Polar POLICRYPS diffractive structures generate cylindrical vector beams

Local shaping of the polarization state of a light beam is appealing for a number of applications. This can be achieved by employing devices containing birefringent materials. In this article, we present one such enables converting a uniformly circularly polarized beam into a cylindrical vector beam (CVB). This device has been fabricated by exploiting the POLICRYPS (POlymer-LIquid CRYstals-Polymer-Slices) photocuring technique. It is a liquid-crystal-based optical diffraction grating featuring polar symmetry of the director alignment. We have characterized the resulting CVB profile and polarization for the cases of left and right circularly polarized incoming beams. © 2015 AIP Publishing LLC

OREMPdb: a semantic dictionary of computational pathway models

<p>Abstract</p> <p>Background</p> <p>The information coming from biomedical ontologies and computational pathway models is expanding continuously: research communities keep this process up and their advances are generally shared by means of dedicated resources published on the web. In fact, such models are shared to provide the characterization of molecular processes, while biomedical ontologies detail a semantic context to the majority of those pathways. Recent advances in both fields pave the way for a scalable information integration based on aggregate knowledge repositories, but the lack of overall standard formats impedes this progress. Indeed, having different objectives and different abstraction levels, most of these resources "speak" different languages. Semantic web technologies are here explored as a means to address some of these problems.</p> <p>Methods</p> <p>Employing an extensible collection of interpreters, we developed OREMP (Ontology Reasoning Engine for Molecular Pathways), a system that abstracts the information from different resources and combines them together into a coherent ontology. Continuing this effort we present OREMPdb; once different pathways are fed into OREMP, species are linked to the external ontologies referred and to reactions in which they participate. Exploiting these links, the system builds species-sets, which encapsulate species that operate together. Composing all of the reactions together, the system computes all of the reaction paths from-and-to all of the species-sets.</p> <p>Results</p> <p>OREMP has been applied to the curated branch of BioModels (2011/04/15 release) which overall contains 326 models, 9244 reactions, and 5636 species. OREMPdb is the semantic dictionary created as a result, which is made of 7360 species-sets. For each one of these sets, OREMPdb links the original pathway and the link to the original paper where this information first appeared. </p

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics

The BITS2011 meeting, held in Pisa on June 20-22, 2011, brought together more than 120 Italian researchers working in the field of Bioinformatics, as well as students in Bioinformatics, Computational Biology, Biology, Computer Sciences, and Engineering, representing a landscape of Italian bioinformatics research

A "Candidate-Interactome" Aggregate Analysis of Genome-Wide Association Data in Multiple Sclerosis

Though difficult, the study of gene-environment interactions in multifactorial diseases is crucial for interpreting the relevance of non-heritable factors and prevents from overlooking genetic associations with small but measurable effects. We propose a “candidate interactome” (i.e. a group of genes whose products are known to physically interact with environmental factors that may be relevant for disease pathogenesis) analysis of genome-wide association data in multiple sclerosis. We looked for statistical enrichment of associations among interactomes that, at the current state of knowledge, may be representative of gene-environment interactions of potential, uncertain or unlikely relevance for multiple sclerosis pathogenesis: Epstein-Barr virus, human immunodeficiency virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, HHV8-Kaposi sarcoma, H1N1-influenza, JC virus, human innate immunity interactome for type I interferon, autoimmune regulator, vitamin D receptor, aryl hydrocarbon receptor and a panel of proteins targeted by 70 innate immune-modulating viral open reading frames from 30 viral species. Interactomes were either obtained from the literature or were manually curated. The P values of all single nucleotide polymorphism mapping to a given interactome were obtained from the last genome-wide association study of the International Multiple Sclerosis Genetics Consortium & the Wellcome Trust Case Control Consortium, 2. The interaction between genotype and Epstein Barr virus emerges as relevant for multiple sclerosis etiology. However, in line with recent data on the coexistence of common and unique strategies used by viruses to perturb the human molecular system, also other viruses have a similar potential, though probably less relevant in epidemiological terms

A “Candidate-Interactome” Aggregate Analysis of Genome-Wide Association Data in Multiple Sclerosis

Though difficult, the study of gene-environment interactions in multifactorial diseases is crucial for interpreting the relevance of non-heritable factors and prevents from overlooking genetic associations with small but measurable effects. We propose a "candidate interactome" (i.e. a group of genes whose products are known to physically interact with environmental factors that may be relevant for disease pathogenesis) analysis of genome-wide association data in multiple sclerosis. We looked for statistical enrichment of associations among interactomes that, at the current state of knowledge, may be representative of gene-environment interactions of potential, uncertain or unlikely relevance for multiple sclerosis pathogenesis: Epstein-Barr virus, human immunodeficiency virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, HHV8-Kaposi sarcoma, H1N1-influenza, JC virus, human innate immunity interactome for type I interferon, autoimmune regulator, vitamin D receptor, aryl hydrocarbon receptor and a panel of proteins targeted by 70 innate immune-modulating viral open reading frames from 30 viral species. Interactomes were either obtained from the literature or were manually curated. The P values of all single nucleotide polymorphism mapping to a given interactome were obtained from the last genome-wide association study of the International Multiple Sclerosis Genetics Consortium & the Wellcome Trust Case Control Consortium, 2. The interaction between genotype and Epstein Barr virus emerges as relevant for multiple sclerosis etiology. However, in line with recent data on the coexistence of common and unique strategies used by viruses to perturb the human molecular system, also other viruses have a similar potential, though probably less relevant in epidemiological terms

A Cross-Format Framework for Consistent Information Integration among Molecular Pathways and Ontologies

Abstract — The information coming from biomedical ontologies and runnable pathways is expanding continuously: research communities keep this process up and their advances are generally shared by means of dedicated resources published on the web. Having different objectives and different abstraction levels, most of these resources “speak ” different languages. Employing an extensible collection of interpreters, we propose a system that abstracts the information from different resources and combines them together into a common meta-format. Preserving the resource independence, we provide an alignment service that can be used for multiple purposes. Two recent examples are: 1) The new web application Cytosolve uses an embedded version of this system to provide congruous parallel simulation of multiple models; 2) Using the BioModels.net database, a searchable dictionary of equivalent molecular reaction paths was built. Finally, the enriched knowledge can be exported in OWL and queried by semantically-enabled tools such as Protégé. In this approach, we see a valuable tool to integrate and test information originating from different sources, while preserving the independence of the model curation process. Keywords — Algorithms in Bioinformatics; Multi-scale modeling: algorithm development &amp; applications

Plasmon resonance tunability of gold nanoparticles embedded in a confined cholesteric liquid crystal host

Gold nanoparticles have been dissolved in a cholesteric liquid crystal and then infiltrated in a micro-periodic polymeric structure. This has been realized by combining a holographic step and a microfluidic etching process. The spectral behavior of the nano-composite soft-structure has been investigated in the UV-Vis range for two different polarization directions of an impinging probe light and in presence of external perturbations (electric field, temperature variation). Obtained results show a highly tunable plasmonic response of the material. Copyright © 2012 Taylor and Francis Group, LLC

A new kind of photo-polymerisation induced diffraction gratings in liquid crystalline composite materials

In this paper we report on the first results of a new technique used to obtain good quality holographic diffraction gratings. This technique represents an improvement with respect to the traditional one, the so called polymerisation induced phase separation technique. Gratings are obtained by exposing the initial homogeneous mixture of liquid crystal and monomer molecules to the pattern produced by two interfering UV laser beams. The polymerisation process, which is photo-induced by this pattern, is thus spatially inhomogeneous: It leads to a redistribution of the mixture components and hence to the grating formation

Realization of POLICRYPS gratings. Optical and electro-optical properties

In this paper we report a detailed characterization of a new structure (POLICRYPS) in which liquid crystal films are completely separated by polymer slices. This structure behaves as a Bragg diffraction grating and exhibits efficiencies that can become as high as 96-98%. The temperature dependence of the diffraction efficiency can be explained in terms of a Kogelnik-like model. A numerical simulation has been implemented which makes use only of real values of physical quantities and accounts for the experimental results with good accuracy. An applied electric field is able to switch off the grating, with a characteristic switching time which is lower than 1 ms. Threshold values of the field vary in the range 3-5 V/μm for gratings with a 1.39 μm fringe spacing