Population Dynamics on Complex Food Webs

In this work we analyse the topological and dynamical properties of a simple model of complex food webs, namely the niche model. In order to underline competition among species, we introduce "prey" and "predators" weighted overlap graphs derived from the niche model and compare synthetic food webs with real data. Doing so, we find new tests for the goodness of synthetic food web models and indicate a possible direction of improvement for existing ones. We then exploit the weighted overlap graphs to define a competition kernel for Lotka-Volterra population dynamics and find that for such a model the stability of food webs decreases with its ecological complexity.Comment: 11 Pages, 5 Figures, styles enclosed in the submissio

What? Now. Predictive Coding and Enculturation

Regina Fabry has proposed an intriguing marriage of enculturated cognition and predictive processing. I raise some questions for whether this marriage will work and warn against expecting too much from the predictive processing framework. Furthermore I argue that the predictive processes at a sub-personal level cannot be driving the innovations at a social level that lead to enculturated cognitive systems, like those explored in my target paper

Fostering energy efficiency dynamics through ex-ante strategic niche management: the UK perspective

The United Kingdom building sector has been challenged to retrofit a huge stock of existing buildings in order to increase its adaptive capacity for climate change impacts. Addressing such challenges will require systematic structural changes in both, socio-technical and socio-political infrastructure. A numbers of studies have suggested the approach of strategic niche management of transition for sustainable technological regimes. Accordingly, any such transition would follow processes: early stages of niche formation; creation of policy mechanism required to harness the niches; niche expansion into incumbent regime; and the regime transition into more sustainable technological regime. Following this, the UK Government has introduced a raft of initiatives; one of which is “Green Deal” to enable buildings to become energy efficient through retrofit technologies, ultimately contributing towards the national goal of achieving 80% reduction in carbon emission by 2050. This paper serves three purposes. First, the paper introduces multi-level socio-technical system for construction/retrofitting in building industry. Second, the ex-ante strategic niche management approach has been used to analyse the dynamic of “Green Deal” initiative. Thereby the paper would critically assess technological, organisational and institutional reforms undertaken for the initiative in the processes for sustainable socio-technical transition. Third, the paper would contribute towards strategic niche management literature which lacks in practical examples of using it as an ex-ante tool for niche building and regime transition

Buckling of a growing tissue and the emergence of two-dimensional patterns

The process of biological growth and the associated generation of residual stress has previously been considered as a driving mechanism for tissue buckling and pattern selection in numerous areas of biology. Here, we develop a two-dimensional thin plate theory to simulate the growth of cultured intestinal epithelial cells on a deformable substrate, with the goal of elucidating how a tissue engineer might best recreate the regular array of invaginations (crypts of Lieberkühn) found in the wall of the mammalian intestine. We extend the standard von Kármán equations to incorporate inhomogeneity in the plate’s mechanical properties and surface stresses applied to the substrate by cell proliferation. We determine numerically the configurations of a homogeneous plate under uniform cell growth, and show how tethering to an underlying elastic foundation can be used to promote higher-order buckled configurations. We then examine the independent effects of localised softening of the substrate and spatial patterning of cellular growth, demonstrating that (within a two-dimensional framework, and contrary to the predictions of one-dimensional models) growth patterning constitutes a more viable mechanism for control of crypt distribution than does material inhomogeneity

Cornea organoids from human induced pluripotent stem cells.

The cornea is the transparent outermost surface of the eye, consisting of a stratified epithelium, a collagenous stroma and an innermost single-cell layered endothelium and providing 2/3 of the refractive power of the eye. Multiple diseases of the cornea arise from genetic defects where the ultimate phenotype can be influenced by cross talk between the cell types and the extracellular matrix. Cell culture modeling of diseases can benefit from cornea organoids that include multiple corneal cell types and extracellular matrices. Here we present human iPS cell-derived organoids through sequential rounds of differentiation programs. These organoids share features of the developing cornea, harboring three distinct cell types with expression of key epithelial, stromal and endothelial cell markers. Cornea organoid cultures provide a powerful 3D model system for investigating corneal developmental processes and their disruptions in diseased conditions

Long-term in vitro 3D hydrogel co-culture model of inflammatory bowel disease

The in vitro study of the pathogenesis of inflammatory bowel disease (IBD) requires a cell model which closely reflects the characteristics of the in vivo intestinal epithelium. This study aimed to investigate the application of L-pNIPAM hydrogel as a scaffold to develop a long-term 3D co-culture model of Caco-2 and HT29-MTX cells under conditions analogous to inflammation, to determine its potential use in studying IBD. Monocultures and co-cultures were layered on L-pNIPAM hydrogel scaffolds and maintained under dynamic culture conditions for up to 12 weeks. Treatments with IL-1β, TNFα, and hypoxia for 1 week were used to create an inflammatory environment. Following prolonged culture, the metabolic activity of Caco-2 monoculture and 90% Caco-2/10% HT29-MTX co-cultures on L-pNIPAM hydrogels were increased, and finger-like structures, similar in appearance to villi were observed. Following treatment with IL-1β, TNFα and hypoxia, ALP and ZO-1 were decreased, MUC2 increased, and MUC5AC remained unchanged. ADAMTS1 was increased in response to hypoxia. Caspase 3 expression was increased in response to TNFα and hypoxic conditions. In conclusion, L-pNIPAM hydrogel supported long-term co-culture within a 3D model. Furthermore, stimulation with factors seen during inflammation recapitulated features seen during IBD

The Markov blankets of life: autonomy, active inference and the free energy principle

This work addresses the autonomous organization of biological systems. It does so by considering the boundaries of biological systems, from individual cells to Home sapiens, in terms of the presence of Markov blankets under the active inference scheme—a corollary of the free energy principle. A Markov blanket defines the boundaries of a system in a statistical sense. Here we consider how a collective of Markov blankets can self-assemble into a global system that itself has a Markov blanket; thereby providing an illustration of how autonomous systems can be understood as having layers of nested and self-sustaining boundaries. This allows us to show that: (i) any living system is a Markov blanketed system and (ii) the boundaries of such systems need not be co-extensive with the biophysical boundaries of a living organism. In other words, autonomous systems are hierarchically composed of Markov blankets of Markov blankets—all the way down to individual cells, all the way up to you and me, and all the way out to include elements of the local environment

Contemporary (2001) and ‘Little Ice Age’ glacier extents in the Buordakh Massif, Cherskiy Range, north east Siberia

The Buordakh Massif of the Cherskiy Range of sub-arctic north east Siberia, Russia has a cold continental climate and supports over 80 glaciers. Despite previous research in the region, a georeferenced map of the glaciers has only recently been completed and an enhanced version of it is reproduced in colour here. The mountains of this region reach heights in excess of 3,000 m and the glaciers on their slopes range in size from 0.1 to 10.4 km2. The mapping has been compiled through the interpretation of Landsat 7 ETM+ satellite imagery from August 2001 which has been augmented by data from a field campaign undertaken at the same time. The glaciers of the region are of the cold, ‘firn-less’ continental type and their mass balance relies heavily on the formation of superimposed ice. Moraines which lie in front of the glaciers by up to a few kilometres are believed to date from the Little Ice Age (ca. 1550-1850 AD). Over half of the glaciers mapped have shown marked retreat from these moraines