P Systems with Minimal Insertion and Deletion

In this paper we consider insertion-deletion P systems with priority of deletion over the insertion.We show that such systems with one symbol context-free insertion and deletion rules are able to generate PsRE. If one-symbol one-sided context is added to insertion or deletion rules but no priority is considered, then all recursively enumerable languages can be generated. The same result holds if a deletion of two symbols is permitted. We also show that the priority relation is very important and in its absence the corresponding class of P systems is strictly included in MAT

P Systems with Minimal Left and Right Insertion and Deletion

In this article we investigate the operations of insertion and deletion performed at the ends of a string. We show that using these operations in a P systems framework (which corresponds to using specific variants of graph control), computational completeness can even be achieved with the operations of left and right insertion and deletion of only one symbol

P Systems with Minimal Left and Right Insertion and Deletion

Summary. In this article we investigate the operations of insertion and deletion performed at the ends of a string. We show that using these operations in a P systems framework (which corresponds to using specific variants of graph control), computational completeness can even be achieved with the operations of left and right insertion and deletion of only one symbol.

On very simple P colonies

We study two very simple variants of P colonies: systems with only one object inside the cells, and systems with insertion-deletion programs, so called P colonies with senders and consumers. We show that both of these extremely simple types of systems are able to compute any recursively enumerable set of vectors of non-negative integers

(Tissue) P Systems with Vesicles of Multisets

We consider tissue P systems working on vesicles of multisets with the very simple operations of insertion, deletion, and substitution of single objects. With the whole multiset being enclosed in a vesicle, sending it to a target cell can be indicated in those simple rules working on the multiset. As derivation modes we consider the sequential mode, where exactly one rule is applied in a derivation step, and the set maximal mode, where in each derivation step a non-extendable set of rules is applied. With the set maximal mode, computational completeness can already be obtained with tissue P systems having a tree structure, whereas tissue P systems even with an arbitrary communication structure are not computationally complete when working in the sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for obtaining computational completeness even for tissue P systems working in the sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622

(Tissue) P Systems with Vesicles of Multisets

We consider tissue P systems working on vesicles of multisets with the very simple operations of insertion, deletion, and substitution of single objects. With the whole multiset being enclosed in a vesicle, sending it to a target cell can be indicated in those simple rules working on the multiset. As derivation modes we consider the sequential mode, where exactly one rule is applied in a derivation step, and the set maximal mode, where in each derivation step a non-extendable set of rules is applied. With the set maximal mode, computational completeness can already be obtained with tissue P systems having a tree structure, whereas tissue P systems even with an arbitrary communication structure are not computationally complete when working in the sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for obtaining computational completeness even for tissue P systems working in the sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622

Not all KIT 557/558 codons mutations have the same prognostic influence on recurrence-free survival: breaking the exon 11 mutations in gastrointestinal stromal tumors (GISTs)

Background: Although the gastrointestinal stromal tumor (GIST) genotype is not currently included in risk-stratification systems, a growing body of evidence shows that the pathogenic variant (PV) type and codon location hold a strong prognostic influence on recurrence-free survival (RFS). This information has particular relevance in the adjuvant setting, where an accurate prognostication could help to better identify high-risk tumors and guide clinical decision-making. Materials and Methods: Between January 2005 and December 2020, 96 patients with completely resected GISTs harboring a KIT proto-oncogene receptor tyrosine kinase (KIT) exon 11 PV were included in the study. We analyzed the type and codon location of the PV according to clinicopathological characteristics and clinical outcome; the metastatic sites in relapsed patients were also investigated. Results: Tumors harboring a KIT exon 11 deletion or deletion/insertion involving the 557 and/or 558 codons, showed a more aggressive clinical behavior compared with tumors carrying deletion/deletion/insertion in other codons, or tumors with duplication/insertion/single-nucleotide variant (SNV) (7-year RFS: 50% versus 73.1% versus 88.2%, respectively; p < 0.001). Notably, among 18 relapsed patients with 557 and/or 558 deletion or deletion/insertion, 14 patients (77.8%) harbored deletions simultaneously involving 557 and 558 codons, while only 4 patients (22.2%) harbored deletions involving only 1 of the 557/558 codons. Thus, when 557 or 558 deletions occurred separately, the tumor showed a prognostic behavior similar to the GIST carrying deletions outside the 557/558 position. Remarkably, patients with GISTs stratified as intermediate risk, but carrying the 557/558 deletion, showed a similar outcome to the high-risk patients with tumors harboring deletions in codons other than 557/558, or duplication/insertion/SNV. Conclusion: Our data support the inclusion of the PV type and codon location in routine risk prediction models, and suggest that intermediate-risk patients whose GISTs harbor 557/558 deletions may also need to be treated with adjuvant imatinib like the high-risk patients

Graph-Controlled Insertion-Deletion Systems

In this article, we consider the operations of insertion and deletion working in a graph-controlled manner. We show that like in the case of context-free productions, the computational power is strictly increased when using a control graph: computational completeness can be obtained by systems with insertion or deletion rules involving at most two symbols in a contextual or in a context-free manner and with the control graph having only four nodes.Comment: In Proceedings DCFS 2010, arXiv:1008.127

On insertion-deletion systems over relational words

We introduce a new notion of a relational word as a finite totally ordered set of positions endowed with three binary relations that describe which positions are labeled by equal data, by unequal data and those having an undefined relation between their labels. We define the operations of insertion and deletion on relational words generalizing corresponding operations on strings. We prove that the transitive and reflexive closure of these operations has a decidable membership problem for the case of short insertion-deletion rules (of size two/three and three/two). At the same time, we show that in the general case such systems can produce a coding of any recursively enumerable language leading to undecidabilty of reachability questions.Comment: 24 pages, 8 figure