cPath: open source software for collecting, storing, and querying biological pathways

BACKGROUND: Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. RESULTS: We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. CONCLUSION: cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling

The Impact of Venous Thromboembolism on Risk of Death or Hemorrhage in Older Cancer Patients

BACKGROUND: Among older cancer patients, there is uncertainty about the degree to which venous thromboembolism (VTE) and its treatment increase the risk of death or major hemorrhage. OBJECTIVE: To determine the prevalence of VTE in a cohort of older cancer patients, as well as the degree to which VTE increased the risk of death or major hemorrhage. METHODS: We conducted a retrospective cohort study of linked Surveillance, Epidemiology, and End Results cancer registry and Medicare administrative claims data. Patients with any of ten invasive cancers diagnosed during 1995 through 1999 were included; the independent variable was VTE diagnosed concomitantly with cancer diagnosis. Outcomes included major hemorrhage during the first year after cancer diagnosis and all-cause mortality; RESULTS: Overall, about 1% of patients who were diagnosed with cancer also had a VTE diagnosed concomitantly. After adjusting for sociodemographic factors and cancer stage and grade, concomitant VTE was associated with a relative increase in the risk of death for 8 of the 10 cancer types; the increase in risk tended to range 20–40% across most cancer types. Approximately 16.8% (95% confidence interval [CI] 14.9–18.8%) of patients with a concomitant VTE and 7.9% (95% CI 7.7–8.0%) of patients without a VTE experienced a major hemorrhage during the year after cancer diagnosis (P value <.001). The excess risk of hemorrhage associated with VTE varied substantially across cancer types, ranging from no significant excess (kidney and uterine cancer) to 11.5% (lymphoma). CONCLUSION: Concomitant VTE is not only a marker and potential mediator of increased risk of death among older cancer patients, but patients with a VTE have a marked increased risk of major hemorrhage

Bioavailability in soils

The consumption of locally-produced vegetables by humans may be an important exposure pathway for soil contaminants in many urban settings and for agricultural land use. Hence, prediction of metal and metalloid uptake by vegetables from contaminated soils is an important part of the Human Health Risk Assessment procedure. The behaviour of metals (cadmium, chromium, cobalt, copper, mercury, molybdenum, nickel, lead and zinc) and metalloids (arsenic, boron and selenium) in contaminated soils depends to a large extent on the intrinsic charge, valence and speciation of the contaminant ion, and soil properties such as pH, redox status and contents of clay and/or organic matter. However, chemistry and behaviour of the contaminant in soil alone cannot predict soil-to-plant transfer. Root uptake, root selectivity, ion interactions, rhizosphere processes, leaf uptake from the atmosphere, and plant partitioning are important processes that ultimately govern the accumulation ofmetals and metalloids in edible vegetable tissues. Mechanistic models to accurately describe all these processes have not yet been developed, let alone validated under field conditions. Hence, to estimate risks by vegetable consumption, empirical models have been used to correlate concentrations of metals and metalloids in contaminated soils, soil physico-chemical characteristics, and concentrations of elements in vegetable tissues. These models should only be used within the bounds of their calibration, and often need to be re-calibrated or validated using local soil and environmental conditions on a regional or site-specific basis.Mike J. McLaughlin, Erik Smolders, Fien Degryse, and Rene Rietr

e-Science and biological pathway semantics

<p>Abstract</p> <p>Background</p> <p>The development of e-Science presents a major set of opportunities and challenges for the future progress of biological and life scientific research. Major new tools are required and corresponding demands are placed on the high-throughput data generated and used in these processes. Nowhere is the demand greater than in the semantic integration of these data. Semantic Web tools and technologies afford the chance to achieve this semantic integration. Since pathway knowledge is central to much of the scientific research today it is a good test-bed for semantic integration. Within the context of biological pathways, the BioPAX initiative, part of a broader movement towards the standardization and integration of life science databases, forms a necessary prerequisite for its successful application of e-Science in health care and life science research. This paper examines whether BioPAX, an effort to overcome the barrier of disparate and heterogeneous pathway data sources, addresses the needs of e-Science.</p> <p>Results</p> <p>We demonstrate how BioPAX pathway data can be used to ask and answer some useful biological questions. We find that BioPAX comes close to meeting a broad range of e-Science needs, but certain semantic weaknesses mean that these goals are missed. We make a series of recommendations for re-modeling some aspects of BioPAX to better meet these needs.</p> <p>Conclusion</p> <p>Once these semantic weaknesses are addressed, it will be possible to integrate pathway information in a manner that would be useful in e-Science.</p

Gender differences in the utilization of health-care services among the older adult population of Spain

BACKGROUND: Compared to men, women report greater morbidity and make greater use of health-care services. This study examines potential determinants of gender differences in the utilization of health-care services among the elderly. METHODS: Cross-sectional study covering 3030 subjects, representative of the non-institutionalized Spanish population aged 60 years and over. Potential determinants of gender differences in the utilization of health services were classified into predisposing factors (age and head-of-family status), need factors (lifestyles, chronic diseases, functional status, cognitive deficit and health-related quality of life (HRQL)) and enabling factors (educational level, marital status, head-of-family employment status and social network). Relative differences in the use of each service between women and men were summarized using odds ratios (OR), obtained from logistic regression. The contribution of the variables of interest to the gender differences in the use of such services was evaluated by comparing the OR before and after adjustment for such variables. RESULTS: As compared to men, a higher percentage of women visited a medical practitioner (OR: 1.24; 95% confidence limits (CL): 1.07–1.44), received home medical visits (OR: 1.67; 95% CL: 1.34–2.10) and took ≥3 medications (OR: 1.54; 95% CL: 1.34–1.79), but there were no gender differences in hospital admission or influenza vaccination. Adjustment for need or enabling factors led to a reduction in the OR of women compared to men for utilization of a number of services studied. On adjusting for the number of chronic diseases, the OR (95% CL) of women versus men for ingestion of ≥3 medications was 1.24 (1.06–1.45). After adjustment for HRQL, the OR was 1.03 (0.89–1.21) for visits to medical practitioners, 1.24 (0.98–1.58) for home medical visits, 0.71 (0.58–0.87) for hospitalization, and 1.14 (0.97–1.33) for intake of ≥3 medications. After adjustment for the number of chronic diseases and HRQL, the OR of hospitalization among women versus men was 0.68 (0.56–0.84). CONCLUSION: The factors that best explain the greater utilization of health-care services by elderly women versus men are the number of chronic diseases and HRQL. For equal need, certain inequality was observed in hospital admission, in that it proved less frequent among women

Forest landscape ecology and global change: an introduction

Forest landscape ecology examines broad-scale patterns and processes and their interactions in forested systems and informs the management of these ecosystems. Beyond being among the richest and the most complex terrestrial systems, forest landscapes serve society by providing an array of products and services and, if managed properly, can do so sustainably. In this chapter, we provide an overview of the field of forest landscape ecology, including major historical and present topics of research, approaches, scales, and applications, particularly those concerning edges, fragmentation, connectivity, disturbance, and biodiversity. In addition, we discuss causes of change in forest landscapes, particularly land-use and management changes, and the expected structural and functional consequences that may result from these drivers. This chapter is intended to set the context and provide an overview for the remainder of the book and poses a broad set of questions related to forest landscape ecology and global change that need answers

The genome of the emerging barley pathogen Ramularia collo-cygni

Background Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph

Chromo- and Fluorogenic Organometallic Sensors

Compounds that change their absorption and/or emission properties in the presence of a target ion or molecule have been studied for many years as the basis for optical sensing. Within this group of compounds, a variety of organometallic complexes have been proposed for the detection of a wide range of analytes such as cations (including H+), anions, gases (e.g. O 2, SO2, organic vapours), small organic molecules, and large biomolecules (e.g. proteins, DNA). This chapter focuses on work reported within the last few years in the area of organometallic sensors. Some of the most extensively studied systems incorporate metal moieties with intense long-lived metal-to-ligand charge transfer (MLCT) excited states as the reporter or indicator unit, such as fac-tricarbonyl Re(I) complexes, cyclometallated Ir(III) species, and diimine Ru(II) or Os(II) derivatives. Other commonly used organometallic sensors are based on Pt-alkynyls and ferrocene fragments. To these reporters, an appropriate recognition or analyte-binding unit is usually attached so that a detectable modification on the colour and/or the emission of the complex occurs upon binding of the analyte. Examples of recognition sites include macrocycles for the binding of cations, H-bonding units selective to specific anions, and DNA intercalating fragments. A different approach is used for the detection of some gases or vapours, where the sensor's response is associated with changes in the crystal packing of the complex on absorption of the gas, or to direct coordination of the analyte to the metal centre