15 research outputs found
Closing International Loopholes: Changing the Corporate Tax Base to Effectively Combat Tax Avoidance
An analysis of allelic variation in the ABCA4 gene
PURPOSE. To assess the allelic variation of the ATP-binding transporter protein (ABCA4). METHODS. A combination of single-strand conformation polymorphism (SSCP) and automated DNA sequencing was used to systematically screen this gene for sequence variations in 374 unrelated probands with a clinical diagnosis of Stargardt disease, 182 patients with age-related macular degeneration (AMD), and 96 normal subjects. RESULTS. There was no significant difference in the proportion of any single variant or class of variant between the control and AMD groups. In contrast, truncating variants, amino acid substitutions, synonymous codon changes, and intronic variants were significantly enriched in patients with Stargardt disease when compared with their presence in subjects without Stargardt disease (Kruskal-Wallis P < 0.0001 for each variant group). Overall, there were 2480 instances of 213 different variants in the ABCA4 gene, including 589 instances of 97 amino acid substitutions, and 45 instances of 33 truncating variants. CONCLUSIONS. Of the 97 amino acid substitutions, 11 occurred at a frequency that made them unlikely to be high-penetrance recessive disease-causing variants (HPRDCV). After accounting for variants in cis, one or more changes that were compatible with HPRDCV were found on 35% of all Stargardt-associated alleles overall. The nucleotide diversity of the ABCA4 coding region, a collective measure of the number and prevalence of polymorphic sites in a region of DNA, was found to be 1.28, a value that is 9 to 400 times greater than that of two other macular disease genes that were examined in a similar fashion (VMD2 and EFEMP1)
dandi/dandi-archive: v0.3.60
<h4> Bug Fix</h4>
<ul>
<li>Add UPLOADED state to Zarr models <a href="https://github.com/dandi/dandi-archive/pull/1698">#1698</a> (<a href="https://github.com/AlmightyYakob">@AlmightyYakob</a> <a href="https://github.com/danlamanna">@danlamanna</a>)</li>
<li>Require Python 3.11 <a href="https://github.com/dandi/dandi-archive/pull/1736">#1736</a> (<a href="https://github.com/brianhelba">@brianhelba</a>)</li>
<li>Add a note to registration page that no account is necessary to access public data <a href="https://github.com/dandi/dandi-archive/pull/1696">#1696</a> (<a href="https://github.com/yarikoptic">@yarikoptic</a> <a href="https://github.com/satra">@satra</a>)</li>
</ul>
<h4> Tests</h4>
<ul>
<li>Revert "Skip broken dandi-cli tests" - fixed up in dandi-cli 0.57.0 <a href="https://github.com/dandi/dandi-archive/pull/1732">#1732</a> (<a href="https://github.com/yarikoptic">@yarikoptic</a>)</li>
</ul>
<h4>Authors: 5</h4>
<ul>
<li>Brian Helba (<a href="https://github.com/brianhelba">@brianhelba</a>)</li>
<li>Dan LaManna (<a href="https://github.com/danlamanna">@danlamanna</a>)</li>
<li>Jacob Nesbitt (<a href="https://github.com/AlmightyYakob">@AlmightyYakob</a>)</li>
<li>Satrajit Ghosh (<a href="https://github.com/satra">@satra</a>)</li>
<li>Yaroslav Halchenko (<a href="https://github.com/yarikoptic">@yarikoptic</a>)</li>
</ul>
dandi/dandi-archive: v0.3.61
<h4> Bug Fix</h4>
<ul>
<li>Fix S308 Use of <code>mark_safe</code> may expose cross-site scripting vulnerabilities <a href="https://github.com/dandi/dandi-archive/pull/1742">#1742</a> (<a href="https://github.com/brianhelba">@brianhelba</a>)</li>
<li>Clean up and improve the performance of manifest file creation <a href="https://github.com/dandi/dandi-archive/pull/1738">#1738</a> (<a href="https://github.com/brianhelba">@brianhelba</a>)</li>
<li>Fix PTH118 <code>os.path.join()</code> should be replaced by <code>Path</code> with <code>/</code> operator <a href="https://github.com/dandi/dandi-archive/pull/1743">#1743</a> (<a href="https://github.com/brianhelba">@brianhelba</a>)</li>
</ul>
<h4>Authors: 1</h4>
<ul>
<li>Brian Helba (<a href="https://github.com/brianhelba">@brianhelba</a>)</li>
</ul>
dandi/dandi-archive: v0.3.58
<h4> Bug Fix</h4>
<ul>
<li>Add sentry profiling <a href="https://github.com/dandi/dandi-archive/pull/1728">#1728</a> (<a href="https://github.com/danlamanna">@danlamanna</a>)</li>
<li>Remove unnecessary atomic decorators from tasks <a href="https://github.com/dandi/dandi-archive/pull/1720">#1720</a> (<a href="https://github.com/mvandenburgh">@mvandenburgh</a>)</li>
<li>Remove pinning on django-storages[boto3] <a href="https://github.com/dandi/dandi-archive/pull/1717">#1717</a> (<a href="https://github.com/mvandenburgh">@mvandenburgh</a>)</li>
<li>Temporarily skip broken dandi-cli tests <a href="https://github.com/dandi/dandi-archive/pull/1718">#1718</a> (<a href="https://github.com/mvandenburgh">@mvandenburgh</a>)</li>
<li>Remove unused <code>modified</code> field on <code>Upload</code> model <a href="https://github.com/dandi/dandi-archive/pull/1713">#1713</a> (<a href="https://github.com/mvandenburgh">@mvandenburgh</a>)</li>
<li>File page index fix <a href="https://github.com/dandi/dandi-archive/pull/1704">#1704</a> (<a href="https://github.com/marySalvi">@marySalvi</a>)</li>
<li>Fix <code>requests</code> type errors <a href="https://github.com/dandi/dandi-archive/pull/1714">#1714</a> (<a href="https://github.com/mvandenburgh">@mvandenburgh</a>)</li>
</ul>
<h4>Authors: 3</h4>
<ul>
<li>Dan LaManna (<a href="https://github.com/danlamanna">@danlamanna</a>)</li>
<li>Mary Salvi (<a href="https://github.com/marySalvi">@marySalvi</a>)</li>
<li>Mike VanDenburgh (<a href="https://github.com/mvandenburgh">@mvandenburgh</a>)</li>
</ul>
dandi/dandi-archive: v0.3.62
<h4> Bug Fix</h4>
<ul>
<li>[DATALAD RUNCMD] Replace youtube URL with the one with @dandiarchive <a href="https://github.com/dandi/dandi-archive/pull/1754">#1754</a> (<a href="https://github.com/yarikoptic">@yarikoptic</a>)</li>
<li>Fix style issues found by Ruff <a href="https://github.com/dandi/dandi-archive/pull/1741">#1741</a> (<a href="https://github.com/brianhelba">@brianhelba</a>)</li>
</ul>
<h4>Authors: 2</h4>
<ul>
<li>Brian Helba (<a href="https://github.com/brianhelba">@brianhelba</a>)</li>
<li>Yaroslav Halchenko (<a href="https://github.com/yarikoptic">@yarikoptic</a>)</li>
</ul>
dandi/dandi-archive: v0.3.59
<h4> Bug Fix</h4>
<ul>
<li>Optimize dandiset listing endpoint <a href="https://github.com/dandi/dandi-archive/pull/1730">#1730</a> (<a href="https://github.com/AlmightyYakob">@AlmightyYakob</a>)</li>
<li>Update <code>django-composed-configuration</code> <a href="https://github.com/dandi/dandi-archive/pull/1731">#1731</a> (<a href="https://github.com/mvandenburgh">@mvandenburgh</a>)</li>
</ul>
<h4> Internal</h4>
<ul>
<li><a href="deps">gh-actions</a>: Bump actions/setup-node from 3 to 4 <a href="https://github.com/dandi/dandi-archive/pull/1726">#1726</a> (<a href="https://github.com/dependabot%5Bbot%5D">@dependabot[bot]</a>)</li>
</ul>
<h4>Authors: 3</h4>
<ul>
<li><a href="https://github.com/dependabot%5Bbot%5D">@dependabot[bot]</a></li>
<li>Jacob Nesbitt (<a href="https://github.com/AlmightyYakob">@AlmightyYakob</a>)</li>
<li>Mike VanDenburgh (<a href="https://github.com/mvandenburgh">@mvandenburgh</a>)</li>
</ul>
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Small intestine and colon tissue-resident memory CD8+ T cells exhibit molecular heterogeneity and differential dependence on Eomes
Tissue-resident memory CD8+ T (TRM) cells are a subset of memory T cells that play a critical role in limiting early pathogen spread and controlling infection. TRM cells exhibit differences across tissues, but their potential heterogeneity among distinct anatomic compartments within the small intestine and colon has not been well recognized. Here, by analyzing TRM cells from the lamina propria and epithelial compartments of the small intestine and colon, we showed that intestinal TRM cells exhibited distinctive patterns of cytokine and granzyme expression along with substantial transcriptional, epigenetic, and functional heterogeneity. The T-box transcription factor Eomes, which represses TRM cell formation in some tissues, exhibited unexpected context-specific regulatory roles in supporting the maintenance of established TRM cells in the small intestine, but not in the colon. Taken together, these data provide previously unappreciated insights into the heterogeneity and differential requirements for the formation vs. maintenance of intestinal TRM cells