Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

Gastric necrosis: A rare complication of chloral hydrate intoxication

A rare complication of chloral hydrate intoxication is described. Added to the initial acute cardiorespiratory and central nervous system depression, subsequent gastric necrosis and perforation provided a difficult problem in management. A satisfactory outcome was finally achieved using the Roux-en-Y technique to by-pass the stricture at the oesophagogastric anastomosis.

Surviving heat shock: control strategies for robustness and performance

Molecular biology studies the cause-and-effect relationships among microscopic processes initiated by individual molecules within a cell and observes their macroscopic phenotypic effects on cells and organisms. These studies provide a wealth of information about the underlying networks and pathways responsible for the basic functionality and robustness of biological systems. At the same time, these studies create exciting opportunities for the development of quantitative and predictive models that connect the mechanism to its phenotype then examine various modular structures and the range of their dynamical behavior. The use of such models enables a deeper understanding of the design principles underlying biological organization and makes their reverse engineering and manipulation both possible and tractable The heat shock response presents an interesting mechanism where such an endeavor is possible. Using a model of heat shock, we extract the design motifs in the system and justify their existence in terms of various performance objectives. We also offer a modular decomposition that parallels that of traditional engineering control architectures.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

MOTIVATION

Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively.

RESULTS

We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.

AVAILABILITY

The specification of SBML Level 1 is freely available from http://www.sbml.org/

Oxygen-mediated regulation of skeletal muscle satellite cell proliferation and adipogenesis in culture

Major problems in stem cell biology revolve around defining the developmental potential of cell populations and understanding how their potential is maintained or progressively restricted. Oxygen (O(2)) is an obvious environmental factor which has received little attention in culturing skeletal muscle progenitor cells. In this work, we examine the effects of O(2) levels on the developmental potential, proliferative capacity, and phenotype of the adult skeletal muscle fiber progenitor population (satellite cells), and cell lines that model multipotential embryonic paraxial mesoderm from which skeletal muscle develops. Both satellite cell proliferation and survival of mature fibers increased in physiologic (6%) O(2) vs. non-physiologic 20% O(2) used in virtually all traditional cell culture. Six percent O(2) conditions also accelerated the up-regulation of multiple MyoD family myogenic regulatory factors (MRFs). An unexpected finding was that fiber-adherent satellite cells could assume a non-myogenic phenotype. By the criteria of molecular markers and gross lipid accumulation, satellite cells were found to assume an adipocyte phenotype, and did so more prominently in 20% O(2) than in physiologic O(2). Selection of the adipogenic fate and execution of adipogenesis by multipotential mesenchymal cell lines was also dramatically higher in traditional 20 vs. 6% O(2), and decreased adipogenesis in physiologic O(2) was associated with significantly less expression of the adipogenic regulator, PPAR gamma. These results suggest that regulatory pathways affected by O(2) are important for satellite cell proliferation, execution of cell fate, and parent muscle survival in culture, and so may play a role in vivo under normal or pathologic conditions.

Prescribing of ACE inhibitors for cardiovascular disorders in general practice

OBJECTIVE

To investigate the prescribing patterns for angiotensin converting enzyme (ACE) inhibitors in the management of patients with heart failure and other cardiovascular disorders as part of a local project on heart failure using information collected from a Primary Care Information Initiative.

METHOD

Patients from a large city-centre practice, who were receiving an ACE inhibitor or with a diagnosis of heart failure at the time of the study, were identified from medical records. Details of concomitant medical conditions and drug treatment were also recorded.

RESULTS

There was extensive prescribing of ACE inhibitors alone, in the treatment of patients with hypertension, where no contraindications for the use of thiazide diuretics or beta-blockers could be identified. ACE inhibitors were being prescribed for post-myocardial infarction patients, but the time for the initiation of treatment was rarely within that recommended in the literature. For those patients diagnosed with heart failure, 60% were not being treated with ACE inhibitors even where there were no contraindications.

CONCLUSION

It is clear from the results of this study that overall prescribing patterns for ACE inhibitors are not always in accord with evidence from the literature. These findings provide valuable information for the initiation and development of clinical guidelines for prescribers.

Carotid stenosis and perioperative stroke risk in symptomatic and asymptomatic patients undergoing vascular or coronary surgery

BACKGROUND AND PURPOSE

The management of asymptomatic carotid stenosis found before vascular or coronary surgery is unclear from the literature. We aimed to define the relation of carotid stenosis to perioperative stroke in all patients, symptomatic and asymptomatic, and so determine a policy for the management of asymptomatic carotid stenosis in patients requiring major surgery.

METHODS

We conducted a prospective clinical and Duplex ultrasound study of 358 consecutive noncarotid major vascular or coronary artery bypass operations, with a moratorium on endarterectomy for asymptomatic carotid stenosis.

RESULTS

There were 145 vascular and 213 coronary bypass operations. Ten of the 49 cases with prior symptoms of cerebral ischemia (38 carotid, 11 vertebrobasilar) had symptomatic stenosis of 50% or greater or occlusion, and 3 of these (30%) had ipsilateral perioperative cerebral infarction (95% confidence interval, 6.67% to 65.25%). Two of these occurred ipsilateral to symptomatic carotid occlusions, and 1 occurred ipsilateral to an 80% symptomatic stenosis. One symptomatic patient with bilateral 30% stenosis had a perioperative infarct in the asymptomatic hemisphere. Among the 309 asymptomatic patients, 1 perioperative infarct occurred ipsilateral to carotid stenosis of 30%. In all there were 5 (1.4%) perioperative (within 72 hours) and 2 late (after 18 days) strokes. All strokes were hemisphere infarcts confirmed by computed tomography. There were 53 cases with 50% or greater asymptomatic carotid stenosis or occlusion, including 28 with 80% or greater stenosis or occlusion. None had an ipsilateral perioperative stroke (95% confidence interval, 0% to 6.72%).

CONCLUSIONS

We conclude that the risk of perioperative stroke related to symptomatic carotid stenosis may be high, but for asymptomatic carotid stenosis the risk is low and does not justify preoperative prophylactic carotid endarterectomy.

Influence of mineral supplementation on bovine serum, liver and endometrium at Day 1 and Day 12 of the estrous cycle

The effects of diet on mineral concentrations in serum, liver and endometrium were determined at points in the reproductive cycle in heifers. Dietary treatments extended 134 d and included feeding a basal hay (negative control), basal hay with concentrate (feed control), feed control with phosphorus and feed control with both phosphorus and trace minerals. Samples of serum and liver were taken at the beginning and end of the trial. Within an estrous cycle during the trial (endometrial biopsy) the cows were sampled either at Day 1 or Day 12 for determining progesterone levels and mineral elements in the blood, liver and endometrial tissue. Trace element concentrations in serum and liver did not differ among collection periods pretrial, endometrial biopsy and post breeding nor among treatment groups. However, endometrial tissue concentrations of copper, manganese and zinc were higher at Day 1 than at Day 12 (P < 0.05) in reverse of serum progesterone, which was higher at Day 12 (P < 0.05). Supplemental trace minerals appeared to increase concentrations of copper (P < 0.20), manganese (P < 0.10) and zinc (P < 0.20) at Day 1 but decrease concentrations of these same elements at Day 12 (P < 0.05, P < 0.10 and P < 0.05, respectively). The large differences in trace element concentrations observed in endometrial tissue at the estral phases and under different diets suggest the possible importance of trace elements and trace element nutrition in fertilization and (or) embryo survival.

Vascular trauma at a university teaching hospital

Fifty-two patients with vascular trauma have been managed by the St Vincent's Hospital Vascular Surgical Unit during the 5 year period 1982-86. The mean age of the patients was 39.7 years; 81% were male. Penetrating, blunt and iatrogenic trauma were equally represented. Forty-nine of the patients underwent 63 operations performed by members of the unit. Twenty-five of the patients had significant non-vascular injuries, requiring 29 other operations. Pre-operative angiography was used rarely in urgent cases. All vascular reconstructions were noted to be patent during the follow-up period, with a mean of 20 months, except in one instance, where an amputation resulted from failed surgery. One patient died from a complication of the vascular surgery.

Human neuroelectric patterns predict performance accuracy

In seven right-handed adults, the brain electrical patterns before accurate performance differed from the patterns before inaccurate performance. Activity overlying the left frontal cortex and the motor and parietal cortices contralateral to the performing hand preceded accurate left- or right-hand performance. Additional strong activity overlying midline motor and premotor cortices preceded left-hand performance. These measurements suggest that brief, spatially distributed neural activity patterns, or "preparatory sets," in distinct cognitive, somesthetic-motor, and integrative motor areas of the human brain may be essential precursors of accurate visuomotor performance.

Improved event-related potential estimation using statistical pattern classification

A new method of ERP estimation with minimal statistical assumptions is presented. A mathematical pattern classification procedure is used to select trials with discriminable event-related signals in a time interval of interest. A method of forming a reference 'baseline' is also presented. Stimulus-registered and response-registered 'enhanced' ERP averages computed from selected trials of a visuo-motor experiment show substantial enhancement of event-related signals, especially for channels with weak signals, while rejected trials have minimal event-related signals.

Shadows of thought: shifting lateralization of human brain electrical patterns during brief visuomotor task

Dynamic spatial patterns of correlation of electrical potentials recorded from the human brain were shown in diagrams generated by mathematical pattern recognition. The patterns for "move" and "no-move" variants of a brief visuospatial task were compared. In the interval spanning the P300 peak of the evoked potential, higher correlations of the right parietal electrode with occipital and central electrodes distinguished the no-move task from the move task. In the next interval, spanning the readiness potential in the move task, higher correlations of the left central electrode with occipital and frontal electrodes characterized the move task. These results conform to neuropsychological expectations of localized processing and their temporal sequence. The rapid change in the side and site of localized processes may account for conflicting reports of lateralization in studies which lacked adequate spatial and temporal resolution.

Electrical potentials in human brain during cognition: new method reveals dynamic patterns of correlation

A new technique has been developed for identifying, in humans, dynamic spatiotemporal electrical patterns of the brain during purposive behaviors. In this method, single-trial time-series correlations between brain macropotentials recorded from different scalp sites are analyzed by distribution-independent mathematical pattern recognition. Dynamic patterns of correlation clearly distinguished two brief visuomotor tasks differing only in type of mental judgement required (spatial or numeric). These complex patterns shifted in the anterior-posterior and left-right axes between successive 175-millisecond intervals, indicating that many areas in both cerebral hemispheres were involved even in these simple judgements. These patterns were not obtainable by conventional analysis of averaged evoked potentials or by linear analysis of correlations, suggesting that the new technique will advance the study of human brain activity related to cognition and goal-directed behaviors.

The vascular complications of cervical rib

The consequences of cervical rib do not appear to be widely understood. Whilst most cervical ribs cause little or no trouble, and, at the most, require shoulder raising exercises, some are the cause of serious nerve compression and sometimes arterial compression. Much confusion has existed in the understanding of the vascular manifestations of cervical rib, and this confusion has often led to incorrect treatment with serious consequences. In this regard it is particularly important for the surgeon to deal with the diseased artery at the same time as the cervical rib is excised. Nine cases of cervical rib with arterial compression are reported. The importance of recognition of arterial compression, before surgery is undertaken, is stressed.

EEG patterns during 'cognitive' tasks. II. Analysis of controlled tasks

This experiment was designed to distinguish possible EEG correlates of the cognitive components of tasks from EEG patterns associated with stimulus characteristics, limb and eye movements, and performance-related factors such as subjects' ability and effort. Thirty-two right-handed adults each performed 30 trials, lasting 6-15 sec each, of four simplified, controlled tasks: mental rotation of geometric forms, serial addition of a column of signed digits, substitution of letters with subsequent word recognition and visual fixation. The first three tasks could not be differentiated from each other. Each of these tasks could be differentiated from visual fixation by approximately 10% generalized reductions in alpha and beta band intensities, and slight increases in theta band intensities frontally and occipitally. We conclude that the EEG patterns which differentiated the complex tasks described in Part I were due to inter-task differences in stimulus characteristics, efferent activities and/or performance-related factors, rather than to cognitive differences. With these controls, no evidence for lateralization of different types of cognitive activity was found in the EEG.

EEG patterns during 'cognitive' tasks. I. Methodology and analysis of complex behaviors

This paper presents a methodology which uses nonlinear pattern recognition to study the spatial distribution of EEG patterns accompanying higher cortical functions. The multivariate decision rules reveal the essential EEG patterns which differentiate performance of two tasks. Cross-validation classification accuracy measures the generality of the findings. Using this method, EEG patterns were derived from a group of 23 adults during performance of several complex tasks, including Koh's block design, writing sentences, mental paper folding, and reading silently. These patterns discriminate between the tasks, are consistent with, and extend the results of, visual EEG interpretations and univariate analysis of spectral intensities. Since writing sentences could not be distinguished from mere scribbling, it is unclear whether the EEG patterns found to distinguish complex behaviors were related to the cognitive components of tasks, or to sensory-motor and performance-related factors.

Electroencephalogram correlates of higher cortical functions

By means of two-stage, nonlinear multivariate pattern recognition, electroencephalograms (EEG's) were analyzed during performance of verbal and spatial tasks. Complex scalp distributions of theta-, beta-, and, to a lesser extent, alpha-band spectral intensities discriminated between the two members of a pair of tasks, such as writing sentences and Koh's block design. Small EEG asymmetries were probably attributable to limb movements and other uncontrolled noncognitive aspects of tasks. Significant EEG differences beteeen cognitive tasks were eliminated when controls for inter-task differences in efferent activity, stimulus characteristics, and performance-related factors were introduced. Each controlled task was associated with an approximately 10 percent reduction, as compared with visual fixation, in the magnitude of alpha- and beta-band spectral intensity. This effect occurred bilaterally and was approximately the same over occipital, parietal, and central regions, with some minor difference over the frontal region in the beta band. With these controls, no evidence for lateralization of different cognitive functions was found in the EEG.

Acute mesenteric ischaemia

The experience of acute mesenteric ischaemia at St Vincent's Hospital, Melbourne, has been reviewed over 17 years. The mortality remains appallingly high. This applies particularly to those patients who had thrombosis of the superior mesenteric artery, amongst whom the mortality in this series was 97%. The mortality was slightly less in the group suffering from embolic occlusion of the superior mesenteric artery (66%), and in those suffering from thrombosis of the superior mesenteric vein (60%). A mortality of 66% was also found in patients suffering from non-occlusive gut ischaemia. Delay in diagnosis accounted for this high mortality. Early diagnosis is all-important, and this depends on the performance of mesenteric angiography in any patient suspected of having mesenteric ischaemia. Appropriate surgery may then be carried out in the occlusive group and supportive treatment, including intraarterial papaverine infusion, given to those with non-occlusive ischaemia. There is a pressing need for simple non-invasive tests to segregate those patients suffering from acute mesenteric ischaemia from those whose acute abdomen is due to some other cause.

The Renal Handling of Dextran 40 by Surgical Patients

A study has been made of the renal handling of low molecular weight dextran (dextran 40) by surgical patients. In spite of the usual fall in glomerular filtration rate during surgery, high urine dextran concentrations may occur, with the formatin of highly viscous urine. In view of the possible association between high dextron concentrations and oliguric renal failure, precautions in its administration are suggested with particular emphasis on the maintenance of urine flow rates.

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