A combined model reduction algorithm for controlled biochemical systems

Background: Systems Biology continues to produce increasingly large models of complex biochemical reaction networks. In applications requiring, for example, parameter estimation, the use of agent-based modelling approaches, or real-time simulation, this growing model complexity can present a significant hurdle. Often, however, not all portions of a model are of equal interest in a given setting. In such situations methods of model reduction offer one possible approach for addressing the issue of complexity by seeking to eliminate those portions of a pathway that can be shown to have the least effect upon the properties of interest. Methods: In this paper a model reduction algorithm bringing together the complementary aspects of proper lumping and empirical balanced truncation is presented. Additional contributions include the development of a criterion for the selection of state-variable elimination via conservation analysis and use of an ‘averaged’ lumping inverse. This combined algorithm is highly automatable and of particular applicability in the context of ‘controlled’ biochemical networks. Results: The algorithm is demonstrated here via application to two examples; an 11 dimensional model of bacterial chemotaxis in Escherichia coli and a 99 dimensional model of extracellular regulatory kinase activation (ERK) mediated via the epidermal growth factor (EGF) and nerve growth factor (NGF) receptor pathways. In the case of the chemotaxis model the algorithm was able to reduce the model to 2 state-variables producing a maximal relative error between the dynamics of the original and reduced models of only 2.8% whilst yielding a 26 fold speed up in simulation time. For the ERK activation model the algorithm was able to reduce the system to 7 state-variables, incurring a maximal relative error of 4.8%, and producing an approximately 10 fold speed up in the rate of simulation. Indices of controllability and observability are additionally developed and demonstrated throughout the paper. These provide insight into the relative importance of individual reactants in mediating a biochemical system’s input-output response even for highly complex networks. Conclusions: Through application, this paper demonstrates that combined model reduction methods can produce a significant simplification of complex Systems Biology models whilst retaining a high degree of predictive accuracy. In particular, it is shown that by combining the methods of proper lumping and empirical balanced truncation it is often possible to produce more accurate reductions than can be obtained by the use of either method in isolation

Development and Validity of the Rating-of-Fatigue Scale

Objective: The purpose of these experiments was to develop a rating-of-fatigue (ROF) scale capable of tracking the intensity of perceived fatigue in a variety of contexts. Methods: Four experiments were carried out. The first provided the evidential basis for the construction of the ROF scale. The second tested the face validity of the ROF, and the third tested the convergent and divergent validity of the ROF scale during ramped cycling to exhaustion and 30 min of resting recovery. The final experiment tested the convergent validity of the ROF scale with time of day and physical activity (accelerometer counts) across a whole week. Results: Modal selections of descriptions and diagrams at different levels of exertion and recovery were found during Experiment 1 upon which the ROF scale was constructed and finalised. In Experiment 2, a high level of face validity was indicated, in that ROF was reported to represent fatigue rather than exertion. Descriptor and diagrammatic elements of ROF reportedly added to the coherence and ease of use of the scale. In Experiment 3, high convergence between ROF and various physiological measures were found during exercise and recovery (heart rate, blood lactate concentration, oxygen uptake, carbon dioxide production, respiratory exchange ratio and ventilation rate were all P < 0.001). During ramped cycling to exhaustion ROF and RPE did correspond (P < 0.0001) but not during recovery, demonstrating discriminant validity. Experiment 4 found ROF to correspond with waking time during each day (Mon–Sun all P < 0.0001) and with physical activity (accelerometer count) (Mon–Sun all P < 0.001). Conclusions: The ROF scale has good face validity and high levels of convergent validity during ramped cycling to exhaustion, resting recovery and daily living activities. The ROF scale has both theoretical and applied potential in understanding changes in fatigue in a variety of contexts

Randomised controlled trial of a psychiatric consultation model for treatment of common mental disorder in the occupational health setting

BACKGROUND: Common mental disorders are the most prevalent of all mental disorders, with the highest burden in terms of work absenteeism and utilization of health care services. Evidence-based treatments are available, but recognition and treatment could be improved, especially in the occupational health setting. The situation in this setting has recently changed in the Netherlands because of new legislation, which has resulted in reduced sickness absence. Severe mental disorder has now become one of the main causes of work absenteeism. Occupational physicians (OPs) are expected to take an active role in diagnosis and treatment, and seem to be in need of support for a new approach to handle cases of more complex mental disorders. Psychiatric consultation can be a collaborative care model to achieve this. METHODS/DESIGN: This is a two-armed cluster-randomized clinical trial, with randomization among OPs. Forty OPs in two big companies providing medical care for multiple companies will be randomized to either the intervention group, i.e. psychiatric consultation embedded in a training programme, or the control group, i.e. only training aimed at recognition and providing Care As Usual. 60 patients will be included who have been absent from work for 6–52 weeks and who, after screening and a MINI interview, are diagnosed with depressive disorder, anxiety disorder or somatoform disorder based on DSM-IV criteria. Baseline measurements and follow up measurements (at 3 months and 6 months) will be assessed with questionnaires and an interview. The primary outcome measure is level of general functioning according to the SF-20. Secondary measures are severity of the mental disorder according to the PHQ and the SCL-90, quality of life (EQ-D5), measures of Return To Work and cost-effectiveness of the treatment assessed with the TiC-P. Process measures will be adherence to the treatment plan and assessment of the treatment provided by the Psychiatric Consultant (PC) in both groups. DISCUSSION: In the current study, a psychiatric consultation model that has already proved to be effective in the primary care setting, and aimed to enhance evidence-based care for patients with work absenteeism and common mental disorder will be evaluated for its efficacy and cost-effectiveness in the occupational health setting

Maintenance of cross-sector partnerships: the role of frames in sustained collaboration

We examine the framing mechanisms used to maintain a cross-sector partnership (XSP) that was created to address a complex long-term social issue. We study the first eight years of existence of an XSP that aims to create a market for recycled phosphorus, a nutrient that is critical to crop growth but whose natural reserves have dwindled significantly. Drawing on 27 interviews and over 3,000 internal documents, we study the evolution of different frames used by diverse actors in an XSP. We demonstrate the role of framing in helping actors to avoid some of the common pitfalls for an XSP, such as debilitating conflict, and in creating sufficient common ground to sustain collaboration. As opposed to a commonly held assumption in the XSP literature, we find that collaboration in a partnership does not have to result in a unanimous agreement around a single or convergent frame regarding a contentious issue. Rather, successful collaboration between diverse partners can also be achieved by maintaining a productive tension between different frames through ‘optimal’ frame plurality – not excessive frame variety that may prevent agreements from emerging, but the retention of a select few frames and the deletion of others towards achieving a narrowing frame bandwidth. One managerial implication is that resources need not be focussed on reaching a unanimous agreement among all partners on a single mega-frame vis-à-vis a contentious issue, but can instead be used to kindle a sense of unity in diversity that allows sufficient common ground to emerge, despite the variety of actors and their positions

A prospective investigation of rumination and executive control in predicting overgeneral autobiographical memory in adolescence

The CaR-FA-X model (Williams et al., 2007), or capture and rumination (CaR), functional avoidance (FA) and impaired executive control (X), is a model of overgeneral autobiographical memory. Two mechanisms of the model, rumination and executive control were examined in isolation and in interaction to investigate overgeneral autobiographical memory over time. Method: Across two time points, six months apart, a total of 149 adolescents (13-16 years) completed a minimal instruction autobiographical memory test, a measure of executive control with emotional and non-emotional stimuli, and measures of brooding rumination and reflective pondering. Results: It was found that executive control for emotional information was negatively associated with OGM, but only when reflective pondering levels were high. Conclusion: In the context of higher levels of reflective pondering, greater switch costs (i.e. lower executive control) when processing emotional information predict a decrease in OGM over time

Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms

Rate variation in genes from all three genomes has been observed frequently in plant lineages with a parasitic and mycoheterotrophic mode of life. While the loss of photosynthetic ability leads to a relaxation of evolutionary constraints in genes involved in the photosynthetic apparatus, it remains to be determined how prevalent increased substitution rates are in nuclear DNA of non-photosynthetic angiosperms. In this study we infer rates of molecular evolution of 18S rDNA of all parasitic and mycoheterotorphic plant families (except Lauraceae and Polygalaceae) using relative rate tests. In several holoparasitic and mycoheterotrophic plant lineages extremely high substitution rates are observed compared to other photosynthetic angiosperms. The position and frequency of these substitutions have been identified to understand the mutation dynamics of 18S rRNA in achlorophyllous plants. Despite the presence of significantly elevated substitution rates, very few mutations occur in major functional and structural regions of the small ribosomal molecule, providing evidence that the efficiency of the translational apparatus in non-photosynthetic plants has not been affected

Simultaneous islet-kidney vs pancreas-kidney transplantation in type 1 diabetes mellitus: a 5 year single centre follow-up

AIMS/HYPOTHESIS: The aim of this study was to compare the long-term outcomes-in terms of glucose control, renal function and procedure-related complications-of simultaneous islet-kidney (SIK) transplantation with those of simultaneous pancreas-kidney (SPK) transplantation in patients with type 1 diabetes mellitus. METHODS: HbA(1c), need for insulin, GFR and complication rate were compared between 13 recipients of SIK and 25 recipients of SPK transplants at the same institution. The mean follow-up was 41 months. RESULTS: Two primary organ non-functions occurred in the SIK group. HbA(1c) did not differ at any time point during follow-up in the SIK group compared with the SPK group (mean during follow-up 6.3 vs 5.9%). Similarly, kidney function over time was not different between the two groups. A higher rate of insulin independence following SPK transplantation (after 1 year 96 vs 31% in the SIK group) was counterbalanced by a higher rate of serious adverse events (40% relaparotomies vs 0% in the SIK group). CONCLUSIONS/INTERPRETATION: The endogenous insulin production achieved by islet transplantation, combined with optimal insulin therapy, was sufficient for maintaining near-normal glucose levels. In terms of glucose control, islet transplantation provides results comparable to those achieved with pancreas transplantation. However, SPK results in a higher rate of insulin independence, albeit at the cost of more surgical complications. These results have led to a new paradigm in islet transplantation at our institution, where the primary goal is not insulin independence, but good glucose control and avoidance of severe hypoglycaemia