Simulation and optimization of dynamic flux balance analysis models using an interior point method reformulation

This work presents a novel, differentiable, way of solving dynamic Flux Balance Analysis (dFBA) problems by embedding flux balance analysis of metabolic network models within lumped bulk kinetics for biochemical processes. The proposed methodology utilizes transformation of the bounds of the embedded linear programming problem of flux balance analysis via a logarithmic barrier (interior point) approach. By exploiting the first-order optimality conditions of the interior-point problem, and with further transformations, the approach results in a system of implicit ordinary differential equations. Results from four case studies, show that the CPU and wall-times obtained using the proposed method are competitive with existing state-of-the-art approaches for solving dFBA simulations, for problem sizes up to genome-scale. The differentiability of the proposed approach allows, using existing commercial packages, its application to the optimal control of dFBA problems at a genome-scale size, thus outperforming existing formulations as shown by two dynamic optimization case studies.• R. Conejeros would like to thank CONICYT’s research grant FONDECYT 1151295 for funding this research. • F. Scott gratefully acknowledges financial support from CONICYT (Proyectos REDES ETAPA INICIAL, Convocatoria 2017, REDI170254)

Errata: Heat exchanger network cleaning scheduling: From optimal control to mixed-integer decision making

Errata to the article by Al Ismaili et al. [1], on the optimal scheduling of cleaning actions for Heat Exchanger Networks under fouling, are presented. Errors present in the equations of the Pontryagin Minimum Principle analysis of the original article are indicated and rectified. It is noted that despite these errors, there is no change to the conclusions of the analysis given in Al Ismaili et al. [1]

Optimisation of heat exchanger network cleaning schedules: incorporating uncertainty in fouling and cleaning model parameters

The optimisation of the cleaning schedule in heat exchanger networks (HENs) subject to fouling is presented in which the impact of parametric uncertainty is considered. This work is based on the realisation that these HEN cleaning scheduling problems are multistage mixed-integer optimal control problems (MIOCPs) in which the controls, i.e. cleaning actions, exhibit bang-bang behaviour as they occur linearly in the system equations. A multiple scenario feasible path MIOCP approach is proposed, whereby many scenarios of the HEN multiperiod problem are stacked, sharing the same control actions. This is implemented on a 10 unit and a 25 unit HEN case studies representing crude oil refinery preheat trains (PHTs). Results show that there is a large difference in financial performance for the deterministic case versus the parametric uncertainty problem and hence it is vital that uncertainty be taken into account during the optimisation of schedules for HEN maintenance problems.This research was supported by the Ministry of Higher Education in the Sultanate of Oman and Petroleum Development Oman (PDO)

Validation tools: can they indicate the information content of macromolecular crystal structures?

AbstractThe explosive increase in the number of published three-dimensionsal structures of macromolecules determined by X-ray analysis places a responsibility on experimentalists, referees and curators of databases to ensure correspondence between the structure parameters and data. Validation tools will evolve as more appropriate statistical techniques and new information, such as that from proteins analysed at atomic resolution, becomes available

St George's Respiratory Questionnaire Score Predicts Outcomes in Patients with COPD: Analysis of Individual Patient Data in the COPD Biomarkers Qualification Consortium Database.

Background: We aimed to estimate the usefulness of a disease specific health status measure, the St George's Respiratory Questionnaire (SGRQ), to predict outcomes in patients with chronic obstructive pulmonary disease (COPD). Methods: Individual patient-data of 12043 patients from long-term randomized clinical trials (2-4 years' duration) in the COPD Biomarkers Qualification Consortium database were analyzed. The adverse COPD outcomes were: exacerbations of COPD, hospital admissions due to exacerbation and all-cause mortality. Cox proportional hazards regression was used to calculate adjusted hazard ratios (HR) and 95% confidence intervals (CIs) for quartiles of SGRQ scores at baseline and time to first event, and time from first to second event, where appropriate. Results: The risk of adverse COPD outcomes increased with each increasing quartile of SGRQ score for all time to first event analyses. When comparing the lowest versus the highest quartile, the event risk (HRs [95% CIs]) increased by 40% for exacerbations (1.40 [1.29, 1.51]); 2-fold for hospital admissions (2.01 [1.78, 2.28]) and more than 2-fold for all-cause mortality (2.30 [1.91, 2.78]). For second event analyses in a subset of eligible patients, these trends persisted albeit with reduced risk estimates for exacerbations. Conclusions: Among patients with COPD, health status measured by a SGRQ score predicted exacerbations of COPD, hospital admissions due to exacerbations and their recurrence and death after adjustment. These data support the rationale for a health status measure use as a drug development tool and suggest that a health status measure may also have a role in risk assessment for COPD patients in routine medical care

Heat Exchanger Network Cleaning Scheduling: From Optimal Control to Mixed-Integer Decision Making

An approach for optimising the cleaning schedule in heat exchanger networks (HENs) subject to fouling is presented. This work focuses on HEN applications in crude oil preheat trains located in refineries. Previous approaches have focused on using mixed-integer nonlinear programming (MINLP) methods involving binary decision variables describing when and which unit to clean in a multi-period formulation. This work is based on the discovery that the HEN cleaning scheduling problem is in actuality a multistage optimal control problem (OCP), and further that cleaning actions are the controls which appear linearly in the system equations. The key feature is that these problems exhibit bang-bang behaviour, obviating the need for combinatorial optimisation methods. Several case studies are considered; ranging from a single unit up to 25 units. Results show that the feasible path approach adopted is stable and efficient in comparison to classical methods which sometimes suffer from failure in convergence.Support of this research by the Ministry of Higher Education in the Sultanate of Oman and Petroleum Development Oman (PDO) is gratefully acknowledged

Socioeconomic Status as a Determinant of Health Status Treatment Response in COPD Trials.

Background: Randomized controlled trials (RCTs) often recruit patients from low and high socioeconomic status (SES) countries, but little is known about the effect of SES on clinical outcomes, particularly patient-centered measures of symptomatic benefit. Methods: Combined individual chronic obstructive pulmonary disease (COPD) patient data from the placebo and long-acting bronchodilator arms of 17 RCTs (from the COPD Biomarkers Qualification Consortium database) were analyzed. Health status was measured using the St George's Respiratory Questionnaire (SGRQ) (minimum clinically important difference [MCID]: 4 units). Trials were grouped into short-term (≤12 months) and medium-term (>12 months to 48 months). A participant's country of residence was categorized into Low/Medium or High SES using World Health Organization criteria. Results: Data from 19765 individuals (6109 Low/Medium SES) were available. Patients in Low/Medium SES countries had more severe disease at baseline. Improvement in SGRQ score with placebo was ≈2 units greater in Low/Medium than in High SES countries; at its greatest, the improvement from baseline exceeded the MCID in Low/Medium countries. This difference was maintained for at least 1 year. Improvement with bronchodilator was also greater in Low/Medium versus High SES countries; overall there was no evidence that the treatment effect versus placebo was different between countries of different SES status. Conclusions: Participants in Low/Medium SES countries experienced significantly larger treatment effects, irrespective of treatment group (placebo and bronchodilator). Despite this, COPD patients in Low/Medium SES countries experienced a health status gain from long-acting bronchodilator treatment that is similar to that seen in High SES countries

The COPD Biomarkers Qualification Consortium Database: Baseline Characteristics of the St George's Respiratory Questionnaire Dataset.

The COPD Biomarkers Qualification Consortium (CBQC) is a public-private partnership formed in 2010 with a goal of qualifying biomarkers and clinical assessment tools for use in clinical or nonclinical decision-making and particularly within the regulatory context. The St George's Respiratory Questionnaire (SGRQ) is a measure of health-related quality of life widely used in clinical research. The aim of the CBQC working group on SGRQ was to construct an individual patient level database of clinical trial data that included the SGRQ, to use this to confirm the reliability and validity of the SGRQ as an outcome measure of health status, and investigate its use as a predictor of future events (exacerbations and mortality). This manuscript describes the formulation of the CBQC database and presents the baseline demographic and clinical characteristics of the integrated SGRQ database overall, and by study type (short-term [≤1 year], medium-term [2-4 years] and observational studies). Distribution of baseline SGRQ scores varied little by demographic determinants except for income region in the observational data set (low-middle income countries +10 units compared with high income, p<0.0001) and this observation held across studies. SGRQ scores increased with increasing modified Medical Research Council dyspnea scores (mean differences ranged 6.9-17.9 units) and with increasing airflow limitations (Global initiative for chronic Obstructive Lung Disease grades 1 to 4; differences ranged 4.5-16.1 units), consistent across study types. As a method of cross-sectional comparison, the SGRQ appears to be relatively free of bias from demographic factors although care should be taken when making cross sectional comparisons of scores between patients in countries at different levels of socio-economic development/

Interplay of quantum and classical fluctuations near quantum critical points

For a system near a quantum critical point (QCP), above its lower critical dimension $d_L$, there is in general a critical line of second order phase transitions that separates the broken symmetry phase at finite temperatures from the disordered phase. The phase transitions along this line are governed by thermal critical exponents that are different from those associated with the quantum critical point. We point out that, if the effective dimension of the QCP, $d_{eff}=d+z$ ($d$ is the Euclidean dimension of the system and $z$ the dynamic quantum critical exponent) is above its upper critical dimension $d_C$, there is an intermingle of classical (thermal) and quantum critical fluctuations near the QCP. This is due to the breakdown of the generalized scaling relation $\psi=\nu z$ between the shift exponent $\psi$ of the critical line and the crossover exponent $\nu z$, for $d+z>d_C$ by a \textit{dangerous irrelevant interaction}. This phenomenon has clear experimental consequences, like the suppression of the amplitude of classical critical fluctuations near the line of finite temperature phase transitions as the critical temperature is reduced approaching the QCP.Comment: 10 pages, 6 figures, to be published in Brazilian Journal of Physic

Electrophysiological Heterogeneity of Fast-Spiking Interneurons: Chandelier versus Basket Cells

In the prefrontal cortex, parvalbumin-positive inhibitory neurons play a prominent role in the neural circuitry that subserves working memory, and alterations in these neurons contribute to the pathophysiology of schizophrenia. Two morphologically distinct classes of parvalbumin neurons that target the perisomatic region of pyramidal neurons, chandelier cells (ChCs) and basket cells (BCs), are generally thought to have the same "fast-spiking" phenotype, which is characterized by a short action potential and high frequency firing without adaptation. However, findings from studies in different species suggest that certain electrophysiological membrane properties might differ between these two cell classes. In this study, we assessed the physiological heterogeneity of fast-spiking interneurons as a function of two factors: species (macaque monkey vs. rat) and morphology (chandelier vs. basket). We showed previously that electrophysiological membrane properties of BCs differ between these two species. Here, for the first time, we report differences in ChCs membrane properties between monkey and rat. We also found that a number of membrane properties differentiate ChCs from BCs. Some of these differences were species-independent (e.g., fast and medium afterhyperpolarization, firing frequency, and depolarizing sag), whereas the differences in the first spike latency between ChCs and BCs were species-specific. Our findings indicate that different combinations of electrophysiological membrane properties distinguish ChCs from BCs in rodents and primates. Such electrophysiological differences between ChCs and BCs likely contribute to their distinctive roles in cortical circuitry in each species. © 2013 Povysheva et al