Transmission of viruses via our microbiomes.

BackgroundBacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the human body, but their ecology suggests they may be shared between close contacts.ResultsHere, we report the ecology of viruses in the guts and mouths of a cohort and demonstrate that substantial numbers of gut and oral viruses were shared amongst genetically unrelated, cohabitating individuals. Most of these viruses were bacteriophages, and each individual had distinct oral and gut viral ecology from their housemates despite the fact that some of their bacteriophages were shared. The distribution of bacteriophages over time within households indicated that they were frequently transmitted between the microbiomes of household contacts.ConclusionsBecause bacteriophages may shape human oral and gut bacterial ecology, their transmission to household contacts suggests they could have substantial roles in shaping the microbiota within a household

Interacting damage models mapped onto Ising and percolation models

We introduce a class of damage models on regular lattices with isotropic interactions, as e.g. quasistatic fiber bundles. The system starts intact with a surface-energy threshold required to break any cell sampled from an uncorrelated quenched-disorder distribution. The evolution of this heterogeneous system is ruled by Griffith's principle which states that a cell breaks when the release in elastic energy in the system exceeds the surface-energy barrier necessary to break the cell. By direct integration over all possible realizations of the quenched disorder, we obtain the probability distribution of each damage configuration at any level of the imposed external deformation. We demonstrate an isomorphism between the distributions so obtained and standard generalized Ising models, in which the coupling constants and effective temperature in the Ising model are functions of the nature of the quenched-disorder distribution and the extent of accumulated damage. In particular, we show that damage models with global load sharing are isomorphic to standard percolation theory, that damage models with local load sharing rule are isomorphic to the standard Ising model, and draw consequences thereof for the universality class and behavior of the autocorrelation length of the breakdown transitions corresponding to these models. We also treat damage models having more general power-law interactions, and classify the breakdown process as a function of the power-law interaction exponent. Last, we also show that the probability distribution over configurations is a maximum of Shannon's entropy under some specific constraints related to the energetic balance of the fracture process, which firmly relates this type of quenched-disorder based damage model to standard statistical mechanics.Comment: 16 pages, 3 figure

Largeness and SQ-universality of cyclically presented groups

Largeness, SQ-universality, and the existence of free subgroups of rank 2 are measures of the complexity of a finitely presented group. We obtain conditions under which a cyclically presented group possesses one or more of these properties. We apply our results to a class of groups introduced by Prishchepov which contains, amongst others, the various generalizations of Fibonacci groups introduced by Campbell and Robertson

No-splitting property and boundaries of random groups

We prove that random groups in the Gromov density model, at any density, satisfy property (FA), i.e. they do not act non-trivially on trees. This implies that their Gromov boundaries, defined at density less than 1/2, are Menger curves.Comment: 20 page

Fracture of disordered solids in compression as a critical phenomenon: I. Statistical mechanics formalism

This is the first of a series of three articles that treats fracture localization as a critical phenomenon. This first article establishes a statistical mechanics based on ensemble averages when fluctuations through time play no role in defining the ensemble. Ensembles are obtained by dividing a huge rock sample into many mesoscopic volumes. Because rocks are a disordered collection of grains in cohesive contact, we expect that once shear strain is applied and cracks begin to arrive in the system, the mesoscopic volumes will have a wide distribution of different crack states. These mesoscopic volumes are the members of our ensembles. We determine the probability of observing a mesoscopic volume to be in a given crack state by maximizing Shannon's measure of the emergent crack disorder subject to constraints coming from the energy-balance of brittle fracture. The laws of thermodynamics, the partition function, and the quantification of temperature are obtained for such cracking systems.Comment: 11 pages, 2 figure

Time evolution of damage under variable ranges of load transfer

We study the time evolution of damage in a fiber bundle model in which the range of interaction of fibers varies through an adjustable stress transfer function recently introduced. We find that the lifetime of the material exhibits a crossover from mean field to short range behavior as in the static case. Numerical calculations showed that the value at which the transition takes place depends on the system's disorder. Finally, we have performed a microscopic analysis of the failure process. Our results confirm that the growth dynamics of the largest crack is radically different in the two limiting regimes of load transfer during the first stages of breaking.Comment: 8 pages, 7 figures, revtex4 styl

Chemostat culture systems support diverse bacteriophage communities from human feces

BACKGROUND: Most human microbiota studies focus on bacteria inhabiting body surfaces, but these surfaces also are home to large populations of viruses. Many are bacteriophages, and their role in driving bacterial diversity is difficult to decipher without the use of in vitro ecosystems that can reproduce human microbial communities. RESULTS: We used chemostat culture systems known to harbor diverse fecal bacteria to decipher whether these cultures also are home to phage communities. We found that there are vast viral communities inhabiting these ecosystems, with estimated concentrations similar to those found in human feces. The viral communities are composed entirely of bacteriophages and likely contain both temperate and lytic phages based on their similarities to other known phages. We examined the cultured phage communities at five separate time points over 24 days and found that they were highly individual-specific, suggesting that much of the subject-specificity found in human viromes also is captured by this culture-based system. A high proportion of the community membership is conserved over time, but the cultured communities maintain more similarity with other intra-subject cultures than they do to human feces. In four of the five subjects, estimated viral diversity between fecal and cultured communities was highly similar. CONCLUSIONS: Because the diversity of phages in these cultured fecal communities have similarities to those found in humans, we believe these communities can serve as valuable ecosystems to help uncover the role of phages in human microbial communities

Human oral viruses are personal, persistent and gender-consistent.

Viruses are the most abundant members of the human oral microbiome, yet relatively little is known about their biodiversity in humans. To improve our understanding of the DNA viruses that inhabit the human oral cavity, we examined saliva from a cohort of eight unrelated subjects over a 60-day period. Each subject was examined at 11 time points to characterize longitudinal differences in human oral viruses. Our primary goals were to determine whether oral viruses were specific to individuals and whether viral genotypes persisted over time. We found a subset of homologous viral genotypes across all subjects and time points studied, suggesting that certain genotypes may be ubiquitous among healthy human subjects. We also found significant associations between viral genotypes and individual subjects, indicating that viruses are a highly personalized feature of the healthy human oral microbiome. Many of these oral viruses were not transient members of the oral ecosystem, as demonstrated by the persistence of certain viruses throughout the entire 60-day study period. As has previously been demonstrated for bacteria and fungi, membership in the oral viral community was significantly associated with the sex of each subject. Similar characteristics of personalized, sex-specific microflora could not be identified for oral bacterial communities based on 16S rRNA. Our findings that many viruses are stable and individual-specific members of the oral ecosystem suggest that viruses have an important role in the human oral ecosystem

Developing a sense of place toolkit: Identifying destination uniqueness

It has long been recognised that the tangible and intangible characteristics that make a location distinctive and memorable, contribute significantly to destination image. How this destination feel is communicated, has largely been the domain of place branding and destination marketing, which have the potential to miss stakeholder voices. Recently though, practitioners are starting to carefully consider ‘sense of place’; that is an emotional attachment to place, which is defined more carefully in the literature review of this article, and which corresponds with long-running academic discussions. This paper attempts to identify some of these and bridge the gap between academic theory on sense of place and practice. In the UK, many rural areas are now seeking to operationalise sense of place through toolkit documents that might inform landscape interpretation and destination branding. A scenario echoed internationally, where local distinctiveness features in both rural and urban planning. However, sense of place in a tourism context, and more specifically the development of these toolkits, has received limited academic attention. Hence, this paper presents the case of Morecambe Bay, and the development of a dedicated sense of place toolkit. The subsequent case emerges from a collaboration between academics and practitioners and draws on participant observation, semi-structured interviews and document analysis. Specifically, the paper outlines a series of workshop activities developed with destination stakeholders and identifies how these inform subsequent toolkit design. It offers a critical analysis of the benefits and potential pitfalls of employing this approach. This case is of value to academics and destination stakeholders interested in identifying and communicating the uniqueness and emotional tone of the destination. Key lessons and recommendations are identified for those engaging in similar toolkit development initiatives

Toward Forecasting Volcanic Eruptions using Seismic Noise

During inter-eruption periods, magma pressurization yields subtle changes of the elastic properties of volcanic edifices. We use the reproducibility properties of the ambient seismic noise recorded on the Piton de la Fournaise volcano to measure relative seismic velocity variations of less than 0.1 % with a temporal resolution of one day. Our results show that five studied volcanic eruptions were preceded by clearly detectable seismic velocity decreases within the zone of magma injection. These precursors reflect the edifice dilatation induced by magma pressurization and can be useful indicators to improve the forecasting of volcanic eruptions.Comment: Supplementary information: http://www-lgit.obs.ujf-grenoble.fr/~fbrengui/brenguier_SI.pdf Supplementary video: http://www-lgit.obs.ujf-grenoble.fr/~fbrengui/brenguierMovieVolcano.av