1,720,975 research outputs found
The AddACO: A bio-inspired modified version of the ant colony optimization algorithm to solve travel salesman problems
Full text linkThe Travel Salesman Problem (TSP) consists in finding the minimal-length closed tour that connects the entire group of nodes of a given graph. We propose to solve such a combinatorial optimization problem with the AddACO algorithm: it is a version of the Ant Colony Optimization method that is characterized by a modified probabilistic law at the basis of the exploratory movement of the artificial insects. In particular, the ant decisional rule is here set to amount in a linear convex combination of competing behavioral stimuli and has therefore an additive form (hence the name of our algorithm), rather than the canonical multiplicative one. The AddACO intends to address two conceptual shortcomings that characterize classical ACO methods: (i) the population of artificial insects is in principle allowed to simultaneously minimize/maximize all migratory guidance cues (which is in implausible from a biological/ecological point of view) and (ii) a given edge of the graph has a null probability to be explored if at least one of the movement trait is therein equal to zero, i.e., regardless the intensity of the others (this in principle reduces the exploratory potential of the ant colony). Three possible variants of our method are then specified: the AddACO-V1, which includes pheromone trail and visibility as insect decisional variables, and the AddACO-V2 and the AddACO-V3, which in turn add random effects and inertia, respectively, to the two classical migratory stimuli. The three versions of our algorithm are tested on benchmark middle-scale TPS instances, in order to assess their performance and to find their optimal parameter setting. The best performing variant is finally applied to large-scale TSPs, compared to the naive Ant-Cycle Ant System, proposed by Dorigo and colleagues, and evaluated in terms of quality of the solutions, computational time, and convergence speed. The aim is in fact to show that the proposed transition probability, as long as its conceptual advantages, is competitive from a performance perspective, i.e., if it does not reduce the exploratory capacity of the ant population w.r.t. the canonical one (at least in the case of selected TSPs). A theoretical study of the asymptotic behavior of the AddACO is given in the appendix of the work, whose conclusive section contains some hints for further improvements of our algorithm, also in the perspective of its application to other optimization problems
Selected aspects of avascular tumor growth reproduced by a hybrid model of cell dynamics and chemical kinetics
Full text linkWe here propose a hybrid computational framework to reproduce and analyze aspects of the avascular progression of a generic solid tumor. Our method first employs an individual-based approach to represent the population of tumor cells, which are distinguished in viable and necrotic agents. The active part of the disease is in turn differentiated according to a set of metabolic states. We then describe the spatio-temporal evolution of the concentration of oxygen and of tumor-secreted proteolytic enzymes using partial differential equations (PDEs). A differential equation finally governs the local degradation of the extracellular matrix (ECM) by the malignant mass. Numerical realizations of the model are run to reproduce tumor growth and invasion in a number scenarios that differ for cell properties (adhesiveness, duplication potential, proteolytic activity) and/or environmental conditions (level of tissue oxygenation and matrix density pattern). In particular, our simulations suggest that tumor aggressiveness, in terms of invasive depth and extension of necrotic tissue, can be reduced by (i) stable cell–cell contact interactions, (ii) poor tendency of malignant agents to chemotactically move upon oxygen gradients, and (iii) presence of an overdense matrix, if coupled by a disrupted proteolytic activity of the disease
Computational approaches for translational oncology: Concepts and patents
Full text linkBackground: Cancer is a heterogeneous disease, which is based on an intricate network of processes at different spatiotemporal scales, from the genome to the tissue level. Hence the necessity for the biomedical and pharmaceutical research to work in a multiscale fashion. In this respect, a significant help derives from the collaboration with theoretical sciences. Mathematical models can in fact provide insights into tumor-related processes and support clinical oncologists in the design of treatment regime, dosage, schedule and toxicity. Objective and Method: The main objective of this article is to review the recent computational-based patents which tackle some relevant aspects of tumor treatment. We first analyze a series of patents concerning the purposing the purposing or repurposing of anti-tumor compounds. These approaches rely on pharmacokinetics and pharmacodynamics modules, that incorporate data obtained in the different phases of clinical trials. Similar methods are also at the basis of other patents included in this paper, which deal with treatment optimization, in terms of maximizing therapy efficacy while minimizing side effects on the host. A group of patents predicting drug response and tumor evolution by the use of kinetics graphs are commented as well. We finally focus on patents that implement informatics tools to map and screen biological, medical, and pharmaceutical knowledge. Results and Conclusions: Despite promising aspects (and an increasing amount of the relative literature), we found few computational-based patents: There is still a significant effort to do for allowing modelling approaches to become an integral component of the pharmaceutical research
A discrete particle model reproducing collective dynamics of a bee swarm
Full text linkIn this article, we present a microscopic discrete mathematical model describing collective dynamics of a bee swarm. More specifically, each bee is set to move according to individual strategies and social interactions, the former involving the desire to reach a target destination, the latter accounting for repulsive/attractive stimuli and for alignment processes. The insects tend in fact to remain sufficiently close to the rest of the population, while avoiding collisions, and they are able to track and synchronize their movement to the flight of a given set of neighbors within their visual field. The resulting collective behavior of the bee cloud therefore emerges from non-local short/long-range interactions. Differently from similar approaches present in the literature, we here test different alignment mechanisms (i.e., based either on an Euclidean or on a topological neighborhood metric), which have an impact also on the other social components characterizing insect behavior. A series of numerical realizations then shows the phenomenology of the swarm (in terms of pattern configuration, collective productive movement, and flight synchronization) in different regions of the space of free model parameters (i.e., strength of attractive/repulsive forces, extension of the interaction regions). In this respect, constraints in the possible variations of such coefficients are here given both by reasonable empirical observations and by analytical results on some stability characteristics of the defined pairwise interaction kernels, which have to assure a realistic crystalline configuration of the swarm. An analysis of the effect of unconscious random fluctuations of bee dynamics is also provided
Extension of tumor fingers: A comparison between an individual-cell based model and a measure theoretic approach
Full text linkThe invasive capability is fundamental in determining the malignancy of a solid tumor. In particular, tumor invasion fronts are characterized by different morphologies, which result both from cell-based processes (such as cell elasticity, adhesive properties and motility) and from subcellular molecular dynamics (such as growth factor internalization, ECM protein digestion and MMP secretion). Of particular relevance is the development of tumors with unstable fingered morphologies: they are in fact more aggressive and hard to be treated than smoother ones as, even if their invasive depth is limited, they are diffcult to be surgically removed. The phenomenon of malignant fingering has been reproduced with several mathematical approaches. In this respect, we here present a qualitative comparison between the results obtained by an individual cell-based model (an extended version of the cellular Potts model) and by a measure-based theoretic method. In particular, we show that in both cases a fundamental role in nger extension is played by intercellular adhesive forces and taxis-like migration
Collective migration and patterning during early development of zebrafish posterior lateral line
Full text linkThe morphogenesis of zebrafish posterior lateral line (PLL) is a good predictive model largely used in biology to study cell coordinated reorganization and collective migration regulating pathologies and human embryonic processes. PLL development involves the formation of a placode formed by epithelial cells with mesenchymal characteristics which migrates within the animal myoseptum while cyclically assembling and depositing rosette-like clusters (progenitors of neuromast structures). The overall process mainly relies on the activity of specific diffusive chemicals, which trigger collective directional migration and patterning. Cell proliferation and cascade of phenotypic transitions play a fundamental role as well. The investigation on the mechanisms regulating such a complex morphogenesis has become a research topic, in the last decades, also for the mathematical community. In this respect, we present a multiscale hybrid model integrating a discrete approach for the cellular level and a continuous description for the molecular scale. The resulting numerical simulations are then able to reproduce both the evolution of wild-type (i.e. normal) embryos and the pathological behaviour resulting form experimental manipulations involving laser ablation. A qualitative analysis of the dependence of these model outcomes from cell-cell mutual interactions, cell chemical sensitivity and internalization rates is included. The aim is first to validate the model, as well as the estimated parameter values, and then to predict what happens in situations not tested yet experimentally. This article is part of the theme issue 'Multi-scale analysis and modelling of collective migration in biological systems'
A phenotype-structured model to reproduce the avascular growth of a tumor and its interaction with the surrounding environment
Full text linkWe here propose a one-dimensional spatially explicit phenotype-structured model to analyze selected aspects of avascular tumor progression. In particular, our approach distinguishes viable and necrotic cell fractions. The metabolically active part of the disease is, in turn, differentiated according to a continuous trait, that identifies cell variants with different degrees of motility and proliferation potential. A parabolic partial differential equation (PDE) then governs the spatio-temporal evolution of the phenotypic distribution of active cells within the host tissue. In this respect, active tumor agents are allowed to duplicate, move upon haptotactic and pressure stimuli, and eventually undergo necrosis. The mutual influence between the emerging malignancy and its environment (in terms of molecular landscape) is implemented by coupling the evolution law of the viable tumor mass with a parabolic PDE for oxygen kinetics and a differential equation that accounts for local consumption of extracellular matrix (ECM) elements. The resulting numerical realizations reproduce tumor growth and invasion in a number scenarios that differ for cell properties (i.e., individual migratory behavior, duplication, and mutation potential) and environmental conditions (i.e., level of tissue oxygenation and homogeneity in the initial matrix profile). In particular, our simulations show that, in all cases, more mobile cell variants occupy the front edge of the tumor, whereas more proliferative clones are selected at more internal regions. A necrotic core constantly occupies the bulk of the mass due to nutrient deprivation. This work may eventually suggest some biomedical strategies to partially reduce tumor aggressiveness, i.e., to enhance necrosis of malignant tissue and to promote the presence of more proliferative cell phenotypes over more invasive ones
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
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
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