Large Graph Analysis in the GMine System

Current applications have produced graphs on the order of hundreds of thousands of nodes and millions of edges. To take advantage of such graphs, one must be able to find patterns, outliers and communities. These tasks are better performed in an interactive environment, where human expertise can guide the process. For large graphs, though, there are some challenges: the excessive processing requirements are prohibitive, and drawing hundred-thousand nodes results in cluttered images hard to comprehend. To cope with these problems, we propose an innovative framework suited for any kind of tree-like graph visual design. GMine integrates (a) a representation for graphs organized as hierarchies of partitions - the concepts of SuperGraph and Graph-Tree; and (b) a graph summarization methodology - CEPS. Our graph representation deals with the problem of tracing the connection aspects of a graph hierarchy with sub linear complexity, allowing one to grasp the neighborhood of a single node or of a group of nodes in a single click. As a proof of concept, the visual environment of GMine is instantiated as a system in which large graphs can be investigated globally and locally

Towards Scalable Visual Exploration of Very Large RDF Graphs

In this paper, we outline our work on developing a disk-based infrastructure for efficient visualization and graph exploration operations over very large graphs. The proposed platform, called graphVizdb, is based on a novel technique for indexing and storing the graph. Particularly, the graph layout is indexed with a spatial data structure, i.e., an R-tree, and stored in a database. In runtime, user operations are translated into efficient spatial operations (i.e., window queries) in the backend.Comment: 12th Extended Semantic Web Conference (ESWC 2015

The effects of arbuscular mycorrhizal fungi (AMF) and Rhizophagus irregularis on soil microorganisms assessed by metatranscriptomics and metaproteomics

Arbuscular mycorrhizal fungi (AMF) form symbioses with approximately 80% of plant species and potentially benefit their hosts (e.g. nutrient acquisition) and the soil environment (e.g. soil aggregation). AMF also affect soil microbiota and soil multifunctionality. We manipulated AMF presence (via inoculation of non-sterile soil with Rhizophagus irregularis and using a hyphal compartment design) and used RNA-seq and metaproteomics to assess AMF roles in soil. The results indicated that AMF drove an active soil microbial community expressing transcripts and proteins related to nine metabolic functions, including the metabolism of C and N. We suggest two possible mechanisms: 1) the AMF hyphae produce exudates that select a beneficial community, or, 2) the hyphae compete with other soil microbes for available nutrients and consequently induce the community to mineralize nutrients from soil organic matter. We also identified candidate proteins that are potentially related to soil aggregation, such as Lpt and HSP60. Our results bridge microbial ecology and ecosystem functioning. We show that the AMF hyphosphere contains an active community related to soil respiration and nutrient cycling, thus potentially improving nutrient mineralization from soil organic matter and nutrient supply to the plants

Community detection applied on big linked data

The Linked Open Data (LOD) Cloud has more than tripled its sources in just six years (from 295 sources in 2011 to 1163 datasets in 2017). The actual Web of Data contains more then 150 Billions of triples. We are assisting at a staggering growth in the production and consumption of LOD and the generation of increasingly large datasets. In this scenario, providing researchers, domain experts, but also businessmen and citizens with visual representations and intuitive interactions can significantly aid the exploration and understanding of the domains and knowledge represented by Linked Data. Various tools and web applications have been developed to enable the navigation, and browsing of the Web of Data. However, these tools lack in producing high level representations for large datasets, and in supporting users in the exploration and querying of these big sources. Following this trend, we devised a new method and a tool called H-BOLD (High level visualizations on Big Open Linked Data). H-BOLD enables the exploratory search and multilevel analysis of Linked Open Data. It offers different levels of abstraction on Big Linked Data. Through the user interaction and the dynamic adaptation of the graph representing the dataset, it will be possible to perform an effective exploration of the dataset, starting from a set of few classes and adding new ones. Performance and portability of H-BOLD have been evaluated on the SPARQL endpoint listed on SPARQL ENDPOINT STATUS. The effectiveness of H-BOLD as a visualization tool is described through a user study

Immunomics-guided antigen discovery for praziquantel-induced vaccination inurogenital human schistosomiasis

Despite the enormous morbidity attributed to schistosomiasis, there is still no vaccine to combat the disease for the hundreds of millions of infected people. The anthelmintic drug, praziquantel, is the mainstay treatment option, although its molecular mechanism of action remains poorly defined. Praziquantel treatment damages the outermost surface of the parasite, the tegument, liberating surface antigens from dying worms that invoke a robust immune response which in some subjects results in immunologic resistance to reinfection. Herein we term this phenomenon Drug-Induced Vaccination (DIV). To identify the antigenic targets of DIV antibodies in urogenital schistosomiasis, we constructed a recombinant proteome array consisting of approximately 1,000 proteins informed by various secretome datasets including validated proteomes and bioinformatic predictions. Arrays were screened with sera from human subjects treated with praziquantel and shown 18 months later to be either reinfected (chronically infected subjects, CI) or resistant to reinfection (DIV). IgG responses to numerous antigens were significantly elevated in DIV compared to CI subjects, and indeed IgG responses to some antigens were completely undetectable in CI subjects but robustly recognized by DIV subjects. One antigen in particular, a cystatin cysteine protease inhibitor stood out as a unique target of DIV IgG, so recombinant cystatin was produced, and its vaccine efficacy assessed in a heterologous Schistosoma mansoni mouse challenge model. While there was no significant impact of vaccination with adjuvanted cystatin on adult worm numbers, highly significant reductions in liver egg burdens (45-55%, P<0.0001) and intestinal egg burdens (50-54%, P<0.0003) were achieved in mice vaccinated with cystatin in two independent trials. This study has revealed numerous antigens that are targets of DIV antibodies in urogenital schistosomiasis and offer promise as subunit vaccine targets for a drug-linked vaccination approach to controlling schistosomiasis

Psychopharmacological Analysis of Central Muscarinic and Nicotinic Receptors

Arecoline and nicotine are two psychoactive cholinergic alkaloids. Arecoline is primarily a muscarinic agonist while nicotine, at low doses, is a nicotinic agonist. The experiments in this dissertation investigated two major areas: (1) the role of different factors in the development of tolerance to the behavioral effects of arecoline and nicotine, and (2) the possible mechanism and site of action of the discriminative stimulus (DS) effects of arecoline and nicotine. The role of dispositional and physiological factors comfiared to behavioral factors in the development of tolerance to the effects of arecoline and nicotine on operant behavior was assessed in Experiments I and II, respectively. In part one of Experiment I, rats were trained to respond (M1 a variable-interval 15 second (VI-15) schedule for milk reinforcement. Dose-effect relationships were assessed prior to and during chronic arecoline (1.74 mg/kg/day) treatment. After 21 days Of arecoline administration prior to the session, the dose-effect relationship for total responses was not shifted. However, the dose-effect relationship for total reinforcements was shifted to the right. In part two of Experiment I, rats were trained to respond on a fixed-ratio 20 (FR-ZG) schedule for milk reinforcement. Dose-effect relationships were assessed prior to and during chronic arecoline (0.87 mg/kg/day) administration. One group of rats received daily injections of arecoline prior to the seSsion and a second group received arecoline injections after the session. Daily administration of arecoline resulted in a greater shift to the right of the dose-effect relationship in the pre-session group compared to the post-session group. These data demonstrate the importance cflf behavioral factors in the development of tolerance to arecoline. In Experiment II, rats were trained to respond on a VI-15 second schedule of milk reinforcement. Dose-effect relationships were determined prior to and during chronic nicotine (2.28 mg/kg/day) administration. One group of rats received daily injections Of nicotine prior to the session, another group received nicotine injections after the session. After 36 days of chronic treatment, similar degrees of tolerance were observed in both groups, however the group receiving post-session nicotine developed tolerance at a faster rate. The data suggested that 21 complex interaction of nicotine and the experimental environment affected the rate of tolerance development. Experiment III characterized the DS effect of arecoline. Using a two-lever operant paradigm, rats were trained to discriminate arecoline from saline on a VI-12 second schedule of milk reinforcement. Rats could learn to discriminate 1.74 mg/kg arecoline from saline, but not 0.58 mg/kg from saline. Agonist and antagonist studies demonStrated that the DS effect of arecoline is mediated through central muscarinic receptors. In Experiment IV, the ability of physostigmine to interact fiith the DS effect of nicotine (1.14 mg/kg) and arecoline (1.74 mg/kg) was assessed. Physostigmine (0.125 mg/kg) pretreatment shifted the dose-effect relationship for arecoline to the left but did not affect that of nicotine. Physostigmine (0.25 mg/kg) almost completely generalized to the DS effect of arecoline but not to the DS effect of nicotine. These data suggest an interaction of endogenous acetylcholine with muscarinic receptors but not with nicotinic receptors. In Experiment V, the ability hf arecoline and nicotine injected directly into the dorsal hippocampus (DH) and mesencephalic reticular formation (MRF) to generalize to the DS effect of peripherally administered arecoline (1.74 mg/kg) and nicotine (1.14 mg/kg) was assessed; Nicotine injected into these sites generalized in a dose-related manner to nicotine. The MRF was slightly more sensitive than the DH. Arecoline injected into either site did not generalize to the DS effect of, peripherally administered arecoline. However, a decrease in response rates was observed