Agent-Based Modeling of Complex Molecular Systems

The seamless integration of laboratory experiments and detailed computational modeling provides an exciting route to uncovering many new insights into complex biological processes. In particular, the development of agent-based modeling using supercomputers has provided new opportunities for highly detailed, validated simulations that provide the researcher with greater understanding of these processes and new directions for investigation. This chapter examines some of the principles behind the powerful computational framework FLAME and its application in a number of different areas with a more detailed look at a particular signaling example involving the NF-κB cascade.

Indacaterol/glycopyrronium versus salmeterol/fluticasone in the prevention of clinically important deterioration in COPD: results from the FLAME study

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a progressive disease and a composite endpoint could be an indicator of treatment effect on disease worsening. This post-hoc analysis assessed whether indacaterol/glycopyrronium (IND/GLY) 110/50 μg once daily reduced the risk of clinically important deterioration (CID) versus salmeterol/fluticasone (SFC) 50/500 μg twice daily in moderate-to-very severe COPD patients from the FLAME study.

METHODS

CID was defined as ≥100 mL decrease in forced expiratory volume in 1 s (FEV1) or ≥ 4-unit increase in St. George's Respiratory Questionnaire (SGRQ) total score or a moderate-to-severe COPD exacerbation. Changes from baseline in the rate of moderate and severe exacerbations, time to first moderate-to-severe exacerbation, and change from baseline in the SGRQ score, measured after Week 12 up to Week 52, were assessed by presence of early CID (CID+) or absence of CID (CID-) at Week 12.

RESULTS

IND/GLY significantly delayed the time to CID (hazard ratio [HR] (95% confidence interval [CI]), 0.72 [0.67-0.78]; P < 0.0001), and reduced the incidences of CID versus SFC. Additionally, IND/GLY delayed the time to CID in all patient subgroups. After 12 weeks until 52 weeks, CID+ patients had a significantly higher rate of moderate-to-severe exacerbations versus CID- patients (P < 0.0001); moreover, CID+ patients experienced moderate-to-severe exacerbations significantly earlier versus CID- patients (P < 0.0001). CID+ patients had a comparable change in the SGRQ total score versus CID- patients.

CONCLUSIONS

IND/GLY reduced the risk of CID versus SFC. CID had a significant impact on long-term exacerbation outcomes in patients with moderate-to-very severe COPD and a history of ≥1 exacerbations in the previous year.

TRIAL REGISTRATION

Clinicaltrials.gov NCT01782326 .

Contouring of prostate tumors on multiparametric MRI: Evaluation of clinical delineations in a multicenter radiotherapy trial

PURPOSE

To date no guidelines are available for contouring prostate cancer inside the gland, as visible on multiparametric (mp-) MRI. We assessed inter-institutional differences in interpretation of mp-MRI in the multicenter phase III FLAME trial.

METHODS

We analyzed clinical delineations on mp-MRI and clinical characteristics from 260 patients across three institutes. We performed a logistic regression analysis to examine each institute's weighting of T2w, ADC and K^trans intensity maps in the delineation of the cancer. As reviewing of all delineations by an expert panel is not feasible, we made a selection based on discrepancies between a published tumor probability (TP) model and each institute's clinical delineations using Areas Under the ROC Curve (AUC) analysis.

RESULTS

Regression coefficients for the three institutes were -0.07, -0.27 and -0.11 for T2w, -1.96, -0.53 and -0.65 for ADC and 0.15, 0.20 and 0.62 for K^trans, with significant differences between institutes for ADC and K^trans. AUC analysis showed median AUC values of 0.92, 0.80 and 0.79. Five patients with lowest AUC values were reviewed by a uroradiologist.

CONCLUSION

Regression coefficients revealed considerably different interpretations of mp-MRI in tumor contouring between institutes and demonstrated the need for contouring guidelines. Based on AUC values outlying delineations could efficiently be identified for review.

Adult Stem Cell Therapies for Wound Healing: Biomaterials and Computational Models

The increased incidence of diabetes and tumors, associated with global demographic issues (aging and life styles), has pointed out the importance to develop new strategies for the effective management of skin wounds. Individuals affected by these diseases are in fact highly exposed to the risk of delayed healing of the injured tissue that typically leads to a pathological inflammatory state and consequently to chronic wounds. Therapies based on stem cells (SCs) have been proposed for the treatment of these wounds, thanks to the ability of SCs to self-renew and specifically differentiate in response to the target bimolecular environment. Here, we discuss how advanced biomedical devices can be developed by combining SCs with properly engineered biomaterials and computational models. Examples include composite skin substitutes and bioactive dressings with controlled porosity and surface topography for controlling the infiltration and differentiation of the cells. In this scenario, mathematical frameworks for the simulation of cell population growth can provide support for the design of bioconstructs, reducing the need of expensive, time-consuming, and ethically controversial animal experimentation.

Septicaemia in scald and flame burns: appraisal of significant differences

One hundred and sixty burn patients suffering from septicaemia, hospitalized in the Al-Babtain Centre burns unit, Kuwait, between June 1992 and May 2001, were studied. Thirty-two patients (20%) had scalds and 128 (80%) flame burns, thus representing a ratio of 1:4 among septicaemic patients. There were 20 males (62.5%) in the scald group, compared to 73 (57%) with flame burns. Flame burns were significantly higher (p &lt; 0.01) among non-Kuwaiti patients. The mean ages of the scald and flame burn patients were respectively 6.2 and 31.5 yr. The mean total body surface area burn in scalds was 20% and in flame burns 49%, which was significantly higher (p < 0.001). The 34 septicaemic episodes in 32 scald patients and 212 such episodes in 128 flame burn patients showed a significantly higher incidence in the latter group. The majority of septicaemic episodes, in scalds (82.4%) and flame burns (57.6%), were due to gram-positive organisms, mainly methicillin-resistant Staphylococcus aureus and methicillin-resistant Staphylococcus epidermidis. A significantly increased number of episodes were due to S. aureus (p < 0.001) and Enterococcus (p < 0.05) in scald patients. More surgical operations were performed in flame burn patients and survival increased significantly with an increasing number of grafting sessions (p < 0.001). The mean hospital stay in flame burn patients (56 days) was significantly higher than in scald patients (23 days) (p < 0.001). It is significant to record that all the 38 deaths (29.7%) were in flame burn septicaemic patients (p < 0.001). The scald and flame burn patients were quite distinct in their demographic and clinical characteristics. The flame burn patients were more vulnerable to septicaemia, with a high risk of mortality.