Abstract Upon antigen recognition, activation-induced cytosine deaminase initiates affinity maturation of the B-cell receptor by somatic hypermutation (SHM) through error-prone DNA repair pathways. SHM typically creates single nucleotide substitutions, but tandem substitutions may also occur. While have been described in mice and other species, incidence this phenomenon its underlying mechanism...

The-calculus adds explicit substitutions to the-calculus so as to provide a theoretical framework within which the implementation of functional programming languages can be studied. This paper gen-eralises the-calculus to provide a linear calculus of explicit substitutions , called xDILL, which analogously describes the implementation of linear functional programming languages. Our main observa...

We analyze a normalization function for the simply typed λ-calculus based on hereditary substitutions, a technique developed by Pfenning et al. The normalizer is implemented in Agda, a total language where all programs terminate. It requires no termination proof since it is structurally recursive which is recognized by Agda’s termination checker. Using Agda as an interactive theorem prover we e...

We consider a substitutive version of the Arnoux-Yoccoz Interval Exchange Transformation (IET) related to the Tribonacci substitution. We construct the so-called stepped lines associated to the fixed points of the substitution in the Abelianisation (symbolic) space. We analyse various projections of the stepped line recovering the Rauzy Fractal, a Peano Curve related to the work of Arnoux [1], ...

When inferring phylogenetic relationships, not all sites in a sequence alignment are equally informative. One recently proposed approach that takes advantage of this inequality relies on sites that contain amino acids whose replacement requires multiple substitutions. Identifying these so-called RGC_CAM substitutions (after Rare Genomic Changes as Conserved Amino acids-Multiple substitutions) r...

The D-loop region is a hot spot for mitochondrial DNA (mtDNA) alterations, containing two hypervariable segments, HVS-I and HVS-II. In order to identify polymorphic sites and potential genetic background accounting for Hypertrophic CardioMyopathy (HCM) disease, the complete non-coding region of mtDNA from 31 unrelated HCM patients and 45 normal controls were sequenced. The sequences were aligne...

Different tumor types vary greatly in their distribution of driver substitutions. Here, we analyzed how mutation and natural selection contribute to differences in the distribution of KRAS driver substitutions between lung, colon and pancreatic adenocarcinomas. We were able to demonstrate that both differences in mutation and differences in selection drive variation in the distribution of KRAS ...

This paper proposes an implementation of objects and functions via a calculus with explicit substitutions which is connuent and preserves strong normal-ization. The source calculus corresponds to the combination of the &-calculus of Abadi and Cardelli AC96] and the-calculus, and the target calculus corresponds to an extension of the former calculus with explicit substitutions. The interesting f...

quinones are a class of compounds which have widespread importance in chemistry, biology and medicine. because of their appropriate performance in electron transferring rate, quinones are among the most applicable mediators in biosensors. recently, the effects of different non-metal substitutions on redox potential of quinone have been investigated to design suitable mediators for different ele...