Oyster – Sharing and Re-using Ontologies in a Peer-to-Peer Community

In this paper, we present Oyster, a Peer-to-Peer system for exchanging ontology metadata among communities in the Semantic Web. Oyster exploits semantic web techniques in data representation, query formulation and query result presentation to provide an online solution for sharing ontologies, thus assisting researchers in re-using existing ontologies

Interactions and magnetic moments near vacancies and resonant impurities in graphene

The effect of electronic interactions in graphene with vacancies or resonant scatterers is investigated. We apply dynamical mean-field theory in combination with quantum Monte Carlo simulations, which allow us to treat non-perturbatively quantum fluctuations beyond Hartree-Fock approximations. The interactions narrow the width of the resonance and induce a Curie magnetic susceptibility, signaling the formation of local moments. The absence of saturation of the susceptibility at low temperatures suggests that the coupling between the local moment and the conduction electrons is ferromagnetic

Winnowing ontologies based on application use

The requirements of specific applications and services are often over estimated when ontologies are reused or built. This sometimes results in many ontologies being too large for their intended purposes. It is not uncommon that when applications and services are deployed over an ontology, only a few parts of the ontology are queried and used. Identifying which parts of an ontology are being used could be helpful to winnow the ontology, i.e., simplify or shrink the ontology to smaller, more fit for purpose size. Some approaches to handle this problem have already been suggested in the literature. However, none of that work showed how ontology-based applications can be used in the ontology-resizing process, or how they might be affected by it. This paper presents a study on the use of the AKT Reference Ontology by a number of applications and services,and investigates the possibility of relying on this usage information to winnow that ontology

Actors and factors - bridging social science findings and urban land use change modeling

Recent uneven land use dynamics in urban areas resulting from demographic change, economic pressure and the cities’ mutual competition in a globalising world challenge both scientists and practitioners, among them social scientists, modellers and spatial planners. Processes of growth and decline specifically affect the urban environment, the requirements of the residents on social and natural resources. Social and environmental research is interested in a better understanding and ways of explaining the interactions between society and landscape in urban areas. And it is also needed for making life in cities attractive, secure and affordable within or despite of uneven dynamics.\ud The position paper upon “Actors and factors – bridging social science findings and urban land use change modeling” presents approaches and ideas on how social science findings on the interaction of the social system (actors) and the land use (factors) are taken up and formalised using modelling and gaming techniques. It should be understood as a first sketch compiling major challenges and proposing exemplary solutions in the field of interest

Vitamin C inhibits endothelial cell apoptosis in congestive heart failure

Background - Proinflammatory cytokines like tumor necrosis factor- and oxidative stress induce apoptotic cell death in endothelial cells (ECs). Systemic inflammation and increased oxidative stress in congestive heart failure (CHF) coincide with enhanced EC apoptosis and the development of endothelial dysfunction. Therefore, we investigated the effects of antioxidative vitamin C therapy on EC apoptosis in CHF patients. Methods and Results - Vitamin C dose dependently suppressed the induction of EC apoptosis by tumor necrosis factor- and angiotensin II in vitro as assessed by DNA fragmentation, DAPI nuclear staining, and MTT viability assay. The antiapoptotic effect of vitamin C was associated with reduced cytochrome C release from mitochondria and the inhibition of caspase-9 activity. To assess EC protection by vitamin C in CHF patients, we prospectively randomized CHF patients in a double-blind trial to vitamin C treatment versus placebo. Vitamin C administration to CHF patients markedly reduced plasma levels of circulating apoptotic microparticles to 32±8% of baseline levels, whereas placebo had no effect (87±14%, P<0.005). In addition, vitamin C administration suppressed the proapoptotic activity on EC of the serum of CHF patients (P<0.001). Conclusions - Administration of vitamin C to CHF patients suppresses EC apoptosis in vivo, which might contribute to the established functional benefit of vitamin C supplementation on endothelial function

Synthetic routes toward MOF nanomorphologies.

As metal–organic frameworks (MOFs) are coming of age, their structural diversity, exceptional porosity and inherent functionality need to be transferred into useful applications. Fashioning MOFs into various shapes and at the same time controlling their size constitute an essential step toward MOF-based devices. Moreover, downsizing MOFs to the nanoscale triggers a whole new set of properties distinguishing nanoMOFs from their bulk counterparts. Therefore, dimensionality-controlled miniaturization of MOFs enables the customised use of nanoMOFs for specific applications where suitable size and shape are key prerequisites. In this feature article we survey the burgeoning field of nanoscale MOF synthesis, ranging from classical protocols such as microemulsion synthesis all the way to microfluidic-based techniques and template-directed epitaxial growth schemes. Along these lines, we will fathom the feasibility of rationally designing specific MOF nanomorphologies—zero-, one- and two-dimensional nanostructures—and we will explore more complex “second-generation” nanostructures typically evolving from a high level of interfacial control. As a recurring theme, we will review recent advances made toward the understanding of nucleation and growth processes at the nanoscale, as such insights are expected to further push the borders of nanoMOF science

Sustained gene expression in the retina by improved episomal vectors

Gene and cellular therapies are nowadays part of therapeutic strategies for the treatment of diverse pathologies. The drawbacks associated with gene therapy-low levels of transgene expression, vector loss during mitosis, and gene silencing-need to be addressed. The pEPI-1 and pEPito family of vectors was developed to overcome these limitations. It contains a scaffold/matrix attachment region, which anchors its replication to cell division in eukaryotic cells while in an extrachromosomal state and is less prone to silencing, due to a lower number of CpG motifs. Recent success showed that ocular gene therapy is an important tool for the treatment of several diseases, pending the overcome of the aforementioned limitations. To achieve sustained gene delivery in the retina, we evaluated several vectors based on pEPito and pEPI-1 for their ability to sustain transgene expression in retinal cells. These vectors stably transfected and replicated in retinal pigment epithelial (RPE) cells. Expression levels were promoter dependent with constitutive promoters cytomegalovirus immediate early promoter (CMV) and human CMV enhancer/human elongation factor 1 alpha promoter yielding the highest levels of transgene expression compared with the retina-specific RPE65 promoter. When injected in C57Bl6 mice, transgene expression was sustained for at least 32 days. Furthermore, the retina-specific RPE65 promoter showed higher efficiency in vivo compared to in vitro. In this study, we demonstrate that by combining tissue-specific promoters with a mitotic stable system, less susceptible to epigenetic silencing such as pEPito-based plasmids, we can achieve prolonged gene expression and a sustained therapeutic effect.Fundacao para a Ciencia e Tecnologia, Portugal [PEst/OE/EQB-LA 0023/2013, SFRH/BD/76873/2011, SFRH/BD/70318/2010, PTDC/SAU/BEB/098475/2008]; European Union [PIRG-GA-2009-249314

Discrete model for laser driven etching and microstructuring of metallic surfaces

We present a unidimensional discrete solid-on-solid model evolving in time using a kinetic Monte Carlo method to simulate micro-structuring of kerfs on metallic surfaces by means of laser-induced jet-chemical etching. The precise control of the passivation layer achieved by this technique is responsible for the high resolution of the structures. However, within a certain range of experimental parameters, the microstructuring of kerfs on stainless steel surfaces with a solution of $\mathrm{H}_3\mathrm{PO}_4$ shows periodic ripples, which are considered to originate from an intrinsic dynamics. The model mimics a few of the various physical and chemical processes involved and within certain parameter ranges reproduces some morphological aspects of the structures, in particular ripple regimes. We analyze the range of values of laser beam power for the appearance of ripples in both experimental and simulated kerfs. The discrete model is an extension of one that has been used previously in the context of ion sputtering and is related to a noisy version of the Kuramoto-Sivashinsky equation used extensively in the field of pattern formation.Comment: Revised version. Etching probability distribution and new simulations adde