Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX

MOTIVATION: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. RESULTS: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.     

Computer-aided decision support in clinical medicine

This paper reviews the problems and prospects involved in providing computer-aided decision support in clinical medicine. First, the evaluation of medical innovation is discussed. It is suggested that there are three criteria by which an innovation may be judged, namely (1) a need for the innovation, (2) the ability of the innovation to fulfil that need and (3) the ability to do so without transgressing practical, ethical or legal boundaries. These problems are addressed in turn. The paper suggests, taking one area of clinical medicine as an example (acute abdominal pain) there is a clear need for decision support — since the area is not handled well by doctors in current practice. Evidence is adduced to suggest that the computer can provide decision support and do so without transgressing professional, ethical or legal boundaries. The obstacles to progress, which stand in the way of widespread implementation are briefly discussed. These are lack of medical terminology, poor man-machine interface and above all a lack of co-ordination. Finally, it is suggested that the most valuable facet of current systems is the discipline and precision in data collection they impose upon practicing doctors.     

Reciprocity of agonistic support in ravens

Cooperative behaviour through reciprocation or interchange of valuable services in primates has received considerable attention, especially regarding the timeframe of reciprocation and its ensuing cognitive implications. Much less, however, is known about reciprocity in other animals, particularly birds. We investigated patterns of agonistic support (defined as a third party intervening in an ongoing conflict to attack one of the conflict participants, thus supporting the other) in a group of 13 captive ravens, Corvus corax. We found support for long-term, but not short-term, reciprocation of agonistic support. Ravens were more likely to support individuals who preened them, kin and dominant group members. These results suggest that ravens do not reciprocate on a calculated tit-for-tat basis, but aid individuals from whom reciprocated support would be most useful and those with whom they share a good relationship. Additionally, dyadic levels of agonistic support and consolation (postconflict affiliation from a bystander to the victim) correlated strongly with each other, but we found no evidence to suggest that receiving agonistic support influences the victim's likelihood of receiving support (consolation) after the conflict ends. Our findings are consistent with an emotionally mediated form of reciprocity in ravens and provide additional support for convergent cognitive evolution in birds and mammals.     

Mechanical circulatory support

Currently, almost five million Americans and 23 million people worldwide are living with congestive heart failure (CHF), with 2 million new cases diagnosed each year. The etiology is mostly ischemic, idiopathic, or viral, and more than $36 billion is spent each year on the care of congestive heart failure patients. Treatment of advanced CHF takes three forms: medical therapy, surgical therapy and cardiac replacement. Medical therapy, including inotropes and vasodilators, relieves symptoms by reducing cardiac work and increasing myocardial contractility. This has helped improve quality of life, but mortality remains unaffected. Surgical therapy, including revascularization, ventricular restoration and valve replacement/repair, relieves symptoms and improves function, but in most cases does not stop the underlying disease process from progressing. When conventional medical or surgical therapies are exhausted, cardiac assist or replacement, including ventricular assist device (VAD), heart transplant or a total artificial heart (TAH) may become the only therapeutic options. This article will not discuss the use of extracorporeal membrane oxygenation for cardiac support that is described in an additional article in this issue of Organogenesis.     

Cercopithecid locomotion,support use,and support availability in the Tai Forest,Ivory Coast

Habitat heterogeneity is widely theorized to be important in the evolution of Old World monkeys, yet the impact of architecturally distinct forest types on the positional repertoires of African monkeys is largely unknown. As part of a wider project, this study investigates how the locomotor behavior of five sympatric cercopithecids varies in structurally distinct forest areas. Fieldwork took place in the Tai Forest, Ivory Coast, from June 1993 to August 1994. Data were collected on Colobus badius, C. polykomos, C. verus, Cercopithecus diana, and C. campbelli ranging throughout a common forest mosaic. The behavior of adult females was sampled using an instantaneous time point scheme at 3 min time intervals. Vegetative differences within each 100 × 100 m grid cell used by all species were quantified. Further, the relative numbers of different sized substrates at 10 m intervals within the canopy were recorded in each cell sampled. Data indicate that consistency of locomotor behavior across forest types is maintained because most monkeys select the same set of preferred supports in both forest types. The conservative nature of Tai monkey locomotor behavior is discussed within the context of additional proximate and ultimate influences and constraints. © 1996 Wiley-Liss, Inc.     

Enzyme immobilization in a biomimetic silica support

Robust immobilization techniques that preserve the activity of biomolecules have many potential applications. Silicates, primarily in the form of sol-gel composites or functionalized mesoporous silica, have been used to encapsulate a wide variety of biomolecules but the harsh conditions required for chemical synthesis limit their applicability. Silaffin polypeptides from diatoms catalyze the formation of silica in vitro at neutral pH and ambient temperature and pressure. Here we show that butyrylcholinesterase entrapped during the precipitation of silica nanospheres retained all of its activity. Ninety percent of the soluble enzyme was immobilized, and the immobilized enzyme was substantially more stable than the free enzyme. The mechanical properties of silica nanospheres facilitated application in a flow-through reactor. The use of biosilica for enzyme immobilization combines the excellent support properties of a silica matrix with a benign immobilization method that retains enzyme activity.     

Literature mining in support of drug discovery

The drug discovery enterprise provides strong drivers for data integration. While attention in this arena has tended to focus on integration of primary data from omics and other large platform technologies contributing to drug discovery and development, the scientific literature remains a major source of information valuable to pharmaceutical enterprises, and therefore tools for mining such data and integrating it with other sources are of vital interest and economic impact. This review provides a brief overview of approaches to literature mining as they relate to drug discovery, and offers an illustrative case study of a 'lightweight' approach we have implemented within an industrial context.     

Constructed wetlands support bats in agricultural landscapes

Bats are known to use aquatic habitats as foraging habitats. Agricultural intensification is perceived to be a main reason for the loss of wetlands. However, artificial wetland creation (i.e. the construction of retention-ponds) in the agricultural landscape aiming at water or nutrient retention has recently gained importance. We evaluated to what extent bats use these artificial wetlands as foraging habitats in an agricultural landscape.Bat activity and prey density were compared in matched pairs at retention-ponds and neighbouring vineyard sites using stationary bat-detectors and sticky-traps, respectively. To examine if bat activity is related to the number of bat individuals, a thermal infrared imaging camera was used. Pipistrellus pipistrellus, the dominant species, served as an example to assess habitat selection between retention-ponds and vineyards. This was performed by relating foraging activity to the available area available within the potential home-range.Total bat activity and nocturnal prey density were significantly higher above the retention-ponds than above vineyards. High differences of activity levels between the ponds and the respective vineyard sites were found for Pipistrellus spp. (P. pipistrellus and P. nathusii) and Myotis spp. (M. daubentonii and M. mystacinus), being about 180 times and 50 times higher above the retention-ponds, respectively. A significant correlation was found between recorded bat activity and the maximum number of bat individuals observed with a thermal infrared imaging camera. When relating foraging activity to habitat availability within the assumed home-range of P. pipistrellus, retention-ponds had on average a higher importance as a foraging habitat than the complete vineyard area although they covered less than 0.1% of its area.This study indicates that artificial wetlands such as retention-ponds provide foraging habitats for bats. Therefore, creation of wetlands in intensively used agricultural landscapes benefits bats.