antigenomics/vdjdb-db: Celebrate the summer 2023 release

Content updates accumulated from the last releas

Particle approximation for first order stochastic partial differential equations

SIGLEAvailable at INIST (FR), Document Supply Service, under shelf-number : 14802 E, issue : a.1991 n.1502 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Edizione Nazionale del Carteggio di L.A. Muratori, vol. 11, Carteggi con Cacciago .... Capilupi

Questo carteggio conferma, al pari degli altri volumi, la straordinaria capacit\ue0 dell\u2019erudito modenese di tessere una rete di contatti e scambi culturali che andava dagli angoli pi\uf9 remoti della Penisola alle grandi sedi della cultura europea. Tra i carteggi raccolti nel presente volume \u2013 in tutto cinquantasei \u2013 spiccano, per consistenza e interesse, quelli con il veneto Angelo Caloger\ue0, esponente di rilievo del giornalismo scientifico, il filosofo siciliano Tommaso Campailla, l\u2019erudito marchigiano Filippo Camerini, l\u2019abate Pietro Canneti e il geografo Giacomo Cantelli. Non mancano inoltre lettere che gettano luce sulla multiforme personalit\ue0 muratoriana, i cui interessi spaziavano dalla medicina (carteggio con P. Capilupi), alla pratica pastorale (Campi Cervelli), al diritto canonico (C.L. Calcagnini), ai molti volti della storia. Interessanti infine i contatti pi\uf9 o meno occasionali di quanti si rivolsero al modenese per ricevere consigli in materia di genealogia, educazione e linguistica

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

<div><p>Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at <a href="https://github.com/mikessh/vdjtools" target="_blank">https://github.com/mikessh/vdjtools</a>.</p></div

Validation of the potentially somatic retroelement insertions.

<p>Black arrows show the primers. GP primers are complementary to the flanking sequences, RE primers are complementary to the retroelement sequence (RE).</p

The number of potentially somatic L1 and Alu insertions detected in different tissue samples and the data on their distribution in genome.

<p>The number of potentially somatic L1 and Alu insertions detected in different tissue samples and the data on their distribution in genome.</p

Number of the retroelement insertions detected within genes and promoters (for each library, predictions are derived from 1000 simulations of coordinates sample sets).

<p>Error bars show 1 SD. (A)—L1 in genes; (B)—L1 in promoters; (C)—Alu in genes; (D)—Alu in promoters.</p

The oligonucleotides used for the preparation of the DNA libraries.

<p>The oligonucleotides used for the preparation of the DNA libraries.</p

The orientation of somatic L1 and Alu insertions relative to nearby genes.

<p>*—p-value based on Monte-Carlo test, 1000 permutations (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117854#sec007" target="_blank">Materials and Methods</a> for details), NS—non-significant (p>0.05)</p><p>The orientation of somatic L1 and Alu insertions relative to nearby genes.</p

Retroelements flanking sequences library preparation.

<p>Small vertical arrows show the restriction sites. Horizontal arrows show PCR primers.</p