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.

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.

Connections between signal processing and complex analysis

We describe one of the research lines of the Grup de Teoria de Funcions de la UAB UB, which deals with sampling and interpolation problems in signal analysis and their connections with complex function theory.

Option valuation as an expectation in the complex domain: The Black-Scholes case

It is very well known that the first succesful valuation of a stock option was done by solving a deterministic partial differential equation (PDE) of the parabolic type with some complementary conditions specific for the option. In this approach, the randomness in the option value process is eliminated through a no-arbitrage argument. An alternative approach is to construct a replicating portfolio for the option. From this viewpoint the payoff function for the option is a random process which, under a new probabilistic measure, turns out to be of a special type, a martingale. Accordingly, the value of the replicating portfolio (equivalently, of the option) is calculated as an expectation, with respect to this new measure, of the discounted value of the payoff function. Since the expectation is, by definition, an integral, its calculation can be made simpler by resorting to powerful methods already available in the theory of analytic functions. In this paper we use precisely two of those techniques to find the well-known value of a European call

Using spatially distributed parameters and multi-response objective functions to solve parameterization of complex applications of semi-distributed hydrological models

Application of semi-distributed hydrological models to large, heterogeneous watersheds deals with several problems. On one hand, the spatial and temporal variability in catchment features should be adequately represented in the model parameterization, while maintaining the model complexity in an acceptable level to take advantage of state-of-the-art calibration techniques. On the other hand, model complexity enhances uncertainty in adjusted model parameter values, therefore increasing uncertainty in the water routing across the watershed. This is critical for water quality applications, where not only streamflow, but also a reliable estimation of the surface versus subsurface contributions to the runoff is needed. In this study, we show how a regularized inversion procedure combined with a multiobjective function calibration strategy successfully solves the parameterization of a complex application of a water quality-oriented hydrological model. The final value of several optimized parameters showed significant and consistentdifferences across geological and landscape features. Although the number of optimized parameters was significantly increased by the spatial and temporal discretization of adjustable parameters, the uncertainty in water routing results remained at reasonable values. In addition, a stepwise numerical analysis showed that the effects on calibration performance due to inclusion of different data types in the objective function could be inextricably linked. Thus caution should be taken when adding or removing data from an aggregated objective function.

Rapid and sensitive hormonal profiling of complex plant samples by liquid chromatography coupled to electrospray ionization tandem mass spectrometry

Background Plant hormones play a pivotal role in several physiological processes during a plant's life cycle, from germination to senescence, and the determination of endogenous concentrations of hormones is essential to elucidate the role of a particular hormone in any physiological process. Availability of a sensitive and rapid method to quantify multiple classes of hormones simultaneously will greatly facilitate the investigation of signaling networks in controlling specific developmental pathways and physiological responses. Due to the presence of hormones at very low concentrations in plant tissues (10-9 M to 10-6 M) and their different chemistries, the development of a high-throughput and comprehensive method for the determination of hormones is challenging. Results The present work reports a rapid, specific and sensitive method using ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UPLC/ESI-MS/MS) to analyze quantitatively the major hormones found in plant tissues within six minutes, including auxins, cytokinins, gibberellins, abscisic acid, 1-amino-cyclopropane-1-carboxyic acid (the ethylene precursor), jasmonic acid and salicylic acid. Sample preparation, extraction procedures and UPLC-MS/MS conditions were optimized for the determination of all plant hormones and are summarized in a schematic extraction diagram for the analysis of small amounts of plant material without time-consuming additional steps such as purification, sample drying or re-suspension. Conclusions This new method is applicable to the analysis of dynamic changes in endogenous concentrations of hormones to study plant developmental processes or plant responses to biotic and abiotic stresses in complex tissues. An example is shown in which a hormone profiling is obtained from leaves of plants exposed to salt stress in the aromatic plant, Rosmarinus officinalis.

Essential residues in the H-NS binding site of Hha, a co-regulator of horizontally acquired genes in Enterobacteria

Proteins of the Hha/YmoA family co-regulate with H-NS the expression of horizontally acquired genes in Enterobacteria. Systematic mutations of conserved acidic residues in Hha have allowed the identification of D48 as an essential residue for H-NS binding and the involvement of E25. Mutations of these residues resulted in deregulation of sensitive genes in vivo. D48 is only partially solvent accessible, yet it defines the functional binding interface between Hha and H-NS confirming that Hha has to undergo a conformational change to bind H-NS. Exposed acidic residues, such as E25, may electrostatically facilitate and direct the approach of Hha to the positively charged region of H-NS enabling the formation of the final complex when D48 becomes accessible by a conformational change of Hha.

Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases

AbstractBACKGROUND: Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult.PRINCIPAL FINDINGS: We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell.CONCLUSIONS: For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases.AVAILABILITY: The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download

Les Basíliques paleocristianes del suburbi occidental de Tarraco : el temple septentrional i el complex martirial de Sant Fructuós

Les basíliques paleocristianes del suburbi occidental de Tarraco. El temple septentrional i el complex martirial de Sant Fructuós és el resultat de 10 anys d’investigació desenvolupada al voltant del sector septentrional del Conjunt Paleocristià del Francolí, originada arran de les excavacions efectuades entre els anys 1994 i 1997 a la zona on actualment s’ubica el Parc Central. L’extraordinària importància del jaciment va despertar de seguida l’interès de l’autor, Jordi López, i de la comunitat científica, tant pel valor mateix de les restes com per la seva relació amb l’extensa necròpolis paleocristiana que al llarg de diverses campanyes havia excavat el Dr. Mn. Joan Serra i Vilaró. Es tracta d’una presentació de les últimes investigacions desenvolupades a l’ampli conjunt funerari i cristià del Francolí, al suburbium occidental de Tarraco. Consta de dos volums. El primer està estructurat en tres grans parts. Primerament, la presentació dels resultats dels treballs d’excavació duts a terme entre els anys 1994 i 1997 al sector septentrional del centre de culte cristià del Francolí, que inclou un estudi arquitectònic exhaustiu de la nova basílica excavada. En segon lloc, una revisió de les diferents intervencions desenvolupades en el sector meridional a principi de segle XX per Mn. Serra Vilaró i dels treballs dels anys 70 de M. D. del Amo, amb la proposta d’una nova interpretació arquitectònica de l’antiga basílica i de l’edifici situat al sud d’aquesta. I, finalment, una exposició general de l’evolució d’aquest sector occidental del suburbium de la ciutat, que reflecteix un especial dinamisme entre els segles IV i V dC, moment de màxima expansió de les grans àrees funeràries del segle III dC i de la monumentalització d’un gran centre de culte martirial al Francolí. El text està il·lustrat amb una àmplia documentació gràfica (plantes, seccions, fotografia, reconstruccions tridimensionals). A més, inclou 22 pàgines de conclusions amb la corresponent traducció a l’anglès. El segon volum conté set annexos específics: la relació d’unitats estratigràfiques, un inventari de materials, la descripció dels sepulcres, l’estudi osteoarqueològic i paleopatològic de les restes humanes, una anàlisi epigràfica, una de numismàtica i una última d’escultòrica.

Courtyard Houses and Other Complex Buildings in the Protohistory of Southern Gaul: From Architectural to Social Changes

Courtyard houses are attested at several sites in southern Gaul between the 5th and the 1st centuries BC. They represent a new concept when compared to the traditional protohistoric houses of the region and have often been interpreted in terms of Mediterranean, Greek or Italic influences. Regardless of their origin, exogenous influences or evolution, these houses suggest the emergence of social differentiation and elites in several of the main settlements. This article analyses the significance of the various courtyard house categories in the context of local, indigenous societies, while trying to understand the social implications of this new type of residence. In a wider context, the development of domestic architecture during the Iron Age is analysed alongside the relationships between changing uses of space and social changes.