1,721,004 research outputs found
Verification of spatial and temporal modalities in biochemical systems.
Full text linkBiochemical systems such as metabolic and signaling pathways tend to be arranged in a physical space: the product of one reaction must be in the right place to become the reactant for the subsequent reaction in the pathway. Moreover, in some cases, the behavior of the systems can depend on both, the location of the reactants as well as on the time needed for the reaction to occur. We address the problem of specifying and verifying properties of biochemical systems that exhibit both temporal and spatial modalities at the same time. For that, we use as specification language a fragment of intuitionistic linear logic with subexponentials (SELL). The subexponential signature allows us to capture the spatial relations among the different components of the system and the timed constraints for reactions to occur. We show that our framework is general enough to give a declarative semantics to P-Systems and we show that such logical characterization has a strong level of adequacy. Hence, derivations in SELL follow exactly the behavior of the modeled system
A Toolkit Supporting Formal Reasoning about Causality in Metabolic Networks
No full textWe propose a formal analysis approach aiming at featuring both expressiveness and
ease of use. Its main ingredients are: i) a minimal notation to precisely represent bio-chemical
interactions, and ii) an automated tool allowing the human expert to easily vary conditions of
the in silico experiment. In particular, we exploit an analogy between logical implication and
chemical reaction, i.e., roughly, the reaction of two molecules A and B producing a third one,
C, can be interpreted as A and B logically imply C. Starting from a description of a
metabolic network, in terms of reaction rules and initial conditions, chains of reactions,
causally depending one from the another, can be mechanically deduced. Then, both the
components of the initial state and, noticeably, the clauses ruling reactions can be changed
and a new trial of the experiment started, according to a what-if investigation strategy. The
method is supported by a computational logic counterpart, based on a Prolog implementation,
which allows for a representation language closely correspondent to the adopted chemical
abstract notation. The proposed framework has been validated by studying the robustness of the metabolic network of Escherichia coli K12. Selected genes have been knocked-out by
disabling the rules regarding the encoded enzymes. Results are coherent with the actual
biological behaviour
Control Flow Analysis of Generalised Boolean Networks
No full textGeneralised Boolean Networks are a well known qualitative model used to analyse the evolution of genetic networks as well as generic biological pathways. Despite the qualitative abstraction due to the few threshold concentration values considered for each biological element in the model, the complexity of the execution of a Generalised Boolean model could be non trivial. In this paper, we propose a tailored process algebra, called Sim-πn, reminiscent of the π-calculus to model GBNs. We further apply the Control Flow Analysis methodology to the resulting computational model for making static (and therefore less computationally expensive) predictions on the dynamical evolution of the investigated networks. The scope is twofold: helping in the setting up of the model, for checking its completeness, and checking the evolution of the model, in terms of the possibility to reach particular threshold values of the biological elements in the model, when varying the initial conditions
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
On Deducing Causality in Metabolic Networks
Full text linkMetabolic networks present a complex interconnected structure, whose understanding is in general a non-trivial task. Several formal approaches have been developed to support the investigation of such networks. One of the relevant problems in this context is the comprehension of causality dependencies amongst the molecules involved in the metabolic process
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
A framework for modelling spatially dependent interactions of biological systems in CCP.
No full textIn this paper we show how to model biochemical reactions in Concurrent Constraint Programming (CCP) taking into account space and locality. In fact, in many cases, the distribution of the reactants in the cellular space is critical for the correct dynamics of the reactions. Thus, we propose a modelling framework which allows us to take into account space domains. Resorting on our approach, it is possible to de- scribe accurately biochemical processes without abstracting away from features related to the spatial localisation. In order to describe locality in CCP, we add subexponentials, a concept coming from linear logic, to the constraint system and then, we can model declaratively when a certain reaction occurs within one location of the space domain. Clearly we can also express interactions between agents, taking place either in different spaces or in the same space. Metabolic pathways and, in par- ticular, signalling pathways tend to be arranged in a physical space such that the product of one reaction is in the right place to become the re- actant for the subsequent reaction in the pathway. Following this idea, we show through a simple case study how we can model a signalling cascade. Then, we exploit our framework to model a more complex sig- nalling pathway, namely the TWEAK (TNF related Weak inducer of apoptosis), whose misfunctioning has implications in several important diseases
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