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.

A gamma camera count rate saturation correction method for whole-body planar imaging.

Whole-body (WB) planar imaging has long been one of the staple methods of dosimetry, and its quantification has been formalized by the MIRD Committee in pamphlet no 16. One of the issues not specifically addressed in the formalism occurs when the count rates reaching the detector are sufficiently high to result in camera count saturation. Camera dead-time effects have been extensively studied, but all of the developed correction methods assume static acquisitions. However, during WB planar (sweep) imaging, a variable amount of imaged activity exists in the detector's field of view as a function of time and therefore the camera saturation is time dependent. A new time-dependent algorithm was developed to correct for dead-time effects during WB planar acquisitions that accounts for relative motion between detector heads and imaged object. Static camera dead-time parameters were acquired by imaging decaying activity in a phantom and obtaining a saturation curve. Using these parameters, an iterative algorithm akin to Newton's method was developed, which takes into account the variable count rate seen by the detector as a function of time. The algorithm was tested on simulated data as well as on a whole-body scan of high activity Samarium-153 in an ellipsoid phantom. A complete set of parameters from unsaturated phantom data necessary for count rate to activity conversion was also obtained, including build-up and attenuation coefficients, in order to convert corrected count rate values to activity. The algorithm proved successful in accounting for motion- and time-dependent saturation effects in both the simulated and measured data and converged to any desired degree of precision. The clearance half-life calculated from the ellipsoid phantom data was calculated to be 45.1 h after dead-time correction and 51.4 h with no correction; the physical decay half-life of Samarium-153 is 46.3 h. Accurate WB planar dosimetry of high activities relies on successfully compensating for camera saturation which takes into account the variable activity in the field of view, i.e. time-dependent dead-time effects. The algorithm presented here accomplishes this task.

Format of medical order sheet improves security of antibiotics prescription: The experience of an intensive care unit.

OBJECTIVE: To assess whether formatting the medical order sheet has an effect on the accuracy and security of antibiotics prescription. DESIGN: Prospective assessment of antibiotics prescription over time, before and after the intervention, in comparison with a control ward. SETTING: The medical and surgical intensive care unit (ICU) of a university hospital. PATIENTS: All patients hospitalized in the medical or surgical ICU between February 1 and April 30, 1997, and July 1 and August 31, 2000, for whom antibiotics were prescribed. INTERVENTION: Formatting of the medical order sheet in the surgical ICU in 1998. MEASUREMENTS AND MAIN RESULTS: Compliance with the American Society of Hospital Pharmacists' criteria for prescription safety was measured. The proportion of safe orders increased in both units, but the increase was 4.6 times greater in the surgical ICU (66% vs. 74% in the medical ICU and 48% vs. 74% in the surgical ICU). For unsafe orders, the proportion of ambiguous orders decreased by half in the medical ICU (9% vs. 17%) and nearly disappeared in the surgical ICU (1% vs. 30%). The only missing criterion remaining in the surgical ICU was the drug dose unit, which could not be preformatted. The aim of antibiotics prescription (either prophylactic or therapeutic) was indicated only in 51% of the order sheets. CONCLUSIONS: Formatting of the order sheet markedly increased security of antibiotics prescription. These findings must be confirmed in other settings and with different drug classes. Formatting the medical order sheet decreases the potential for prescribing errors before full computerized prescription is available.

Comparison of fundus autofluorescence images acquired by the confocal scanning laser ophthalmoscope (488 nm excitation) and the modified Topcon fundus camera (580 nm excitation).

To compare autofluorescence (AF) images obtained with the confocal scanning laser ophthalmoscope (using the Heidelberg retina angiograph; HRA) and the modified Topcon fundus camera, in a routine clinical setting. A prospective comparative study conducted at the Jules-Gonin Eye Hospital. Fifty-six patients from the medical retina clinic. All patients had complete ophthalmic slit-lamp and fundus examinations, colour and red-free fundus photography, AF imaging with both instruments, and fluorescein angiography. Cataract and fixation were graded clinically. AF patterns were analyzed for healthy and pathological features. Differences of image noise were analyzed by cataract grading and fixation. A total of 105 eyes were included. AF patterns discovered by the retina angiograph and the fundus camera images, respectively, were a dark optic disc in 72 % versus 15 %, a dark fovea in 92 % versus 4 %, sub- and intraretinal fluid visible as hyperautofluorescence on HRA images only, lipid exudates visible as hypoautofluorescence on HRA images only. The same autofluorescent pattern was found on both images for geographic atrophy, retinal pigment changes, drusen and haemorrhage. Image noise was significantly associated with the degree of cataract and/or poor fixation, favouring the fundus camera. Images acquired by the fundus camera before and after fluorescein angiography were identical. Fundus AF images differ according to the technical differences of the instruments used. Knowledge of these differences is important not only for correctly interpreting images, but also for selecting the most appropriate instrument for the clinical situation.

The policy-making structure of European regulatory networks and the domestic adoption of standards

European regulatory networks (ERNs) constitute the main governance instrument for the informal co-ordination of public regulation at the European Union (EU) level. They are in charge of co-ordinating national regulators and ensuring the implementation of harmonized regulatory policies across the EU, while also offering sector-specific expertise to the Commission. To this aim, ERNs develop 'best practices' and benchmarking procedures in the form of standards, norms and guidelines to be adopted in member states. In this paper, we focus on the Committee of European Securities Regulators and examine the consequences of the policy-making structure of ERNs on the domestic adoption of standards. We find that the regulators of countries with larger financial industries tend to occupy more central positions in the network, especially among newer member states. In turn, network centrality is associated with a more prompt domestic adoption of standards.

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.

SUMMARY: MetaNetX.org is a website for accessing, analysing and manipulating genome-scale metabolic networks (GSMs) as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Currently, it provides access to hundreds of GSMs and pathways that can be interactively compared (two or more), analysed (e.g. detection of dead-end metabolites and reactions, flux balance analysis or simulation of reaction and gene knockouts), manipulated and exported. Users can also upload their own metabolic models, choose to automatically map them into the common namespace and subsequently make use of the website's functionality. Availability and implementation: MetaNetX.org is available at http://metanetx.org. CONTACT: help@metanetx.org.

Patterns of recovery following focal hemispheric lesions : relationship between lasting deficit and damage to specialized networks

Rapport de synthèse : Objectif : Les déficits cognitifs présents dans la phase aiguë d'une lésion hémisphérique focale ont tendance à être de nature plus importante et plus générale que les déficits résiduels qui persistent dans la phase chronique de récupération. Nous avons investigué, dans le cadre de ce travail, les modèles de récupération auditive et la relation qui se dessine entre les déficits et les dommages relatifs à des réseaux spécifiques, pris comme modèle cognitif des fonctions auditives. De nombreuses études humaines dans les domaines de la neuropsychologie, de la psychophysique ainsi que des études d'activation suggèrent que les processus de reconnaissance et de localisation sonores sont effectués par l'intermédiaire de réseaux distincts tant sur le plan anatomique que fonctionnel : il s'agit des zones de traitement du «What» et du «Where », qui sont toutes deux présentes dans les deux hémisphères. Des études ont démontré que des lésions hémisphériques focales gauches ou droites, centrées sur ces réseaux, sont associées dans la phase chronique de récupération à des déficits correspondant en ce qui concerne la reconnaissance et/ou la localisation sonore. Méthode : Dans le cadre de ce travail, nous avons analysé les résultats concernant les performances auditives chez 24 patients ayant subi des lésions hémisphériques focales avec déficits secondaires dans des tâches de reconnaissance, de localisation et/ou de perception du mouvement sonore lors d'un premier testing effectué en phase aiguë (9 patients), en phase subaiguë (6 patients) ou en phase chronique précoce (9 patients). La totalité de ces patients ont bénéficié d'un second testing en phase chronique. Les observations effectuées ont servi à l'élaboration de patterns de récupération auditive. Résultats : Tous les 24 patients avaient initialement un déficit dans le domaine de la localisation et/ou de la perception du mouvement sonore. Dans la phase aiguë, ce déficit survenait sans atteinte spécifique du réseau «Where » chez presque la moitié des patients ; en revanche, cette situation n'était jamais observée chez les patients testés en phase chronique précoce. Une absence de récupération avait tendance à être associée à un dommage spécifique au réseau concerné ainsi qu'à la persistance d'un déficit au-delà de la phase aiguë. Les déficits résiduels n'étaient par ailleurs pas strictement en lien avec la taille lésionnelle ou l'étendue de l'atteinte du réseau spécifique. Conclusion : Nos résultats suggèrent que des mécanismes distincts sous-tendent la récupération et la plasticité à différentes périodes temporelles post-lésionnelles.

Conditioning of stochastic 3-D fracture networks to hydrological and geophysical data

The geometry and connectivity of fractures exert a strong influence on the flow and transport properties of fracture networks. We present a novel approach to stochastically generate three-dimensional discrete networks of connected fractures that are conditioned to hydrological and geophysical data. A hierarchical rejection sampling algorithm is used to draw realizations from the posterior probability density function at different conditioning levels. The method is applied to a well-studied granitic formation using data acquired within two boreholes located 6 m apart. The prior models include 27 fractures with their geometry (position and orientation) bounded by information derived from single-hole ground-penetrating radar (GPR) data acquired during saline tracer tests and optical televiewer logs. Eleven cross-hole hydraulic connections between fractures in neighboring boreholes and the order in which the tracer arrives at different fractures are used for conditioning. Furthermore, the networks are conditioned to the observed relative hydraulic importance of the different hydraulic connections by numerically simulating the flow response. Among the conditioning data considered, constraints on the relative flow contributions were the most effective in determining the variability among the network realizations. Nevertheless, we find that the posterior model space is strongly determined by the imposed prior bounds. Strong prior bounds were derived from GPR measurements and helped to make the approach computationally feasible. We analyze a set of 230 posterior realizations that reproduce all data given their uncertainties assuming the same uniform transmissivity in all fractures. The posterior models provide valuable statistics on length scales and density of connected fractures, as well as their connectivity. In an additional analysis, effective transmissivity estimates of the posterior realizations indicate a strong influence of the DFN structure, in that it induces large variations of equivalent transmissivities between realizations. The transmissivity estimates agree well with previous estimates at the site based on pumping, flowmeter and temperature data.