Markov chain aggregation and its application to rule-based modelling

Rule-based modelling allows to represent molecular interactions in a compact and natural way. The underlying molecular dynamics, by the laws of stochastic chemical kinetics, behaves as a continuous-time Markov chain. However, this Markov chain enumerates all possible reaction mixtures, rendering the analysis of the chain computationally demanding and often prohibitive in practice. We here describe how it is possible to efficiently find a smaller, aggregate chain, which preserves certain properties of the original one. Formal methods and lumpability notions are used to define algorithms for automated and efficient construction of such smaller chains (without ever constructing the original ones). We here illustrate the method on an example and we discuss the applicability of the method in the context of modelling large signalling pathways

Metrics with Prescribed Ricci Curvature near the Boundary of a Manifold

Suppose $M$ is a manifold with boundary. Choose a point $o\in\partial M$. We investigate the prescribed Ricci curvature equation \Ric(G)=T in a neighborhood of $o$ under natural boundary conditions. The unknown $G$ here is a Riemannian metric. The letter $T$ in the right-hand side denotes a (0,2)-tensor. Our main theorems address the questions of the existence and the uniqueness of solutions. We explain, among other things, how these theorems may be used to study rotationally symmetric metrics near the boundary of a solid torus $\mathcal T$. The paper concludes with a brief discussion of the Einstein equation on $\mathcal T$.Comment: 13 page

Hide and seek: The theory of mind of visual concealment and search

Researchers have investigated visual search behavior for almost a century. During that time, few studies have examined the cognitive processes involved in hiding items rather than finding them. To investigate this, we developed a paradigm that allowed participants to indicate where they would hide (or find) an item that was to be found (or hidden) by a friend or a foe. We found that (i) for friends more than foes, participants selected the pop-out item in the display, and (ii) when the display was homogeneous, they selected nearby and corner items. These behaviors held for both hiding and finding, although hide and find behaviors were not identical. For pop-out displays, decision times were unusually long when hiding an item from a foe. These data converge on the conclusion that the principles of search and concealment are similar, but not the same. They also suggest that this paradigm will provide researchers a powerful method for investigating theory of mind in adults

Electrical behaviour, characteristics and properties of anodic aluminium oxide films coloured by nickel electrodeposition

Porous anodic films on 1050 aluminium substrate were coloured by AC electrodeposition of nickel. Several experiments were performed at different deposition voltages and nickel concentrations in the electrolyte in order to correlate the applied electrical power to the electrical behaviour, as well as the characteristics and properties of the coatings. The content of nickel inside the coatings reached 1.67 g/m2, depending on the experimental conditions. According to the applied AC voltage in comparison with the threshold voltage Ut, the coating either acted only as a capacitor when U\Ut and, when U[Ut, the behaviour during the anodic and cathodic parts of the power sine wave was different. In particular, due to the semi-conducting characteristics of the barrier layer, additional oxidation of the aluminium substrate occurred during the anodic part of the electrical signal, whilst metal deposition (and solvent reduction) occurred during the cathodic part; these mechanisms correspond to the blocked and pass directions of the barrier layer/electrolyte junction, respectively

Continuous Interaction with a Virtual Human

Attentive Speaking and Active Listening require that a Virtual Human be capable of simultaneous perception/interpretation and production of communicative behavior. A Virtual Human should be able to signal its attitude and attention while it is listening to its interaction partner, and be able to attend to its interaction partner while it is speaking – and modify its communicative behavior on-the-fly based on what it perceives from its partner. This report presents the results of a four week summer project that was part of eNTERFACE’10. The project resulted in progress on several aspects of continuous interaction such as scheduling and interrupting multimodal behavior, automatic classification of listener responses, generation of response eliciting behavior, and models for appropriate reactions to listener responses. A pilot user study was conducted with ten participants. In addition, the project yielded a number of deliverables that are released for public access

Western Indian Ocean marine and terrestrial records of climate variability: a review and new concepts on land-ocean interactions since AD 1660

We examine the relationship between three tropical and two subtropical western Indian Ocean coral oxygen isotope time series to surface air temperatures (SAT) and rainfall over India, tropical East Africa and southeast Africa. We review established relationships, provide new concepts with regard to distinct rainfall seasons, and mean annual temperatures. Tropical corals are coherent with SAT over western India and East Africa at interannual and multidecadal periodicities. The subtropical corals correlate with Southeast African SAT at periodicities of 16–30 years. The relationship between the coral records and land rainfall is more complex. Running correlations suggest varying strength of interannual teleconnections between the tropical coral oxygen isotope records and rainfall over equatorial East Africa. The relationship with rainfall over India changed in the 1970s. The subtropical oxygen isotope records are coherent with South African rainfall at interdecadal periodicities. Paleoclimatological reconstructions of land rainfall and SAT reveal that the inferred relationships generally hold during the last 350 years. Thus, the Indian Ocean corals prove invaluable for investigating land–ocean interactions during past centuries

BRCA1 and BRCA2 mutations in a population-based study of male breast cancer

Background: The contribution of BRCA1 and BRCA2 to the incidence of male breast cancer (MBC) in the United Kingdom is not known, and the importance of these genes in the increased risk of female breast cancer associated with a family history of breast cancer in a male first-degree relative is unclear. Methods: We have carried out a population-based study of 94 MBC cases collected in the UK. We screened genomic DNA for mutations in BRCA1 and BRCA2 and used family history data from these cases to calculate the risk of breast cancer to female relatives of MBC cases. We also estimated the contribution of BRCA1 and BRCA2 to this risk. Results: Nineteen cases (20%) reported a first-degree relative with breast cancer, of whom seven also had an affected second-degree relative. The breast cancer risk in female first-degree relatives was 2.4 times (95% confidence interval [CI] = 1.4–4.0) the risk in the general population. No BRCA1 mutation carriers were identified and five cases were found to carry a mutation in BRCA2. Allowing for a mutation detection sensitivity frequency of 70%, the carrier frequency for BRCA2 mutations was 8% (95% CI = 3–19). All the mutation carriers had a family history of breast, ovarian, prostate or pancreatic cancer. However, BRCA2 accounted for only 15% of the excess familial risk of breast cancer in female first-degree relatives. Conclusion: These data suggest that other genes that confer an increased risk for both female and male breast cancer have yet to be found

Comparative historical sociology and the State : problems of method

Historical sociology can be understood both as a specific sub-field of sociology and as providing general conceptual underpinnings of the discipline, to the extent that it provides an understanding of the specificity of the modern state and the perceived emergence of modernity within Europe. The association of modernity with Europe (and with a European history limited to the self-identified boundaries of the continent) is commonplace and pervasive within the social sciences and humanities. What such an understanding fails to take into consideration, however, are the connections between Europe and the rest of the world that constitute the broader context for the emergence of what is understood to be the modern world and its institutions, such as the state and market. In this article, I suggest that integral to this misunderstanding, and its reproduction over time, is the methodology of comparative historical sociology as represented by ideal types. In contrast, I argue for ‘connected sociologies’ as a more appropriate way to understand our shared past and its continuing impact upon the present. I examine these issues in the context of historical sociological understandings of nation-state formation

Identification of the initial molecular changes in response to circulating angiogenic cells-mediated therapy in critical limb ischemia

BackgroundCritical limb ischemia (CLI) constitutes the most aggressive form of peripheral arterial occlusive disease, characterized by the blockade of arteries supplying blood to the lower extremities, significantly diminishing oxygen and nutrient supply. CLI patients usually undergo amputation of fingers, feet, or extremities, with a high risk of mortality due to associated comorbidities.Circulating angiogenic cells (CACs), also known as early endothelial progenitor cells, constitute promising candidates for cell therapy in CLI due to their assigned vascular regenerative properties. Preclinical and clinical assays with CACs have shown promising results. A better understanding of how these cells participate in vascular regeneration would significantly help to potentiate their role in revascularization.Herein, we analyzed the initial molecular mechanisms triggered by human CACs after being administered to a murine model of CLI, in order to understand how these cells promote angiogenesis within the ischemic tissues.MethodsBalb-c nude mice (n:24) were distributed in four different groups: healthy controls (C, n:4), shams (SH, n:4), and ischemic mice (after femoral ligation) that received either 50 mu l physiological serum (SC, n:8) or 5x10(5) human CACs (SE, n:8). Ischemic mice were sacrificed on days 2 and 4 (n:4/group/day), and immunohistochemistry assays and qPCR amplification of Alu-human-specific sequences were carried out for cell detection and vascular density measurements. Additionally, a label-free MS-based quantitative approach was performed to identify protein changes related.ResultsAdministration of CACs induced in the ischemic tissues an increase in the number of blood vessels as well as the diameter size compared to ischemic, non-treated mice, although the number of CACs decreased within time. The initial protein changes taking place in response to ischemia and more importantly, right after administration of CACs to CLI mice, are shown.ConclusionsOur results indicate that CACs migrate to the injured area; moreover, they trigger protein changes correlated with cell migration, cell death, angiogenesis, and arteriogenesis in the host. These changes indicate that CACs promote from the beginning an increase in the number of vessels as well as the development of an appropriate vascular network.Institute of Health Carlos III, ISCIII; Junta de Andaluci

Expression quantitative trait loci are highly sensitive to cellular differentiation state

Blood cell development from multipotent hematopoietic stem cells to specialized blood cells is accompanied by drastic changes in gene expression for which the triggers remain mostly unknown. Genetical genomics is an approach linking natural genetic variation to gene expression variation, thereby allowing the identification of genomic loci containing gene expression modulators (eQTLs). In this paper, we used a genetical genomics approach to analyze gene expression across four developmentally close blood cell types collected from a large number of genetically different but related mouse strains. We found that, while a significant number of eQTLs (365) had a consistent “static” regulatory effect on gene expression, an even larger number were found to be very sensitive to cell stage. As many as 1,283 eQTLs exhibited a “dynamic” behavior across cell types. By looking more closely at these dynamic eQTLs, we show that the sensitivity of eQTLs to cell stage is largely associated with gene expression changes in target genes. These results stress the importance of studying gene expression variation in well-defined cell populations. Only such studies will be able to reveal the important differences in gene regulation between different ce