A set of ontologies to drive tools for the control of vector-borne diseases

We are developing a set of ontologies that deal with vector-borne diseases and the arthropod vectors that transmit them. For practical reasons (application priorities), we initiated this project with an ontology of insecticide resistance followed by a series of ontologies that describe malaria as well as physiological processes of mosquitoes that are relevant to, and involved in, disease transmission. These will be expanded to encompass other vector-borne diseases as well as non-mosquito vectors. The aim of the whole undertaking, which is worked out in the frame of the international IDO (Infectious Disease Ontology) project, is to provide the community with a set of ontological tools that can be used both in the development of specific databases and, most importantly, in the construction of decision support systems to control these diseases

Discovery of a transient radiation belt at Saturn

Radiation belts have been detected in situ at five planets. Only at Earth however has any variability in their intensity been heretofore observed, in indirect response to solar eruptions and high altitude nuclear explosions. The Cassini spacecraft's MIMI/LEMMS instrument has now detected systematic radiation belt variability elsewhere. We report three sudden increases in energetic ion intensity around Saturn, in the vicinity of the moons Dione and Tethys, each lasting for several weeks, in response to interplanetary events caused by solar eruptions. However, the intensifications, which could create temporary satellite atmospheres at the aforementioned moons, were sharply restricted outside the orbit of Tethys. Unlike Earth, Saturn has almost unchanging inner ion radiation belts: due to Saturn's near-symmetrical magnetic field, Tethys and Dione inhibit inward radial transport of energetic ions, shielding the planet's main, inner radiation belt from solar wind influences

MIRO and IRbase: IT Tools for the Epidemiological Monitoring of Insecticide Resistance in Mosquito Disease Vectors

It is a historical fact that a successful campaign against vector populations is one of the prerequisites for effectively fighting and eventually eradicating arthropod-borne diseases, be that in an epidemic or, even more so, in endemic cases. Based mostly on the use of insecticides and environmental management, vector control is now increasingly hampered by the occurrence of insecticide resistance that manifests itself, and spreads rapidly, briefly after the introduction of a (novel) chemical substance. We make use here of a specially built ontology, MIRO, to drive a new database, IRbase, dedicated to storing data on the occurrence of insecticide resistance in mosquito populations worldwide. The ontological approach to the design of databases offers the great advantage that these can be searched in an efficient way. Moreover, it also provides for an increased interoperability of present and future epidemiological tools. IRbase is now being populated by both older data from the literature and data recently collected from field

DEM-resolution control on rainfall-triggered landslide modeling within a triangulated network-based model

Catchment slope distribution significantly controls rainfall-triggered landslide modeling, in both direct and indirect ways. Slope directly determines the soil volume associated with instability. Indirectly, it affects the subsurface lateral redistribution of soil moisture across the basin, which in turn determines the water pore pressure conditions that impact slope stability. It is thus clear that the accuracy in reproducing slope distribution may be crucial in slope stability analysis. The resolution of Digital Elevation Model (DEM) regulates the description of topography. The correlation between raster resolution and landslide model outputs has been investigated in literature, both in terms of landslide susceptibility and landslide dynamics. Results demonstrate that the optimal DEM resolution may not necessarily exclude the use of coarser DEMs. This study evaluates the influence of DEM resolution on the slope stability analysis by using a distributed eco-hydrological-landslide model, which implements a Triangulated Irregular Network (TIN) to describe the topography; as well, the model is capable of evaluating vegetation dynamics and predicting shallow landslides triggered by rainfall

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.

VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community

Topographic variability and the influence of soil erosion on the carbon cycle

Soil erosion, particularly that caused by agriculture, is closely linked to the global carbon (C) cycle. There is a wide range of contrasting global estimates of how erosion alters soil-atmosphere C exchange. This can be partly attributed to limited understanding of how geomorphology, topography, and management practices affect erosion and oxidation of soil organic C (SOC). This work presents a physically based approach that stresses the heterogeneity at fine spatial scales of SOC erosion, SOC burial, and associated soil-atmosphere C fluxes. The Holcombe's Branch watershed, part of the Calhoun Critical Zone Observatory in South Carolina, USA, is the case study used. The site has experienced some of the most serious agricultural soil erosion in North America. We use SOC content measurements from contrasting soil profiles and estimates of SOC oxidation rates at multiple soil depths. The methodology was implemented in the tRIBS-ECO (Triangulated Irregular Network-based Real-time Integrated Basin Simulator-Erosion and Carbon Oxidation), a spatially and depth-explicit model of SOC dynamics built within an existing coupled physically based hydro-geomorphic model. According to observations from multiple soil profiles, about 32% of the original SOC content has been eroded in the study area. The results indicate that C erosion and its replacement exhibit significant topographic variation at relatively small scales (tens of meters). The episodic representation of SOC erosion reproduces the history of SOC erosion better than models that use an assumption of constant erosion in space and time. The net atmospheric C exchange at the study site is estimated to range from a maximum source of 14.5 g m−2 yr−1 to a maximum sink of −18.2 g m−2 yr−1. The small-scale complexity of C erosion and burial driven by topography exerts a strong control on the landscape's capacity to serve as a C source or a sink

The Structure of the Large-Scale Heliosphere as Seen by Current Models.

This review summarizes the current state of research aiming at a description of the global heliosphere using both analytical and numerical modeling efforts, particularly in view of the overall plasma/neutral flow and magnetic field structure, and its relation to energetic neutral atoms. Being part of a larger volume on current heliospheric research, it also lays out a number of key concepts and describes several classic, though still relevant early works on the topic. Regarding numerical simulations, emphasis is put on magnetohydrodynamic (MHD), multi-fluid, kinetic-MHD, and hybrid modeling frameworks. Finally, open issues relating to the physical relevance of so-called "croissant" models of the heliosphere, as well as the general (dis)agreement of model predictions with observations are highlighted and critically discussed

IDOMAL: an ontology for malaria

<p>Abstract</p> <p>Background</p> <p>Ontologies are rapidly becoming a necessity for the design of efficient information technology tools, especially databases, because they permit the organization of stored data using logical rules and defined terms that are understood by both humans and machines. This has as consequence both an enhanced usage and interoperability of databases and related resources. It is hoped that IDOMAL, the ontology of malaria will prove a valuable instrument when implemented in both malaria research and control measures.</p> <p>Methods</p> <p>The OBOEdit2 software was used for the construction of the ontology. IDOMAL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.</p> <p>Results</p> <p>The first version of the malaria ontology covers both clinical and epidemiological aspects of the disease, as well as disease and vector biology. IDOMAL is meant to later become the nucleation site for a much larger ontology of vector borne diseases, which will itself be an extension of a large ontology of infectious diseases (IDO). The latter is currently being developed in the frame of a large international collaborative effort.</p> <p>Conclusions</p> <p>IDOMAL, already freely available in its first version, will form part of a suite of ontologies that will be used to drive IT tools and databases specifically constructed to help control malaria and, later, other vector-borne diseases. This suite already consists of the ontology described here as well as the one on insecticide resistance that has been available for some time. Additional components are being developed and introduced into IDOMAL.</p