Dynamic Image-Based Modelling of Kidney Branching Morphogenesis

Kidney branching morphogenesis has been studied extensively, but the mechanism that defines the branch points is still elusive. Here we obtained a 2D movie of kidney branching morphogenesis in culture to test different models of branching morphogenesis with physiological growth dynamics. We carried out image segmentation and calculated the displacement fields between the frames. The models were subsequently solved on the 2D domain, that was extracted from the movie. We find that Turing patterns are sensitive to the initial conditions when solved on the epithelial shapes. A previously proposed diffusion-dependent geometry effect allowed us to reproduce the growth fields reasonably well, both for an inhibitor of branching that was produced in the epithelium, and for an inducer of branching that was produced in the mesenchyme. The latter could be represented by Glial-derived neurotrophic factor (GDNF), which is expressed in the mesenchyme and induces outgrowth of ureteric branches. Considering that the Turing model represents the interaction between the GDNF and its receptor RET very well and that the model reproduces the relevant expression patterns in developing wildtype and mutant kidneys, it is well possible that a combination of the Turing mechanism and the geometry effect control branching morphogenesis

Disordered Type-II Superconductors: A Universal Phase Diagram for Low-Tc_c Systems

A universal phase diagram for weakly pinned low-T$_c$ type-II superconductors is revisited and extended with new proposals. The low-temperature ``Bragg glass'' phase is argued to transform first into a disordered, glassy phase upon heating. This glassy phase, a continuation of the high-field equilibrium vortex glass phase, then melts at higher temperatures into a liquid. This proposal provides an explanation for the anomalies observed in the peak effect regime of 2H-NbSe$_2$ and several other low-T$_c$ materials which is independent of the microscopic mechanisms of superconductivity in these systems.Comment: 23 pages, 9 figure

Utilizing image texture to detect land-cover change in Mediterranean coastal wetlands

Land-use/cover change dynamics were investigated in a Mediterranean coastal wetland. Change Vector Analysis (CVA) without and with image texture derived from the co-occurrence matrix and variogram were evaluated for detecting land-use/cover change. Three Landsat Thematic Mapper (TM) scenes recorded on July 1985, 1993 and 2005 were used, minimizing change detection error caused by seasonal differences. Images were geometrically, atmospherically and radiometrically corrected. CVA without and with texture measures were implemented and assessed using reference images generated by object-based supervised classification. These outputs were used for cross-classification to determine the ‘from–to’ change used to compare between techniques. The Landsat TM image bands together with the variogram yielded the most accurate change detection results, with Kappa statistics of 0.7619 and 0.7637 for the 1985–1993 and 1993–2005 image pairs, respectively

Phase Behavior of Type-II Superconductors with Quenched Point Pinning Disorder: A Phenomenological Proposal

A general phenomenology for phase behaviour in the mixed phase of type-II superconductors with weak point pinning disorder is outlined. We propose that the ``Bragg glass'' phase generically transforms via two separate thermodynamic phase transitions into a disordered liquid on increasing the temperature. The first transition is into a glassy phase, topologically disordered at the largest length scales; current evidence suggests that it lacks the long-ranged phase correlations expected of a ``vortex glass''. This phase has a significant degree of short-ranged translational order, unlike the disordered liquid, but no quasi-long range order, in contrast to the Bragg glass. This glassy phase, which we call a ``multi-domain glass'', is confined to a narrow sliver at intermediate fields, but broadens out both for much larger and much smaller field values. The multi-domain glass may be a ``hexatic glass''; alternatively, its glassy properties may originate in the replica symmetry breaking envisaged in recent theories of the structural glass transition. Estimates for translational correlation lengths in the multi-domain glass indicate that they can be far larger than the interline spacing for weak disorder, suggesting a plausible mechanism by which signals of a two-step transition can be obscured. Calculations of the Bragg glass-multi-domain glass and the multi-domain glass-disordered liquid phase boundaries are presented and compared to experimental data. We argue that these proposals provide a unified picture of the available experimental data on both high-T$_c$ and low-T$_c$ materials, simulations and current theoretical understanding.Comment: 70 pages, 9 postscript figures, modified title and minor changes in published versio

University-industry relationships and open innovation: Towards a research agenda

Accepted versio

New insights into the genetic etiology of Alzheimer's disease and related dementias.

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele