207,996 research outputs found
jonas-fuchs/virHEAT: v.0.7
No full text<h2>Update virHEAT to 0.7</h2>
<h4>New</h4>
<ul>
<li>added <code>-s --scores</code> option that lets you link results from <a href="https://mavedb.org/">deep mutational screens</a> to the heatmap</li>
<li>added some more error catching</li>
<li>added MAVE example data</li>
<li>updated documentation</li>
</ul>
<p></p>
<h2>New Contributors</h2>
<ul>
<li>@PlushZ made their first contribution in https://github.com/jonas-fuchs/virHEAT/pull/13
Thanks a lot! :100:</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/jonas-fuchs/virHEAT/compare/v.0.6...v.0.7</p>
Larval responses to turbulence and temperature in a tidal inlet: Habitat selection by dispersing gastropods?
No full textAuthor Posting. © Sears Foundation for Marine Research, 2010. This article is posted here by permission of Sears Foundation for Marine Research for personal use, not for redistribution. The definitive version was published in Journal of Marine Research 68 (2010): 153-188, doi:10.1357/002224010793079013.Marine larval dispersal is affected by hydrodynamic transport and larval behavior, but little is known about how behavior affects large-scale patterns of dispersal and recruitment. Intertidal habitats are characterized by strong and variable turbulence relative to shelf and pelagic waters, so larval responses to turbulence may affect both dispersal and habitat selection. This study combined observations and theoretical approaches to model gastropod larval responses to multiple physical variables in a well-mixed tidal inlet. Physical measurements and larvae were collected in July 2004 in Barnstable Harbor, Massachusetts (USA). Physical measurements were incorporated in an advection-diffusion model where larval vertical velocity is a function of turbulence dissipation rate, temperature, and the temperature gradient. Modeled larval distributions were fitted to observed concentration profiles by maximum likelihood to estimate larval behavioral velocity (swimming or sinking) as a function of environmental conditions. These quantitative behavior estimates were used to test hypotheses about behavioral differences among groups and to assess the relative impact of different cues on overall larval behavior. Larvae of five common gastropod species from different coastal habitats reacted most strongly to turbulence but had genus-specific responses to environmental cues. Larvae of a species from tidal inlets (the mud snail Nassarius obsoletus) had near-zero velocities under calmer conditions and sank in strong turbulence. In contrast, larvae from exposed beach habitats (Crepidula spp. and Anachis spp.) sank in weak turbulence and swam up in strong turbulence, with additional responses to temperature and temperature gradient. Larval responses also differed between small and large size classes and between flood and ebb tides. Behavior of mud snail larvae would contribute to retention inside the inlet and near adult habitats, whereas behavior of beach snail larvae would contribute to rapid export from muddy inlets lacking suitable adult habitats.This work was funded by the Woods Hole Oceanographic Institution (WHOI) Coastal Ocean
Institute, the WHOI Rinehart Coastal Research Center, the National Science Foundation (NSF OCE-
0326734), NSF and US Office of Naval Research grants to S. Elgar and B. Raubenheimer, and the
WHOI Sea Grant (National Oceanic and Atmospheric Administration, Grant No. NA16RG2273,
project no. R/O-38-PD). Analyses were completed while HLF was a postdoctoral scholar at Scripps
Institution of Oceanography (SIO), supported by the California Current Ecosystem Long-Term Ecological
Research program (NSF OCE-0417616) and by SIO funding to P. Franks
Fuchs-et-alii_supplemental_material – Supplemental material for Infectious diseases and Neolithic transformations: Evaluating biological and archaeological proxies in the German loess zone between 5500 and 2500 BCE
No full textSupplemental material, Fuchs-et-alii_supplemental_material for Infectious diseases and Neolithic transformations: Evaluating biological and archaeological proxies in the German loess zone between 5500 and 2500 BCE by Katharina Fuchs, Christoph Rinne, Clara Drummer, Alexander Immel, Ben Krause-Kyora and Almut Nebel in The Holocene</p
Fuchs-et-alii_InfectiousDiseases_information-supplemental-material_revised – Supplemental material for Infectious diseases and Neolithic transformations: Evaluating biological and archaeological proxies in the German loess zone between 5500 and 2500 BCE
No full textSupplemental material, Fuchs-et-alii_InfectiousDiseases_information-supplemental-material_revised for Infectious diseases and Neolithic transformations: Evaluating biological and archaeological proxies in the German loess zone between 5500 and 2500 BCE by Katharina Fuchs, Christoph Rinne, Clara Drummer, Alexander Immel, Ben Krause-Kyora and Almut Nebel in The Holocene</p
jonas-fuchs/varVAMP: v.1.2.0
No full text<h2><strong>Major varVAMP update to version 1.2</strong></h2>
<p>These changes are credited to @wm75 (https://github.com/jonas-fuchs/varVAMP/pull/39).</p>
<h3><strong>CHANGELOG</strong></h3>
<p><strong>(1) Changes around BLAST functionality:</strong></p>
<ul>
<li>Off-target amplicons are now reported as intended in the logs</li>
<li>Off-target amplicons are now always considered last for the final scheme (no penalty is used, but the fact that they had BLAST matches gets recorded)</li>
<li>The BLAST_PENALTY config option is no longer needed and has been removed</li>
<li>Added a new off_target_amplicons column to the qPCR design, the qPCR primer and the (single/tiled) primer tsv outputs to indicate which final amplicons had BLAST hits</li>
</ul>
<p><strong>(2) General reporting changes:</strong></p>
<ul>
<li>Amplicon numbering now proceeds from 5' to 3' even across pools for the tiled mode and from lowest penalty to highest for the other modes (previously additional BLAST penalties weren't considered during penalty-sorting).</li>
<li>In the primer bed file output in tiled mode, primers are now ordered according to the amplicon number without taking the pool into account</li>
<li>In the primer bed file output in qPCR mode, oligos from the same set are now ordered LEFT, PROBE, RIGHT, i.e. by position on the reference</li>
<li>The per-base mismatch plot now uses final primer names as panel titles</li>
<li>The amplicon bed file, in all modes, is now formatted as proper six-column bed</li>
</ul>
<p><strong>(3) Algorithmic fixes and enhancements:</strong></p>
<ul>
<li>The internal representation of amplicon schemes has been unified/simplified across the different modes and steps of the analysis</li>
<li>Search for final non-overlapping amplicons in single mode and for non-overlapping amplicons passing deltaG in qpcr mode has been optimized and is now significantly faster</li>
<li>Some off-by-one errors in internal primer and amplicon interval calculations have been fixed - generally more primers are now found and considered</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/jonas-fuchs/varVAMP/compare/v.1.1.3...v.1.2.0</p>
Leopold Fuchs Collection 1826-1859
No full textThis collection contains the birth, marriage, and citizenship documents of the Fuchs family of Vienna.Ivan P. Florsheim, 1968The original German language inventory is available in the folder.Processed for digitizationSent for digitizationReturned from digitizationLinked to online manifestationdigitize
Provenienzen des Altbestandes der Gottfried Wilhelm Leibniz Bibliothek
No full textDieses Dataset stellt die Provenienzhinweise dar, welche in den Büchern des Altbestandes der Gottfried Wilhelm Leibniz Bibliothek enthalten sind und löst sie auf.
Es handelt sich hierbei um das Ergebnis eines Referendarsprojektes von Prof. Dr. Thomas Fuchs, welcher sein Referendariat von 2003 bis 2005 an der Gottfried Wilhelm Leibniz Bibliothek absolvierte.
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This dataset presents the provenance references contained in the books of the historical collection of the Gottfried Wilhelm Leibniz Library and decodes them.
It is the result of a project by Prof. Dr. Thomas Fuchs, who completed his traineeship at the Gottfried Wilhelm Leibniz Library from 2003 to 2005.</p
Olivier Fuchs, « Responsabilité administrative extracontractuelle et atteintes environnementales », thèse de doctorat, droit, université de Nantes, 2007
No full textFuchs Olivier. Olivier Fuchs, « Responsabilité administrative extracontractuelle et atteintes environnementales », thèse de doctorat, droit, université de Nantes, 2007. In: Revue Juridique de l'Environnement, n°3, 2009. p. 412
jonas-fuchs/virHEAT: v.0.5.4
No full text<p>NEW:</p>
<ul>
<li>added the <code>-n</code> option that allows to delete mutations that appear in the heatmap n times or less. Will be applied after all filtering steps.</li>
</ul>
<p><em>Example: <code>-n 1</code> will delete all mutations indepent of their frequency if they appear only once in the heatmap. Particular helpful to declutter the heatmap and focus on specific mutations that e.g. appear and increase in frequency over time.</em></p>
jonas-fuchs/virHEAT: v.0.6
No full text<p><strong>NEW</strong></p>
<ul>
<li>added <code>--zoom</code> option that allows to zoom into genomic region specified by <code>start</code> and <code>stop</code> values.</li>
<li>added <code>--name</code> option that allows to customize the name of the plot and the file type. If none is given the default is still <code>virHEAT_plot.pdf</code></li>
</ul>
<p><strong>FIXES</strong></p>
<ul>
<li>Error catching if the gff3 is missing a region annotation (needed to get the correct genome length)</li>
<li>small code structural changes</li>
</ul>
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