Lung function decline in 4-monthly repeated spirometric measurements: Due to silt aerosol exposure or decreasing effort?

Background: Workers on dredgers and lighters on rivers are exposed to the inhalation of aerosols and dusts. Objective: The aim of this study was to investigate effects of river silt aerosol and dust exposure on the respiratory health of dredging employees. Methods: Six era mi nations were performed over a period of 2 years at 4-monthly intervals in 54 seamen with higher silt aerosol exposure and 36 controls of the same employer. Results: No significant differences could be observed between the groups at any time of the study but there was an unexpected significant decrease in the age-corrected expiratory vital capacity (FVC), forced expiratory volume in 1 s (FEV1) and midexpiratory flow rate (MMEF25/75) over the six series in both groups. This may indicate a loss of effort of the participants in re-examinations since biological and technical influences were highly unlikely to be the cause of these findings. Conclusions: Ignoring this possible decline of effort in frequently repeated measurements may result in overestimating potential effects of occupational exposure. Copyright (C) 2000 S. Karger AG, Basel

A new dynamical layout algorithm for complex biochemical reaction networks

BACKGROUND: To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every kind of pathway in biochemical research. This is mainly due to certain conventions to which biochemists/biologists are used to and which are not in accordance to conventional layout algorithms. A number of approaches has been developed to improve this situation. Some of these are used in the context of biochemical databases and make more or less use of the information in these databases to aid the layout process. However, visualisation becomes also more and more important in modelling and simulation tools which mostly do not offer additional connections to databases. Therefore, layout algorithms used in these tools have to work independently of any databases. In addition, all of the existing algorithms face some limitations with respect to the number of edge crossings when it comes to larger biochemical systems due to the interconnectivity of these. Last but not least, in some cases, biochemical conventions are not met properly. RESULTS: Out of these reasons we have developed a new algorithm which tackles these problems by reducing the number of edge crossings in complex systems, taking further biological conventions into account to identify and visualise cycles. Furthermore the algorithm is independent from database information in order to be easily adopted in any application. It can also be tested as part of the SimWiz package (free to download for academic users at [1]). CONCLUSION: The new algorithm reduces the complexity of pathways, as well as edge crossings and edge length in the resulting graphical representation. It also considers existing and further biological conventions to create a drawing most biochemists are familiar with. A lot of examples can be found on [2]

Systems Biology Graphical Notation: Process Diagram Level 1

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps

The NetBuilder project: development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks

Original paper can be found at: http://www.biomedcentral.com/bmcsystbiol/archive --DOI : 10.1186/1752-0509-1-S1-P72Peer reviewe