Synchronous versus asynchronous modeling of gene regulatory networks.

MOTIVATION: In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene-gene, protein-protein and gene-protein interactions. The two dynamical properties that are often experimentally testable are perturbations and stable steady states. Although a lot of work has been done on the identification of steady states, not much work has been reported on in silico modeling of cellular differentiation processes. RESULTS: In this manuscript, we provide algorithms based on reduced ordered binary decision diagrams (ROBDDs) for Boolean modeling of gene regulatory networks. Algorithms for synchronous and asynchronous transition models have been proposed and their corresponding computational properties have been analyzed. These algorithms allow users to compute cyclic attractors of large networks that are currently not feasible using existing software. Hereby we provide a framework to analyze the effect of multiple gene perturbation protocols, and their effect on cell differentiation processes. These algorithms were validated on the T-helper model showing the correct steady state identification and Th1-Th2 cellular differentiation process. AVAILABILITY: The software binaries for Windows and Linux platforms can be downloaded from http://si2.epfl.ch/~garg/genysis.html.

Future trypanosomatid phylogenies: refined homologies, supertrees and networks

There has been good progress in inferring the evolutionary relationships within trypanosomes from DNA data as until relatively recently, many relationships have remained rather speculative. Ongoing molecular studies have provided data that have adequately shown Trypanosoma to be monophyletic and, rather surprisingly, that there are sharply contrasting levels of genetic variation within and between the major trypanosomatid groups. There are still, however, areas of research that could benefit from further development and resolution that broadly fall upon three questions. Are the current statements of evolutionary homology within ribosomal small sub-unit genes in need of refinement? Can the published phylograms be expanded upon to form `supertrees' depicting further relationships? Does a bifurcating tree structure impose an untenable dogma upon trypanosomatid phylogeny where hybridisation or reticulate evolutionary steps have played a part? This article briefly addresses these three questions and, in so doing, hopes to stimulate further interest in the molecular evolution of the group.

Structural Analysis of Networks

Network analysis naturally relies on graph theory and, more particularly, on the use of node and edge metrics to identify the salient properties in graphs. When building visual maps of networks, these metrics are turned into useful visual cues or are used interactively to filter out parts of a graph while querying it, for instance. Over the years, analysts from different application domains have designed metrics to serve specific needs. Network science is an inherently cross-disciplinary field, which leads to the publication of metrics with similar goals; different names and descriptions of their analytics often mask the similarity between two metrics that originated in different fields. Here, we study a set of graph metrics and compare their relative values and behaviors in an effort to survey their potential contributions to the spatial analysis of networks.

Dynamic simulation of regulatory networks using SQUAD.

BACKGROUND: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. RESULTS: We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. CONCLUSION: The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available.

Pork Value Chains: A Comparison of Catalonia, Spain and Manitoba, Canada

The purpose of this paper is to provide a comparative analysis of pork value chains in Catalonia, Spain and Manitoba, Canada. Intensive hog production models were implemented in Catalonia in the 1960s as a result of agriculture crises and fostered by feedstuffs factories. The expansion of the hog sector in Manitoba is more recent (in the 1990s) and brought about in large part by the opening of the Maple Leaf Meats processing plant in Brandon, Manitoba. This plant is capable of processing 90,000 hogs per week. Both hog production models ‐ the ‘older’ one in Catalonia (Spain) and the ‘newer’ in Manitoba‐ have been, until recently, examples of success. Inventories and production have been increasing substantially and both regions have proven to have great export potential. Recently, however, tensions have been developing with the hog production models of both regions, particularly as they relate to environmental concerns. The purpose of the paper is to compare the value chains with respect to their origins (e.g. supply a growing demand for pork, ensure farm profitability) and present states (e.g. environmental concerns, profitability). Keywords: pork value chain, hog farms, agri‐food studies. JEL: Q10, Q13, O57

Environmental Regulations in the Hog Farming Sector: A Comparison of Catalonia, Spain and Manitoba, Canada

This article examines the governance structures for managing the location and operation of Intensive Livestock Farming Operations (ILFOs). The article focuses on the hog sector and compares two very different jurisdictions: the Province of Manitoba, Canada and the Autonomous Community of Catalonia, Spain. Both are regions that have witnessed recent increases in hog production, including increasing spatial concentration of ILFOs and increasing size of those ILFOs. Policy has both fostered and sought to manage the increased production. Following a brief background description of restructuring, the changing legislative framework for Manitoba and Catalonia are described. Keywords: environmental regulations, hog farms, manure management, animal feeding operations. JEL: Q15, Q58, R52, O57

Internal and External Determinants of Radical and incremental Innovation in SMEs: the case of Catalonia

There is a major concern in economic literature about innovation, which is the interaction between internal and external factors.. In this paper those activities are hypothesized as being determined by some territorial characteristics like labour skills, technological infrastructure, educational facilities, agglomeration economies and industrial structure. This assumption allows understanding why those innovative activities are not spread across space and are located into specific areas. We use a detailed survey containing microdata for 497 SMEs located in Catalonia.

Canvi tecnològic i desenvolupament econòmic durant la segona revolució industrial: la transferència tecnològica del sector tèxtil entre Anglaterra i Catalunya

Projecte de recerca elaborat a partir d’una estada a la University of Sussex, Gran Bretanya, entre març i juliol del 2008. L’estada ha estat centrada en obtenir fonts documentals primàries, per avançar en el projecte d’investigació sobre la transferència de tecnologia entre Catalunya i Anglaterra durant la Segona Revolució Industrial. Això ha estat possible gràcies a la consulta de les patents britàniques (Business & Intellectual Property Centre at the British Library). Així mateix, l’obtenció dels recursos documentals especialitzats de diverses biblioteques de referència situades al campus de la University of Sussex (Keith Pavitt Libray (SPRU), Library of Sussex, British Library of Development Studies) i a Ruddignton Framework Knitters’ Library a Nottingham han estat fonamentals, tal i com es pot veure en la relació detallada que es presenta.

Organizational form and business performance

This project deals with the generation of profitability and the distribution of its benefits. Inspired by Davis (1947, 1955), we define profitability as the ratio of revenue to cost. Profitability is not as popular a measure of business financial performance as profit, the difference between revenue and cost. Regardless of its popularity, however, profitability is surely a useful financial performance measure. Our primary objective in this project is to identify the factors that generate change in profitability. One set of factors, which we refer to as sources, consists of changes in quantities and prices of outputs and inputs. Individual quantity changes aggregate to the overall impact of quantity change on profitability change, which we call productivity change. Individual price changes aggregate to the overall impact of price change on profitability change, which we call price recovery change. In this framework profitability change consists exclusively of productivity change and price recovery change. A second set of factors, which we refer to as drivers, consists of phenomena such as technical change, change in the efficiency of resource allocation, and the impact of economies of scale. The ability of management to harness these factors drives productivity change, which is one component of profitability change. Thus the term sources refers to quantities and prices of individual outputs and inputs, whose changes influence productivity change or price recovery change, either of which influences profitability change. The term drivers refers to phenomena related to technology and management that influence productivity change (but not price recovery change), and hence profitability change.

Coevolutionary networks: a novel approach to understanding the relationships of humans with the infectious agents

Human organism is interpenetrated by the world of microorganisms, from the conception until the death. This interpenetration involves different levels of interactions between the partners including trophic exchanges, bi-directional cell signaling and gene activation, besides genetic and epigenetic phenomena, and tends towards mutual adaptation and coevolution. Since these processes are critical for the survival of individuals and species, they rely on the existence of a complex organization of adaptive systems aiming at two apparently conflicting purposes: the maintenance of the internal coherence of each partner, and a mutually advantageous coexistence and progressive adaptation between them. Humans possess three adaptive systems: the nervous, the endocrine and the immune system, each internally organized into subsystems functionally connected by intraconnections, to maintain the internal coherence of the system. The three adaptive systems aim at the maintenance of the internal coherence of the organism and are functionally linked by interconnections, in such way that what happens to one is immediately sensed by the others. The different communities of infectious agents that live within the organism are also organized into functional networks. The members of each community are linked by intraconnections, represented by the mutual trophic, metabolic and other influences, while the different infectious communities affect each other through interconnections. Furthermore, by means of its adaptive systems, the organism influences and is influenced by the microbial communities through the existence of transconnections. It is proposed that these highly complex and dynamic networks, involving gene exchange and epigenetic phenomena, represent major coevolutionary forces for humans and microorganisms.

Les agressions en contextos tancats de Justícia Juvenil

Aquesta recerca explora el fenomen de l'agressivitat originada en entorns tancats, com ho són els centres educatius de Justícia Juvenil de Catalunya. Aquest, però, és només un dels àmbits on la major part de les eines que s'han emprat poden ser d'utilitat. És possible estendre el camp d'aplicació a altres entorns de compliment de mesures o de tractament en règim tancat. L'ús d'eines de valoració estructurades pot ser complementat amb l'obtenció sistemàtica d'informació sobre els comportaments agressius, la qual cosa permet que els equips professionals disposin de més informació útil en termes de prevenció d'incidents. No obstant això, un aspecte rellevant en la prevenció de les agressions és la relació que un individu estableix amb la resta de persones del seu entorn. En aquest cas, s'ha incorporat l'Anàlisi de Xarxes Socials per obtenir indicadors des d'una perspectiva relacional a fi d’efectuar-ne una anàlisi conjunta amb característiques personals i de risc. Els resultats obtinguts permeten valorar aquests aspectes relacionals associats a les agressions que es van produir al Centre Educatiu durant el treball de camp. A més, la utilització d'altres eines permet caracteritzar aquestes agressions com a relativament poc greus i poc freqüents. Pel que fa als resultats de les eines de valoració de risc, s'han obtingut indicis que permeten afirmar la relació d'aquestes eines amb les agressions posteriors, motiu pel qual és factible considerar-les també com a eines vàlides per a la predicció d'incidents.

Information Mobility: Information Dissemination in Mobile Networks

En el nostre projecte, considerem un escenari urbà o interurbà on persones amb dispositius mòbils (smartphones) o vehicles equipats amb interfícies de comunicació, estan interessats en compartir fitxers entre ells o descarregar-los al creuar Punts d’Accés (APs) propers a la carretera. Estudiem la possibilitat d’utilizar la cooperació en les trobades casuals entre nodes per augmentar la velocitat de descàrrega global. Amb aquest objectiu, plantejem algoritmes per a la selecció de quins paquets, per a quins destins i quins transportistes s’escullen en cada moment. Mitjançant extenses simulacions, mostrem com les cooperacions carry&forward dels nodes augmenten significativament la velocitat de descàrrega dels usuaris, i com aquest resultat es manté per a diversos patrons de mobilitat, col•locacions d'AP i càrregues de la xarxa. Per altra banda, aparells com els smartphones, on la targeta de WiFi està encesa contínuament, consumeixen l'energia de la bateria en poques hores. En molts escenaris, una targeta WiFi sempre activa és poc útil, perque sovint no hi ha necessitat de transmissió o recepció. Aquest fet es veu agreujat en les Delay Tolerant Networks (DTN), on els nodes intercanvien dades quan es creuen i en tenen l’oportunitat. Les tècniques de gestió de l’estalvi d’energia permeten extendre la duració de les bateries. El nostre projecte analitza els avantatges i inconvenients que apareixen quan els nodes apaguen períodicament la seva targeta wireless per a estalviar energia en escenaris DTN. Els nostres resultats mostren les condicions en que un node pot desconnectar la bateria sense afectar la probabilitat de contacte amb altres nodes, i les condicions en que aquesta disminueix. Per exemple, es demostra que la vida del node pot ser duplicada mantenint la probabilitat de contacte a 1. I que aquesta disminueix ràpidament en intentar augmentar més la vida útil.