Soledad” (XVI–XVII centuries), located in the province of Huelva in the southwest of Spain. We extracted and analyzed aDNA in three independent laboratories, following specific procedures generally practiced in the aDNA field, including cloning of the amplified DNA fragments and sequencing of several clones. This is the most ancient case, reported to date, from which detection of DNA from T. pallidum subspecies pallidum has been successful in more than one individual, and we put forward a hypothesis to explain this result, taking into account the course of the disease in neonate individuals

indigo-dc/udocker: udocker 1.3.11

<p>udocker 1.3.11 see the changelog and the documentation for further information.</p> <ul> <li>Changelog: https://github.com/indigo-dc/udocker/blob/master/CHANGELOG.md</li> <li>Documentation: https://indigo-dc.github.io/udocker/</li> <li>udocker release for Python 2.7 and >= 3.6</li> </ul> <p>Follow these steps to install and run udocker:</p> <pre><code class="language-bash">wget https://github.com/indigo-dc/udocker/releases/download/1.3.11/udocker-1.3.11.tar.gz tar zxvf udocker-1.3.11.tar.gz export PATH=`pwd`/udocker-1.3.11/udocker:$PATH </code></pre> <p>Test with:</p> <pre><code class="language-bash">udocker --help udocker install </code></pre&gt

common-workflow-language/cwltool: 3.1.20231020113452

<h2>What's Changed</h2> <ul> <li>temporarily downgrade galaxy-tool-util to workaround issue with newer conda by @mr-c in https://github.com/common-workflow-language /cwltool/pull/1930</li> </ul> <h3>Deps</h3> <ul> <li>Bump mypy from 1.6.0 to 1.6.1 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1927</li> <li>Update black requirement from ~=23.9 to ~=23.10 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1926</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231016170136...3.1.20231020113452</p&gt

common-workflow-language/cwltool: 3.1.20231114134824

<h2>What's Changed</h2> <ul> <li>gh-actions: need newer setuptools to run setuptools_scm by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1932</li> <li>Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1934</li> <li>software dependencies: allow newer versions of galaxy-tool-util by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1936</li> <li>skip cwl-utils 0.30 by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1941</li> <li>Update black requirement from ~=23.10 to ~=23.11 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1939</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020140205...3.1.20231114134824</p&gt

common-workflow-language/cwltool: 3.1.20231020140205

<h2>What's Changed</h2> <ul> <li>fix the pickling error for IO objects by @ndonyapour in https://github.com/common-workflow-language/cwltool/pull/1929</li> <li>gh-actions: record version before building container to publish to quay.io by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1931</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020113452...3.1.20231020140205</p&gt

common-workflow-language/cwltool: 3.1.20240112164112

<h2>What's Changed</h2> <ul> <li>Fix fast container job hangs by @kuanyili in https://github.com/common-workflow-language/cwltool/pull/1962</li> <li>Permit calling cwltool.main with preparsed args only even with provenance by @davidjsherman in https://github.com/common-workflow-language/cwltool/pull/1964</li> <li>rename singularity image by @misterbrandonwalker in https://github.com/common-workflow-language/cwltool/pull/1956</li> <li>remove galaxy-tool-util from build dependency by @jfennick in https://github.com/common-workflow-language/cwltool/pull/1955</li> <li>Added new test on loop by @LanderOtto in https://github.com/common-workflow-language/cwltool/pull/1965</li> </ul> <h3>Deps</h3> <ul> <li>Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1952</li> <li>Update black requirement from ~=23.11 to ~=23.12 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1957</li> <li>Bump github/codeql-action from 2 to 3 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1958</li> <li>Bump actions/upload-artifact from 3 to 4 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1959</li> <li>Bump mypy from 1.7.1 to 1.8.0 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1960</li> </ul> <h2>New Contributors</h2> <ul> <li>@kuanyili made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1962</li> <li>@LanderOtto made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1965</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231207110929...3.1.20240112164112</p&gt