77 research outputs found
Membrane Kauffman Networks
A formalization of Kauffman Boolean Networks in terms of P
systems is suggested along two lines: by means of register machines and directly
by means of membranes with receptors
Maximum Search Using P Systems
Several algorithms of maximum search are investigated and eval-
uated in different types of P systems, namely using priorities, multiple nested
membranes and linked transport. The proposed solutions are expected to find
application in a wide range of problems. In particular, the authors are currently working on modeling an algorithm for DNA sequence alignment using
P systems
On Modeling Signal Transduction Networks
Signal transduction networks are very complex processes employed by the
living cell to suitably react to environmental stimuli. Qualitative and quantitative computational
models play an increasingly important role in the representation of these
networks and in the search of new insights about these phenomena. In this work we analyze
some graph-based models used to discover qualitative properties of such networks.
In turn, we show that MP systems can naturally extend these graph-based models by
adding some qualitative elements. The case study of integrins activation during the lymphocyte
recruitment, a crucial phenomenon in inflammatory processes, is described, and
a first MP graph for this network is designed. Finally, we discuss some open problems
related to the qualitative modeling of signaling networks
Computing by Floating Strings
AbstractWe propose a biologically inspired system which computes on double structures of mobile strings by means of rewriting rules that have a biotechnological implementation, by resembling DNA computations. Its computational universality may be straight deduced from a few formal language theoretical results of one of the authors. Such a DNA-like computational device is naturally described by a membrane system which concludes the paper
Toward a Self-replicating Metabolic P System
This work concerns the synthesis of a "minimal cell' by means of a P system, which is a distributed rewriting system inspired by the structure and the functioning of the biological cell. Specifically, we aim to define a dynamical system which exhibits a steady metabolic evolution, resulting in self-maintenance and self-reproduction.
Metabolic P systems represent a class of P systems particularly promising to model
a minimal cell in discrete terms, since they have already successfully modeled several
metabolisms. The main further step is thus to find a simple way to obtain Metabolic P
system self-replication.
This paper deals with ideas presented at the BWMC11 (held in Seville, Feb 2011) and
opens a new trend in membrane computing, based on computational synthetic biology
oriented applications of P systems modeling. The framework is here outlined, and some
problems to tackle the synthesis of a minimal cell are discussed. Moreover, an overview of
literature and a list of appealing research directions is given, along with several references
A word recurrence based algorithm to extract genomic dictionaries
Genomes may be analyzed from an information viewpoint as very long strings,
containing functional elements of variable length, which have been assembled by
evolution. In this work an innovative information theory based algorithm is
proposed, to extract significant (relatively small) dictionaries of genomic
words. Namely, conceptual analyses are here combined with empirical studies, to
open up a methodology for the extraction of variable length dictionaries from
genomic sequences, based on the information content of some factors. Its
application to human chromosomes highlights an original inter-chromosomal
similarity in terms of factor distributions
Two Universality Results for (Mem)Brane Systems
We prove that P systems with mate and drip operations and using at most
five membranes during any step of a computation are universal. This improves a recent
similar result from, where eleven membranes are used. The proof of this result has the
"drawback" that the output of a computation is obtained on an inner membrane of the
system. A universality proof is then given for the case when the result of a computation is
found on the skin membrane (on its external side, hence "visible" from the environment),
but in this case we use one more membrane, as well as another basic brane operation
exo; moreover, the operations are now of the projective type, as introduced in
An Algorithm for Initial Fluxes of Metabolic P Systems
A central issue in systems biology is the study of efficient methods inferring fluxes of biological reactions by starting from experimental data. Among the different techniques proposed in the last years, the theory of Metabolic P systems, which is based on the Log-Gain principle, proved to be helpful for deducing biologi- cal fluxes from temporal series of observed dynamics. According to this approach, the algebraic systems provided by the Log-Gain principle determine the reaction fluxes underlying a system dynamics when initial fluxes are known. Here we propose a heuristic algorithm for estimating the initial fluxes, that is tested in two case studies
Pattern of care for re-irradiation in locally recurrent rectal cancer: a national survey on behalf of the AIRO gastrointestinal tumors study group
PurposeRadical resection (R0) represents the best curative treatment for local recurrence (LR) rectal cancer. Re-irradiation (re-RT) can increase the rate of R0 resection. Currently, there is a lack of guidelines on Re-RT for LR rectal cancer. The Italian Association of Radiation and clinical oncology for gastrointestinal tumors (AIRO-GI) study group released a national survey to investigate the current clinical practice of external beam radiation therapy in these patients.Material and methodsIn February 2021, the survey was designed and distributed to members of the GI working group. The questionnaire consisted of 40 questions regarding center characteristics, clinical indications, doses, and treatment techniques of re-RT for LR rectal cancer.ResultsA total of 37 questionnaires were collected. Re-RT was reported as an option for neoadjuvant treatment in resectable and unresectable disease by 55% and 75% of respondents, respectively. Long-course treatment with 30-40 Gy (1.8-2 Gy/die, 1.2 Gy bid) and hypofractionated regimen of 30-35 Gy in 5 fractions were used in most centers. A total dose of 90-100 Gy as EqD2 dose (& alpha;/& beta; = 5 Gy) was delivered by 46% of the respondents considering the previous treatment. Modern conformal techniques and daily image-guided radiation therapy protocols were used in 94% of centers.ConclusionOur survey showed that re-RT treatment is performed with advanced technology that allow a good management of LR rectal cancer. Significant variations were observed in terms of dose and fractionation, highlighting the need for a consensus on a common treatment strategy that could be validated in prospective studies
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