Self-Enforcing Access Control for Encrypted RDF

The amount of raw data exchanged via web protocols is steadily increasing. Although the Linked Data infrastructure could potentially be used to selectively share RDF data with different individuals or organisations, the primary focus remains on the unrestricted sharing of public data. In order to extend the Linked Data paradigm to cater for closed data, there is a need to augment the existing infrastructure with robust security mechanisms. At the most basic level both access control and encryption mechanisms are required. In this paper, we propose a flexible and dynamic mechanism for securely storing and efficiently querying RDF datasets. By employing an encryption strategy based on Functional Encryption (FE) in which controlled data access does not require a trusted mediator, but is instead enforced by the cryptographic approach itself, we allow for fine-grained access control over encrypted RDF data while at the same time reducing the administrative overhead associated with access control management

An introduction to Graph Data Management

A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

Rapid and Sensitive Lentivirus Vector-Based Conditional Gene Expression Assay to Monitor and Quantify Cell Fusion Activity

Cell-to-cell fusion is involved in multiple fundamental biological processes. Prominent examples include osteoclast and giant cell formation, fertilization and skeletal myogenesis which involve macrophage, sperm-egg and myoblast fusion, respectively. Indeed, the importance of cell fusion is underscored by the wide range of homeostatic as well as pathologic processes in which it plays a key role. Therefore, rapid and sensitive systems to trace and measure cell fusion events in various experimental systems are in demand. Here, we introduce a bipartite cell fusion monitoring system based on a genetic switch responsive to the site-specific recombinase FLP. To allow flexible deployment in both dividing as well as non-dividing cell populations, inducer and reporter modules were incorporated in lentivirus vector particles. Moreover, the recombinase-inducible transcription units were designed in such a way as to minimize basal activity and chromosomal position effects in the “off” and “on” states, respectively. The lentivirus vector-based conditional gene expression assay was validated in primary human mesenchymal stem cells and in a differentiation model based on muscle progenitor cells from a Duchenne muscular dystrophy patient using reporter genes compatible with live- and single-cell imaging and with whole population measurements. Using the skeletal muscle cell differentiation model, we showed that the new assay displays low background activity, a 2-log dynamic range, high sensitivity and is amenable to the investigation of cell fusion kinetics. The utility of the bipartite cell fusion monitoring system was underscored by a study on the impact of drug- and RNAi-mediated p38 MAPK inhibition on human myocyte differentiation. Finally, building on the capacity of lentivirus vectors to readily generate transgenic animals the present FLP-inducible system should be adaptable, alone or together with Cre/loxP-based assays, to cell lineage tracing and conditional gene manipulation studies in vivo

Targeted Chromosomal Insertion of Large DNA into the Human Genome by a Fiber-Modified High-Capacity Adenovirus-Based Vector System

A prominent goal in gene therapy research concerns the development of gene transfer vehicles that can integrate exogenous DNA at specific chromosomal loci to prevent insertional oncogenesis and provide for long-term transgene expression. Adenovirus (Ad) vectors arguably represent the most efficient delivery systems of episomal DNA into eukaryotic cell nuclei. The most advanced recombinant Ads lack all adenoviral genes. This renders these so-called high-capacity (hc) Ad vectors less cytotoxic/immunogenic than those only deleted in early regions and creates space for the insertion of large/multiple transgenes. The versatility of hcAd vectors is been increased by capsid modifications to alter their tropism and by the incorporation into their genomes of sequences promoting chromosomal insertion of exogenous DNA. Adeno-associated virus (AAV) can insert its genome into a specific human locus designated AAVS1. Trans- and cis-acting elements needed for this reaction are the AAV Rep78/68 proteins and Rep78/68-binding sequences, respectively. Here, we describe the generation, characterization and testing of fiber-modified dual hcAd/AAV hybrid vectors (dHVs) containing both these elements. Due to the inhibitory effects of Rep78/68 on Ad-dependent DNA replication, we deployed a recombinase-inducible gene switch to repress Rep68 synthesis during vector rescue and propagation. Flow cytometric analyses revealed that rep68-positive dHVs can be produced similarly well as rep68-negative control vectors. Western blot experiments and immunofluorescence microscopy analyses demonstrated transfer of recombinase-dependent rep68 genes into target cells. Studies in HeLa cells and in the dystrophin-deficient myoblasts from a Duchenne muscular dystrophy (DMD) patient showed that induction of Rep68 synthesis in cells transduced with fiber-modified and rep68-positive dHVs leads to increased stable transduction levels and AAVS1-targeted integration of vector DNA. These results warrant further investigation especially considering the paucity of vector systems allowing permanent phenotypic correction of patient-own cell types with large DNA (e.g. recombinant full-length DMD genes)

Assessing data veracity through domain specific knowledge base inspection

The Internet is nowadays a fantastic source of information thanks to the quantity of the information it provides and its dynamicity. However, these features also represent challenges when we want to consider trustworthy information only. On the Internet, the process of verifying information, known as fact-checking, cannot be performed by human experts given the scale of the information that should be manually checked, and the speed to which it changes. In this paper, we propose an approach to evaluate the trustworthiness of online information modeled as RDF Triples. Given a use case, we select a specific ontology (in the following we use movie reviews as a use case) and match its object properties with WordNet. This allows us to understand, for each input triple, which class the subject and the object belong to. We associate SPARQL queries to each class, which are then used by our approach to search for additional evidences in Wikidata. By doing so, our approach generates feature vectors that are used by machine learning classification models to predict the trustworthiness of new input triples. Experiments on real movie data show that our approach provides results that are on par or better than the state of the art in fact checking

Demonstrating The Entity Registry System : Implementing 5-Star Linked Data Without the Web

Abstract. Linked Data applications often assume that connectivity to data repositories and entity resolution services are always available. This may not be a valid assumption in many cases. Indeed, there are about 4.5 billion people in the world who have no or limited Web access. Many data-driven applications may have a critical impact on the life of those people, but are inaccessible to those populations due to the architecture of today’s data registries. In this paper, we propose and evaluate a new open-source system that can be used as a general-purpose entity registry suitable for deployment in poorly-connected or ad-hoc environments.