Sampling motif-constrained ensembles of networks

The statistical significance of network properties is conditioned on null models which satisfy spec- ified properties but that are otherwise random. Exponential random graph models are a principled theoretical framework to generate such constrained ensembles, but which often fail in practice, either due to model inconsistency, or due to the impossibility to sample networks from them. These problems affect the important case of networks with prescribed clustering coefficient or number of small connected subgraphs (motifs). In this paper we use the Wang-Landau method to obtain a multicanonical sampling that overcomes both these problems. We sample, in polynomial time, net- works with arbitrary degree sequences from ensembles with imposed motifs counts. Applying this method to social networks, we investigate the relation between transitivity and homophily, and we quantify the correlation between different types of motifs, finding that single motifs can explain up to 60% of the variation of motif profiles.Comment: Updated version, as published in the journal. 7 pages, 5 figures, one Supplemental Materia

Boolean networks with reliable dynamics

We investigated the properties of Boolean networks that follow a given reliable trajectory in state space. A reliable trajectory is defined as a sequence of states which is independent of the order in which the nodes are updated. We explored numerically the topology, the update functions, and the state space structure of these networks, which we constructed using a minimum number of links and the simplest update functions. We found that the clustering coefficient is larger than in random networks, and that the probability distribution of three-node motifs is similar to that found in gene regulation networks. Among the update functions, only a subset of all possible functions occur, and they can be classified according to their probability. More homogeneous functions occur more often, leading to a dominance of canalyzing functions. Finally, we studied the entire state space of the networks. We observed that with increasing systems size, fixed points become more dominant, moving the networks close to the frozen phase.Comment: 11 Pages, 15 figure

Redundancy and error resilience in Boolean Networks

We consider the effect of noise in sparse Boolean Networks with redundant functions. We show that they always exhibit a non-zero error level, and the dynamics undergoes a phase transition from non-ergodicity to ergodicity, as a function of noise, after which the system is no longer capable of preserving a memory if its initial state. We obtain upper-bounds on the critical value of noise for networks of different sparsity.Comment: 4 pages, 5 figure

The Network of Epicenters of the Olami-Feder-Christensen Model of Earthquakes

We study the dynamics of the Olami-Feder-Christensen (OFC) model of earthquakes, focusing on the behavior of sequences of epicenters regarded as a growing complex network. Besides making a detailed and quantitative study of the effects of the borders (the occurrence of epicenters is dominated by a strong border effect which does not scale with system size), we examine the degree distribution and the degree correlation of the graph. We detect sharp differences between the conservative and nonconservative regimes of the model. Removing border effects, the conservative regime exhibits a Poisson-like degree statistics and is uncorrelated, while the nonconservative has a broad power-law-like distribution of degrees (if the smallest events are ignored), which reproduces the observed behavior of real earthquakes. In this regime the graph has also a unusually strong degree correlation among the vertices with higher degree, which is the result of the existence of temporary attractors for the dynamics: as the system evolves, the epicenters concentrate increasingly on fewer sites, exhibiting strong synchronization, but eventually spread again over the lattice after a series of sufficiently large earthquakes. We propose an analytical description of the dynamics of this growing network, considering a Markov process network with hidden variables, which is able to account for the mentioned properties.Comment: 9 pages, 10 figures. Smaller number of figures, and minor text corrections and modifications. For version with full resolution images see http://fig.if.usp.br/~tpeixoto/cond-mat-0602244.pd

Multilayer Networks for Text Analysis with Multiple Data Types

We are interested in the widespread problem of clustering documents and finding topics in large collections of written documents in the presence of metadata and hyperlinks. To tackle the challenge of accounting for these different types of datasets, we propose a novel framework based on Multilayer Networks and Stochastic Block Models. The main innovation of our approach over other techniques is that it applies the same non-parametric probabilistic framework to the different sources of datasets simultaneously. The key difference to other multilayer complex networks is the strong unbalance between the layers, with the average degree of different node types scaling differently with system size. We show that the latter observation is due to generic properties of text, such as Heaps' law, and strongly affects the inference of communities. We present and discuss the performance of our method in different datasets (hundreds of Wikipedia documents, thousands of scientific papers, and thousands of E-mails) showing that taking into account multiple types of information provides a more nuanced view on topic- and document-clusters and increases the ability to predict missing links.Comment: 17 pages, 6 figure

Distribution of epicenters in the Olami-Feder-Christensen model

We show that the well established Olami-Feder-Christensen (OFC) model for the dynamics of earthquakes is able to reproduce a new striking property of real earthquake data. Recently, it has been pointed out by Abe and Suzuki that the epicenters of earthquakes could be connected in order to generate a graph, with properties of a scale-free network of the Barabasi-Albert type. However, only the non conservative version of the Olami-Feder-Christensen model is able to reproduce this behavior. The conservative version, instead, behaves like a random graph. Besides indicating the robustness of the model to describe earthquake dynamics, those findings reinforce that conservative and non conservative versions of the OFC model are qualitatively different. Also, we propose a completely new dynamical mechanism that, even without an explicit rule of preferential attachment, generates a free scale network. The preferential attachment is in this case a ``by-product'' of the long term correlations associated with the self-organized critical state. The detailed study of the properties of this network can reveal new aspects of the dynamics of the OFC model, contributing to the understanding of self-organized criticality in non conserving models.Comment: 7 pages, 7 figure

Cross-cultural adaptation and measurement properties of the Portuguese version of the Ankle Instability Instrument

Chronic ankle instability is one of the most common clinical conditions in the general population, especially in adult athletes. The cross-cultural adaptation of self-reported questionnaires that identify and classify this condition contribute to criteria standardization in research but also in rehabilitation. Aim of Study. To validate the Ankle Instability Instrument to the Portuguese population and to investigate its psychometric properties. Material and Methods. Linguistic and semantic equivalence of the original version of the Ankle Instability Instrument to the Portuguese population was firstly performed. The Portuguese version of the Ankle Instability Instrument was then applied to 81 higher education adult students, with (n = 59) and without history of ankle sprain (n = 22). Participants were evaluated two times with an interval of one week to assess the psychometric properties of the Portuguese version of the Ankle Instability Instrument. Results. In the reliability of binary responses based on the test retest, the tetrachoric correlation coefficient ranged from 0.99 to 1.00. In addition, the Kuder–Richardson coefficient was 0.79 suggesting good internal consistency. Conclusions. Test-retest showed an almost perfect match in all answers between the two moments, which seem to be related to sample characteristics. The internal consistency value was similar to the one obtained in the original version. The Portuguese version of the Ankle Instability Instrument is highly reliable and can be used in clinical practice.info:eu-repo/semantics/publishedVersio

Uloga prirodnih spojeva kod raka mliječnih žlijezda u štakora; blagotvorni učinci vodenog ekstrakta Santolina chamaecyparissus L.

Breast cancer is the most diagnosed cancer among women, and a leading cause of death worldwide. Santolina chamaecyparissus L. is a plant with multiple health benefits, including anticancer and anti-diabetic properties. This study aimed to assess the chemopreventive effects of S. chamaecyparissus aqueous extract (SCE) in an animal model of mammary cancer. A total of 28 four-week-old female Wistar rats were divided into four groups: control, MNU-induced (IND), SCE-supplemented (SCE), and SCE+IND. SCE was added to drinking water (12.72 mg/kg body weight) ad libitum. MNU was administered via the intraperitoneal route at 50 days of age. Weekly monitoring of body weight, food/drink intake, humane endpoints, and number of mammary tumours were recorded. Twenty weeks after MNU administration, animals were sacrificed by anaesthetic overdose and a necropsy was performed. Blood samples were used to determine blood count and serum biochemistry analysis, while kidney and liver samples were analysed for oxidative stress. Tumour samples were collected for gene expression and histology studies. SCE chemical composition was analysed by LC-MS and contained 19 phenolic compounds, with the most abundant being myricetin-O-glucuronide and 1,3-O-dicaffeoylquinic acid. Two animals in the IND group were sacrificed due to exceeding the humane endpoint limits. SCE supplementation delayed mammary tumour development, reducing its volume and weight. SCE had a positive impact on haematological parameters, particularly the neutrophil-lymphocyte ratio (P=0.026). No significant differences were observed in serum biochemistry, except for creatinine kinase MB, or in oxidative stress markers. Gene expression analysis showed significantly reduced VEGF expression levels (P=0.0158) in tumours from SCE+IND. These findings suggest that SCE is deserving of further study to identify the individual compounds and to understand its influence on animal models during cancer development.Rak dojke najčešće je dijagnosticiran rak u žena i vodeći uzrok smrti na svijetu. Santolina chamaecyparissus L. je biljka s višestrukim blagotvornim učincima za zdravlje, uključujući antitumorska i antidijabetička svojstva. Cilj je ove studije bio procijeniti kemopreventivne učinke vodenog ekstrakta S. chamaecyparissus (SCE) na životinjama obeljelim od raka mliječnih žlijezda. Dvadeset i osam četiri ženki starih tjedna wistar štakora podijeljeno je u četiri skupine: kontrolnu, MNU-inducirano (IND), s dodatkom SCE (SCE) i SCE+IND. Skupini SCE je dodan vodi za piće (12,72 mg/kg tjelesne mase) ad libitum; MNU je primijenjen intraperitonealnim putem u 50. danu života. Tjedno je bilježeno praćenje tjelesne mase, unosa hrane/tekućine, humano usmrćivanje i broj tumora mliječnih žlijezda. Dvadeset tjedana nakon primjene MNU, životinje su žrtvovane predoziranjem anestetikom i obavljena je razudba. Uzorci krvi su rabljeni za određivanje krvne slike i analizu biokemije seruma, dok su uzeti uzorci bubrega i pluća rabljeni za analize oksidativnog stresa. Uzorci tumora su prikupljeni za studije ekspresije gena i histološke studije. Analiziran je kemijski sastav skupine SCE pomoću LC-MS i otkriveno je da sadrži 19 fenolnih spojeva od kojih su najobilniji bili miricetin-O-glukuronid i 1,3-O-dikafeoilkina kiselina. Dvije životinje iz IND skupini žrtvovane su zbog prekoračenja ograničenja za humano usmrćivanje. Skupini SCE dodatak je odgodio razvoj tumora mliječnih žlijezda, smanjujući njegov volumen i masu. Skupina SCE je imala pozitivni učinak na hematološke parametre, posebice na omjer neutrofila i limfocita (P=0,026). Nikakve značajne razlike nisu otkrivene u biokemiji seruma, osim kreatinin kinaze MB, niti u markerima oksidativnog stresa. Analiza ekspresije gena pokazala je značajno smanjene razina ekspresije VEGF (P=0,0158) u tumora iz skupine SCE+IND. Ovi nalazi ukazuju da bi skupinu SCE trebalo dodatno ispitati da bi se identificirali pojedinačni spojevi i razumio njegov utjecaj na životinjama oboljelih od raka mliječnih žlijezda

New di(hetero)arylethers and di(hetero)arylamines in the thieno[3,2-b]pyridine series: Synthesis, growth inhibitory activity on human tumor cell lines and non-tumor cells, effects on cell cycle and on programmed cell death

New fluorinated and methoxylated di(hetero)arylethers and di(hetero)arylamines were prepared functionalizing the 7-position of the thieno[3,2-blpyridine, using copper (C-O) or palladium (C N) catalyzed couplings, respectively, of the 7-bromothieno[3,2-blpyridine, also prepared, with ortho, meta and para fluoro or methoxy phenols and anilines. The compounds obtained were evaluated for their growth inhibitory activity on the human tumor cell lines MCF-7 (breast adenocarcinoma), NCI-H460 (non-small cell lung cancer), HCI15 (colon carcinoma), HepG2 (hepatocellular carcinoma) and HeLa (cervical carcinoma). The most active compounds, a di(hetero)arylether with a methoxy group in the meta position relative to the ether function and two di(hetero)arylamines with a methoxy group either in the ortho or in the meta position relative to the NH, were further tested at their GI(50) concentrations on NCI-H460 cells causing pronounced alterations in the cell cycle profile and a strong and significant increase in the programmed death of these cells. The fluorinated and the other methoxylated compounds did not show important activity, presenting high GI(50) values in all the cell lines tested. Furthermore, the hepatotoxicity of the compounds was assessed using porcine liver primary cells (PLP2), established by some of us. Results showed that one of the most active compounds was not toxic to the non-tumor cells at their GI(50) concentrations showing to be the most promising as antitumoral.The authors would like to thank to the Foundation for the Science and Technology (PCT Portugal) for financial support through the NMR Portuguese network (Bruker 400 Avance III-Univ Minho); to FCT and FEDER-COMPETE/QREN/EU for financial support through the research unities PEst-C/QUI/UI686/2011 and PEst-OE/AGR/UI0690/2011, the research project PTDC/QUI-QUI/111060/2009 and the post-Doctoral grants attributed to R.C.C. (SFRH/BPD/68344/2010) and R.T.L. (SRH/BPD/68787/2010). IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by FCT