Cycle-based Cluster Variational Method for Direct and Inverse Inference

We elaborate on the idea that loop corrections to belief propagation could be dealt with in a systematic way on pairwise Markov random fields, by using the elements of a cycle basis to define region in a generalized belief propagation setting. The region graph is specified in such a way as to avoid dual loops as much as possible, by discarding redundant Lagrange multipliers, in order to facilitate the convergence, while avoiding instabilities associated to minimal factor graph construction. We end up with a two-level algorithm, where a belief propagation algorithm is run alternatively at the level of each cycle and at the inter-region level. The inverse problem of finding the couplings of a Markov random field from empirical covariances can be addressed region wise. It turns out that this can be done efficiently in particular in the Ising context, where fixed point equations can be derived along with a one-parameter log likelihood function to minimize. Numerical experiments confirm the effectiveness of these considerations both for the direct and inverse MRF inference.Comment: 47 pages, 16 figure

Finite-size scaling analysis of the distributions of pseudo-critical temperatures in spin glasses

Using the results of large scale numerical simulations we study the probability distribution of the pseudo critical temperature for the three-dimensional Edwards-Anderson Ising spin glass and for the fully connected Sherrington-Kirkpatrick model. We find that the behavior of our data is nicely described by straightforward finite-size scaling relations.Comment: 23 pages, 9 figures. Version accepted for publication in J. Stat. Mec

3D City Models and urban information: Current issues and perspectives

Considering sustainable development of cities implies investigating cities in a holistic way taking into account many interrelations between various urban or environmental issues. 3D city models are increasingly used in different cities and countries for an intended wide range of applications beyond mere visualization. Could these 3D City models be used to integrate urban and environmental knowledge? How could they be improved to fulfill such role? We believe that enriching the semantics of current 3D city models, would extend their functionality and usability; therefore, they could serve as integration platforms of the knowledge related to urban and environmental issues allowing a huge and significant improvement of city sustainable management and development. But which elements need to be added to 3D city models? What are the most efficient ways to realize such improvement / enrichment? How to evaluate the usability of these improved 3D city models? These were the questions tackled by the COST Action TU0801 “Semantic enrichment of 3D city models for sustainable urban development”. This book gathers various materials developed all along the four year of the Action and the significant breakthroughs

Progressive and biased divergent evolution underpins the origin and diversification of peridinin dinoflagellate plastids

Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organization of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "minicircles". Previous studies of peridinin plastid genes have found evidence for divergent sequence evolution, including extensive substitutions, novel insertions and deletions, and use of alternative translation initiation codons. Understanding the extent of this divergent evolution has been hampered by the lack of characterized peridinin plastid sequences. We have identified over 300 previously unannotated peridinin plastid mRNAs from published transcriptome projects, vastly increasing the number of sequences available. Using these data, we have produced a well-resolved phylogeny of peridinin plastid lineages, which uncovers several novel relationships within the dinoflagellates. This enables us to define changes to plastid sequences that occurred early in dinoflagellate evolution, and that have contributed to the subsequent diversification of individual dinoflagellate clades. We find that the origin of the peridinin dinoflagellates was specifically accompanied by elevations both in the overall number of substitutions that occurred on plastid sequences, and in the Ka/Ks ratio associated with plastid sequences, consistent with changes in selective pressure. These substitutions, alongside other changes, have accumulated progressively in individual peridinin plastid lineages. Throughout our entire dataset, we identify a persistent bias toward non-synonymous substitutions occurring on sequences encoding photosystem I subunits and stromal regions of peridinin plastid proteins, which may have underpinned the evolution of this unusual organelle.Wellcome Trus

Router-level community structure of the Internet Autonomous Systems

The Internet is composed of routing devices connected between them and organized into independent administrative entities: the Autonomous Systems. The existence of different types of Autonomous Systems (like large connectivity providers, Internet Service Providers or universities) together with geographical and economical constraints, turns the Internet into a complex modular and hierarchical network. This organization is reflected in many properties of the Internet topology, like its high degree of clustering and its robustness. In this work, we study the modular structure of the Internet router-level graph in order to assess to what extent the Autonomous Systems satisfy some of the known notions of community structure. We show that the modular structure of the Internet is much richer than what can be captured by the current community detection methods, which are severely affected by resolution limits and by the heterogeneity of the Autonomous Systems. Here we overcome this issue by using a multiresolution detection algorithm combined with a small sample of nodes. We also discuss recent work on community structure in the light of our results

High modularity creates scaling laws

Scaling laws have been observed in many natural and engineered systems. Their existence can give useful information about the growth or decay of one quantitative feature in terms of another. For example, in the field of city analytics, it is has been fruitful to compare some urban attribute, such as energy usage or wealth creation, with population size. In this work, we use network science and dynamical systems perspectives to explain that the observed scaling laws, and power laws in particular, arise naturally when some feature of a complex system is measured in terms of the system size. Our analysis is based on two key assumptions that may be posed in graph theoretical terms. We assume (a) that the large interconnection network has a well-defined set of communities and (b) that the attribute under study satisfies a natural continuity-type property. We conclude that precise mechanistic laws are not required in order to explain power law effects in complex systems—very generic network-based rules can reproduce the behaviors observed in practice. We illustrate our results using Twitter interaction between accounts geolocated to the city of Bristol, UK

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

© 2015 International Society for Microbial Ecology All rights reserved. Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse hostassociated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals' endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes

A "hair-raising" history of alopecia areata

YesA 3500‐year‐old papyrus from ancient Egypt provides a list of treatments for many diseases including “bite hair loss,” most likely alopecia areata (AA). The treatment of AA remained largely unchanged for over 1500 years. In 30 CE, Celsus described AA presenting as scalp alopecia in spots or the “windings of a snake” and suggested treatment with caustic compounds and scarification. The first “modern” description of AA came in 1813, though treatment still largely employed caustic agents. From the mid‐19th century onwards, various hypotheses of AA development were put forward including infectious microbes (1843), nerve defects (1858), physical trauma and psychological stress (1881), focal inflammation (1891), diseased teeth (1902), toxins (1912) and endocrine disorders (1913). The 1950s brought new treatment developments with the first use of corticosteroid compounds (1952), and the first suggestion that AA was an autoimmune disease (1958). Research progressively shifted towards identifying hair follicle‐specific autoantibodies (1995). The potential role of lymphocytes in AA was made implicit with immunohistological studies (1980s). However, studies confirming their functional role were not published until the development of rodent models (1990s). Genetic studies, particularly genome‐wide association studies, have now come to the forefront and open up a new era of AA investigation (2000s). Today, AA research is actively focused on genetics, the microbiome, dietary modulators, the role of atopy, immune cell types in AA pathogenesis, primary antigenic targets, mechanisms by which immune cells influence hair growth, and of course the development of new treatments based on these discoveries.Alopecia UK

Towards the ontology-based consolidation of production-centric standards

This is an Author's Accepted Manuscript of an article published in the International Journal of Production Research [© Taylor & Francis], available online at: http://www.tandfonline.com/doi/abs/10.1080/00207543.2011.627885.Production-­centric international standards are intended to serve as an important route towards information sharing across manufacturing decision support systems. As a consequence of textual-­based definitions of concepts acknowledged within these standards, their inability to fully interoperate becomes an issue especially since a multitude of standards are required to cover the needs of extensive domains such as manufacturing industries. To help reinforce the current understanding to support the consolidation of production-­centric standards for improved information sharing, this article explores the specification of well-defined core concepts which can be used as a basis for capturing tailored semantic definitions. The potentials of two heavyweight ontological approaches, notably Common Logic (CL) and the Web Ontology Language (OWL) as candidates for the task, are also exposed. An important finding regarding these two methods is that while an OWL-­based approach shows capabilities towards applications which may require flexible hierarchies of concepts, a CL-­based method represents a favoured contender for scoped and facts-­driven manufacturing applications

16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer)

CB was supported on a Daphne Jackson Fellowship sponsored by Natural Environmental Research Council (www.nerc.ac.uk) and the University of Edinburgh via the Daphne Jackson Trust. Field collections were supported by the National Science Foundation (www.nsf.gov) grant number OCE-1261519 to ADR and JSF.Uncovering the complexities of trophic and metabolic interactions among microorganisms is essential for the understanding of marine biogeochemical cycling and modelling climate-driven ecosystem shifts. High-throughput DNA sequencing methods provide valuable tools for examining these complex interactions, although this remains challenging, as many microorganisms are difficult to isolate, identify and culture. We use two species of planktonic foraminifera from the climatically susceptible, palaeoceanographically important genus Neogloboquadrina, as ideal test microorganisms for the application of 16S rRNA gene metabarcoding. Neogloboquadrina dutertrei and Neogloboquadrina incompta were collected from the California Current and subjected to either 16S rRNA gene metabarcoding, fluorescence microscopy, or transmission electron microscopy (TEM) to investigate their species-specific trophic interactions and potential symbiotic associations. 53–99% of 16S rRNA gene sequences recovered from two specimens of N. dutertrei were assigned to a single operational taxonomic unit (OTU) from a chloroplast of the phylum Stramenopile. TEM observations confirmed the presence of numerous intact coccoid algae within the host cell, consistent with algal symbionts. Based on sequence data and observed ultrastructure, we taxonomically assign the putative algal symbionts to Pelagophyceae and not Chrysophyceae, as previously reported in this species. In addition, our data shows that N. dutertrei feeds on protists within particulate organic matter (POM), but not on bacteria as a major food source. In total contrast, of OTUs recovered from three N. incompta specimens, 83–95% were assigned to bacterial classes Alteromonadales and Vibrionales of the order Gammaproteobacteria. TEM demonstrates that these bacteria are a food source, not putative symbionts. Contrary to the current view that non-spinose foraminifera are predominantly herbivorous, neither N. dutertrei nor N. incompta contained significant numbers of phytoplankton OTUs. We present an alternative view of their trophic interactions and discuss these results within the context of modelling global planktonic foraminiferal abundances in response to high-latitude climate change.Publisher PDFPeer reviewe