Gene regulatory networks reconstruction from time series datasets using genetic programming: a comparison between tree-based and graph-based approaches

Genetic programming researchers have shown a growing interest in the study of gene regulatory networks in the last few years. Our team has also contributed to the field, by defining two systems for the automatic reverse engineering of gene regulatory networks called GRNGen and GeNet. In this paper, we revise this work by describing in detail the two approaches and empirically comparing them. The results we report, and in particular the fact that GeNet can be used on large networks while GRNGen cannot, encourage us to pursue the study of GeNet in the future. We conclude the paper by discussing the main research directions that we are planning to investigate to improve GeNet.     

Temporal contexts: Effective text classification in evolving document collections

The management of a huge and growing amount of information available nowadays makes Automatic Document Classification (ADC), besides crucial, a very challenging task. Furthermore, the dynamics inherent to classification problems, mainly on the Web, make this task even more challenging. Despite this fact, the actual impact of such temporal evolution on ADC is still poorly understood in the literature. In this context, this work concerns to evaluate, characterize and exploit the temporal evolution to improve ADC techniques. As first contribution we highlight the proposal of a pragmatical methodology for evaluating the temporal evolution in ADC domains. Through this methodology, we can identify measurable factors associated to ADC models degradation over time. Going a step further, based on such analyzes, we propose effective and efficient strategies to make current techniques more robust to natural shifts over time. We present a strategy, named temporal context selection, for selecting portions of the training set that minimize those factors. Our second contribution consists of proposing a general algorithm, called Chronos, for determining such contexts. By instantiating Chronos, we are able to reduce uncertainty and improve the overall classification accuracy. Empirical evaluations of heuristic instantiations of the algorithm, named WindowsChronos and FilterChronos, on two real document collections demonstrate the usefulness of our proposal. Comparing them against state-of-the-art ADC algorithms shows that selecting temporal contexts allows improvements on the classification accuracy up to 10%. Finally, we highlight the applicability and the generality of our proposal in practice, pointing out this study as a promising research direction.     

Construction of baselines for VoIP traffic management on open MANs

In the last century, owing to the constant evolution of technologies telecommunication networks have become increasingly robust, being able to support multiple services. These services are part of the heterogeneous network traffic that can be carried through the Internet. Many of these services, including VoIP, are latency sensitive. In other words, this means that their quality depends directly on the network quality of service. Since users tend to become more sensitive with the instability and unavailability of the network, it is important to improve traffic management. A particular type of data that could be used to improve VoIP traffic management is the Internet Protocol Detail Record (IPDR). IPDRs are tickets created by all VoIP call attempts which contain a group of information related to the call history. Because of its full range of information, IPDRs can be used to create VoIP traffic baselines. This paper presents the development of baselines based on IPDRs to support VoIP traffic management in open‐access Metropolitan Area Networks (MAN). Copyright © 2013 John Wiley & Sons, Ltd.     

Building a bridge between performance management,radical innovation,and innovation networks: A systematic literature review

Research on performance management (PM) of networks and radical innovation has largely developed along two isolated paths. On the one hand, a growing body of knowledge addresses the use of performance management systems in the context of networks (notably for production and incremental innovation). On the other hand, radical innovation scholars have shown how innovation initiatives that are more uncertain demand the use of new approaches (e.g., new project management routines or different evaluative tools for portfolios). Some scholars even suggest that traditional PM may suppress radical innovation. Our study takes a different approach. It aims to bridge radical innovation and network performance management through a systematic review of the literature. Here, we adopt a hybrid approach that combines bibliometrics with content analysis. Whereas the literature often separates the issues of network performance management and radical innovation, our contribution expands the theory of network management and radical innovation by developing a conceptual framework based on these concepts, thus combining them. We also offer suggestions for further research on this approach. Our framework suggests that overall, the performance management of radical innovation networks presents different features (e.g., recursive rather than linear) and constructs (e.g., openness and unintended performance) from those of innovation network management.     

直流马达的车身电子应用

车内系统的电子产品含量持续成长,原因是市场对自动化、安全性、能耗优化和高质量体验的要求越来越高。在此背景之下,使用直流马达的应用数量也不断上扬。     

Supporting structured parallel program design,development and tuning in FastFlow

The Journal of Supercomputing - The design and tuning of parallel programs is known to be a hard and error-prone process. Structured parallel programming helps overcoming part of the related...     

Geometric theory on the dynamics of a position-dependent mass particle

The connection between geometry and dynamics is a canonical subject of analytical mechanics. A very traditional issue of this topic is the transformation of the mechanical problem at hand into a shortest-path problem. This means the mathematical translation of the dynamical problem into a problem of finding the geodesic of a certain space. In the classical domain of conservative systems, especially following the famous book of Lanczos, this translating bridge is established by the usual condition of constant total energy. By nature, the motion of a particle with position-dependent mass is not a conservative problem. Therefore, the classical geometrical theory of mechanics is not straightforwardly applicable. Given that, we here aim at developing the geometrical theory for the mechanics of a position-dependent mass particle. This is our intended contribution. To our best knowledge, the content of our single investigation is original within this variable mass context. Our theory will be developed in the light of the inverse problem of Lagrangian mechanics, which will accordingly sets the variational framework. From that, we will demonstrate the proper generalization of Euler-Maupertuis’ principle and the following generalization of Jacobi’s principle, which, analogously to the classical procedure, can be seen as intermediate steps to enter geometrical arguments. Then, the corresponding geodesic will appear. Finally, as a closing result, a theorem on the mathematical equivalence between such geodesic and the equation of motion of a position-dependent mass particle will be proved. Our investigation aims at providing the reader with a fundamental contribution to the geometry of variable mass mechanics.     

Changes of the cell surface hydrophobicity of Lactobacillus acidophilus La‐5 in response to pH,temperature and inulin

The main topic of this study was to study how cell surface hydrophobicity (CSH) could change in response to pH, temperature and inulin; Lactobacillus acidophilus La‐5 was used as a model microorganism. pH, temperature, inulin and incubation time (exposure to prebiotic or incubation at pH 4.0 and 9.0) were combined through a full factorial design and a Central Composite Design; the results were analysed using a multifactorial anova (first step) and a stepwise regression (second step). Temperature and pH significantly affected CSH: an increase in the temperature determined a significant increase in CSH, whereas the correlation pH vs. CSH was negative, as an increase in pH caused a significant decrease in CSH. Inulin played a significant role, but its effect could be influenced by temperature, pH and exposure time. This study is the first approach on the effects of some environmental factors on CSH and suggests that the culturing conditions and/or the exposure to some prebiotics could modify it with positive or negative effects.     

Weissella cibaria short-fermented liquid sourdoughs based on quinoa or amaranth flours as fat replacer in focaccia bread formulation

Production of the traditional Italian Focaccia bread (FcBread) requires reformulation to meet the new rules for healthier foods. We tested the applicability of a short-fermented (15 h) liquid sourdough (LS) (dough yield, DY, 250), obtained using quinoa (Q) or amaranth (Am) flour fermented with a Weissella cibaria strain (C43-11) producing exopolysaccharides (EPS) as fat replacer in yeast-leavened FcBread. The LSs were applied during the FcBread-making process at industrial pilot plant, reducing the added fat amount by 20% (FcBread-QLS and FcBread-AmLS) and products were compared with reference samples not containing EPS. All the products were analysed for physico-chemical properties (pH, TTA, organic acids, protein content and profile, instrumental colour), textural properties, sensory quality and glycemic index. The application of both pseudo-cereal-based W. cibaria LSs in FcBread allowed obtaining products with a reduced amount of fat, increased protein amount, mainly due to the albumin and glutenin/glutelin fractions, reduced glycemic index, improved texture and preserved in the traditional sensory profile of ‘focaccia’.