Synchronization reveals topological scales in complex networks

We study the relationship between topological scales and dynamic time scales in complex networks. The analysis is based on the full dynamics towards synchronization of a system of coupled oscillators. In the synchronization process, modular structures corresponding to well-defined communities of nodes emerge in different time scales, ordered in a hierarchical way. The analysis also provides a useful connection between synchronization dynamics, complex networks topology, and spectral graph analysis.

Simple model for nonexponential relaxation in complex fluids

The nonexponential relaxation occurring in complex dynamics manifested in a wide variety of systems is analyzed through a simple model of diffusion in phase space. It is found that the inability of the system to find its equilibrium state in any time scale becomes apparent in an effective temperature field, which leads to a hierarchy of relaxation times responsible for the slow relaxation phenomena.

Clustering in complex networks. II. Percolation properties

The percolation properties of clustered networks are analyzed in detail. In the case of weak clustering, we present an analytical approach that allows us to find the critical threshold and the size of the giant component. Numerical simulations confirm the accuracy of our results. In more general terms, we show that weak clustering hinders the onset of the giant component whereas strong clustering favors its appearance. This is a direct consequence of the differences in the k-core structure of the networks, which are found to be totally different depending on the level of clustering. An empirical analysis of a real social network confirms our predictions.

Generation of uncorrelated random scale-free networks

Uncorrelated random scale-free networks are useful null models to check the accuracy and the analytical solutions of dynamical processes defined on complex networks. We propose and analyze a model capable of generating random uncorrelated scale-free networks with no multiple and self-connections. The model is based on the classical configuration model, with an additional restriction on the maximum possible degree of the vertices. We check numerically that the proposed model indeed generates scale-free networks with no two- and three-vertex correlations, as measured by the average degree of the nearest neighbors and the clustering coefficient of the vertices of degree k, respectively.

Topology of the world trade web

Economy, and consequently trade, is a fundamental part of human social organization which, until now, has not been studied within the network modeling framework. Here we present the first, to the best of our knowledge, empirical characterization of the world trade web, that is, the network built upon the trade relationships between different countries in the world. This network displays the typical properties of complex networks, namely, scale-free degree distribution, the small-world property, a high clustering coefficient, and, in addition, degree-degree correlation between different vertices. All these properties make the world trade web a complex network, which is far from being well described through a classical random network description.

Protein-protein interactions between adenovirus DNA polymerase and nuclear factor I mediate formation of the DNA replication preinitiation complex.

The in vitro adenovirus (Ad) DNA replication system provides an assay to study the interaction of viral and host replication proteins with the DNA template in the formation of the preinitiation complex. This initiation system requires in addition to the origin DNA sequences 1) Ad DNA polymerase (Pol), 2) Ad preterminal protein (pTP), the covalent acceptor for protein-primed DNA replication, and 3) nuclear factor I (NFI), a host cell protein identical to the CCAAT box-binding transcription factor. The interactions of these proteins were studied by coimmunoprecipitation and Ad origin DNA binding assays. The Ad Pol can bind to origin sequences only in the presence of another protein which can be either pTP or NFI. While NFI alone can bind to its origin recognition sequence, pTP does not specifically recognize DNA unless Ad Pol is present. Thus, protein-protein interactions are necessary for the targetting of either Ad Pol or pTP to the preinitiation complex. DNA footprinting demonstrated that the Ad DNA site recognized by the pTP.Pol complex was within the first 18 bases at the end of the template which constitutes the minimal origin of replication. Mutagenesis studies have defined the Ad Pol interaction site on NFI between amino acids 68-150, which overlaps the DNA binding and replication activation domain of this factor. A putative zinc finger on the Ad Pol has been mutated to a product that fails to bind the Ad origin sequences but still interacts with pTP. These results indicate that both protein-protein and protein-DNA interactions mediate specific recognition of the replication origin by Ad DNA polymerase.

Evolution of the Pelagonian carbonate platform complex and the adjacent oceanic realm in response to plate tectonic forcing (Late Triassic and Jurassic), Evvoia, Greece

The Late Triassic and Jurassic platform and the oceanic complexes in Evvoia, Greece, share a complementary plate-tectonic evolution. Shallow marine carbonate deposition responded to changing rates of subsidence and uplift, whilst the adjacent ocean underwent spreading, and then convergence, collision and finally obduction over the platform complex. Late Triassic ocean spreading correlated with platform subsidence and the formation of a long-persisting peritidal passive-margin platform. Incipient drowning occurred from the Sinemurian to the late Middle Jurassic. This subsidence correlated with intra-oceanic subduction and plate convergence that led to supra-subduction calc-alkaline magmatism and the formation of a primitive volcanic arc. During the Middle Jurassic, plate collision caused arc uplift above the carbonate compensation depth (CCD) in the oceanic realm, and related thrust-faulting, on the platform, led to sub-aerial exposures. Patch-reefs developed there during the Late Oxfordian to Kimmeridgian. Advanced oceanic nappe-loading caused platform drowning below the CCD during the Tithonian, which is documented by intercalations of reefal turbidites with non-carbonate radiolarites. Radiolarites and bypass-turbidites, consisting of siliciclastic greywacke, terminate the platform succession beneath the emplaced oceanic nappe during late Tithonian to Valanginian time.

A review of the Tripterygion tripteronotus (Risso, 1810) complex, with a description of a new species from the Mediterranean Sea (Teleostei: Tripterygiidae)

We compared specimens of Tripterygion tripteronotus from 52 localities of the Mediterranean Sea and adjacent waters, using four gene sequences (12S rRNA, tRNA-valine, 16S rRNA and COI) and morphological characters. Two well-differentiated clades with a mean genetic divergence of 6.89±0.73% were found with molecular data, indicating the existence of two different species. These two species have disjunctive geographic distribution areas without any molecular hybrid populations. Subtle but diagnostic morphological differences were also present between the two species. T. tripteronotus is restricted to the northern Mediterranean basin, from the NE coast of Spain to Greece and Turkey, including the islands of Malta and Cyprus. T. tartessicum n. sp. is geographically distributed along the southern coast of Spain, from Cape of La Nao to the Gulf of Cadiz, the Balearic Islands and northern Africa, from Morocco to Tunisia. According to molecular data, these two species could have diverged during the Pliocene glaciations 2.7-3.6 Mya.

L'exploitation des traces dans les accidents de la circulation

Les investigations dans le milieu des accidents de la circulation sont très complexes. Elles nécessitent la mise en oeuvre d'un grand nombre de spécialités venant de domaines très différents. Si certains de ces domaines sont déjà bien exploités, d'autres demeurent encore incomplets et il arrive de nos jours d'observer des lacunes dans la pratique, auxquelles il est primordial de remédier.Ce travail de thèse, intitulé « l'exploitation des traces dans les accidents de la circulation », est issu d'une réflexion interdisciplinaire entre de multiples aspects des sciences forensiques. Il s'agit principalement d'une recherche ayant pour objectif de démontrer les avantages découlant d'une synergie entre les microtraces et l'étude de la dynamique d'un accident. Afin de donner une dimension très opérationnelle à ce travail, l'ensemble des démarches entreprises a été axé de manière à optimiser l'activité des premiers intervenants sur les lieux.Après une partie introductive et ayant trait au projet de recherche, traitant des aspects théoriques de la reconstruction d'une scène d'accident, le lecteur est invité à prendre connaissance de cinq chapitres pratiques, abordés selon la doctrine « du général au particulier ». La première étape de cette partie pratique concerne l'étude de la morphologie des traces. Des séquences d'examens sont proposées pour améliorer l'interprétation des contacts entre véhicules et obstacles impliqués dans un accident. Les mécanismes de transfert des traces de peinture sont ensuite étudiés et une série de tests en laboratoire est pratiquée sur des pièces de carrosseries automobiles. Différents paramètres sont ainsi testés afin de comprendre leur impact sur la fragilité d'un système de peinture. Par la suite, une liste de cas traités (crash-tests et cas réels), apportant des informations intéressantes sur le traitement d'une affaire et permettant de confirmer les résultats obtenus est effectuée. Il s'ensuit un recueil de traces, issu de l'expérience pratique acquise et ayant pour but d'aiguiller la recherche et le prélèvement sur les lieux. Finalement, la problématique d'une banque de données « accident », permettant une gestion optimale des traces récoltées est abordée.---The investigations of traffic accidents are very complex. They require the implementation of a large number of specialties coming from very different domains. If some of these domains are already well exploited, others remain still incomplete and it happens nowadays to observe gaps in the practice, which it is essential to remedy. This thesis, entitled "the exploitation of traces in traffic accidents", arises from a multidisciplinary reflection between the different aspects of forensic science. It is primarily a research aimed to demonstrate the benefits of synergy between microtrace evidence and accidents dynamics. To give a very operational dimension to this work, all the undertaken initiatives were centred so as to optimise the activity of the first participants on the crime scene.After an introductory part treating theoretical aspects of the reconstruction of an accident scene the reader is invited to get acquainted with five practical chapters, according to the doctrine "from general to particular". For the first stage of this practical part, the problem of the morphology of traces is approached and sequences of examinations are proposed to improve the interpretation of the contacts between vehicles and obstacles involved in an accident. Afterwards, the mechanisms of transfer of traces of paint are studied and a series of tests in laboratory is practised on pieces of automobile bodies. Various parameters are thus tested to understand their impact on the fragility of a system of paint. It follows that a list of treated cases (crash-tests and real cases) is created, allowing to bring interesting information on the treatment of a case and confirm the obtained results. Then, this work goes on with a collection of traces, stemming from the acquired experience that aims to steer the research and the taking of evidence on scenes. Finally, the practical part of this thesis ends with the problem of a database « accident », allowing an optimal management of the collected traces.

Partition coefficient and molecular flexibility: the concept of lipophilicity space.

The rationale of this study was to investigate molecular flexibility and its influence on physicochemical properties with a view to uncovering additional information on the fuzzy concept of dynamic molecular structure. Indeed, it is now known that computed molecular interaction fields (MIFs) such as molecular electrostatic potentials (MEPs) and lipophilicity potentials (MLPs) are conformation-dependent, as are dipole moments. A database of 125 compounds was used whose conformational space was explored, while conformation-dependent parameters were computed for each non-redundant conformer found in the conformational space of the compounds. These parameters were the virtual log P (log P(MLP), calculated by a MLP approach), the apolar surface area (ASA), polar surface area (PSA), and solvent-accessible surface (SAS). For each compound, the range taken by each parameter (its property space) was divided by the number of rotors taken as an index of flexibility, yielding a parameter termed 'molecular sensitivity'. This parameter was poorly correlated with others (i.e., it contains novel information) and showed the compounds to fall into two broad classes. 'Sensitive' molecules are those whose computed property ranges are markedly sensitive to conformational effects, whereas 'insensitive' (in fact, less sensitive) molecules have property ranges which are comparatively less affected by conformational fluctuations. A pharmacokinetic application is presented.

Telling the truth: medical students' progress with an ethical skill.

BACKGROUND: Truth-telling is a complex task requiring multiple skills in communication, understanding, and empathy. Its application in the context of breaking bad news (BBN) is distressing and problematic if conducted with insufficient skills. PURPOSE: We investigated the long-term influence of a simulated patient-based teaching intervention integrating the learning of communication skills within an ethical reflection on students' ethical attitudes towards truth-telling, perceived competence and comfort in BBN. METHODS: We followed two cohorts of medical students from the preclinical third year to their clinical rotations (fifth year). We analysed their ethical attitudes and level of comfort and competence in BBN before, after the intervention, and during clinical rotations. RESULTS: Students' ethical attitudes towards truth-telling remained stable. Students feeling uncomfortable or incompetent improved their level of perceived comfort or competence after the intervention, but those feeling comfortable or competent became more aware of the difficulty of the situation, and consequently decreased their level of comfort and competence. CONCLUSIONS: Confronting students with a realistic situation and integrating the practice of communication skills within an ethical reflection may be effective in maintaining ethical attitudes towards truth-telling, in developing new skills and increasing awareness about the difficulty and challenges of a BBN situation.