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)

Constrained NLP via gradient flow penalty continuation: Towards self-tuning robust penalty schemes

This work presents a new numerical solution approach to nonlinear constrained optimization problems based on a gradient flow reformulation. The proposed solution schemes use self-tuning penalty parameters where the updating of the penalty parameter is directly embedded in the system of ODEs used in the reformulation, and its growth rate is linked to the violation of the constraints and variable bounds. The convergence properties of these schemes are analyzed, and it is shown that they converge to a local minimum asymptotically. Numerical experiments using a set of test problems, ranging from a few to several hundred variables, show that the proposed schemes are robust and converge to feasible points and local minima. Moreover, results suggest that the GF formulations were able to find the optimal solution to problems where conventional NLP solvers fail, and in less integration steps and time compared to a previously reported GF formulation

Clinical presentation, auscultation recordings, ultrasonographic findings and treatment response of 12 adult cattle with chronic suppurative pneumonia: case study

Auscultation is considered the critical component of the veterinary clinical examination for the diagnosis of bovine respiratory disease but the accuracy with which adventitious sounds reflect underlying lung pathology remains largely unproven. Modern portable ultrasound machines provide the veterinary practitioner with an inexpensive, non-invasive tool with which to examine the pleural surfaces and superficial lung parenchyma. Simultaneous recording of sounds overlying normal lung and defined pathology allows critical assessment of auscultated sounds in the same animal removing confounding factors such as respiratory rate and thickness of the chest wall (body condition). Twelve cows, referred to the University of Edinburgh Veterinary School, were diagnosed with chronic suppurative pneumonia and enrolled into this prospective study to record and monitor lung sounds, ultrasonographic findings, and response to a standardised antibiotic treatment regimen. Most cows (8/12) had a normal rectal temperature on presentation but all cows had received antibiotic therapy at some time in the previous two weeks and six animals were receiving antibiotic treatment upon admission. All cattle were tachypnoeic (>40 breaths per minute) with frequent and productive coughing, halitosis, and a purulent nasal discharge most noticeable when the head was lowered. Ultrasonographic examination of the chest readily identified pathological changes consistent with severe lung pathology subsequently confirmed as chronic suppurative pneumonia in four cows at necropsy; eight cows recovered well after antibiotic treatment and were discharged two to six weeks after admission. It proved difficult to differentiate increased audibility of normal lung sounds due to tachypnoea from wheezes; coarse crackles were not commonly heard. In general, sounds were reduced in volume over consolidated lung relative to normal lung tissue situated dorsally. Rumen contraction sounds were commonly transmitted over areas of lung pathology. Trueperella (formerly Arcanobacterium) pyogenes was isolated from three of four lung tissue samples at necrospy. Treatment with procaine penicillin for 42 consecutive days resulted in marked improvement with return to normal appetite and improvement in body condition in 8 of 12 cows (67%) where lesions did not extend more than 10-15 cm above the level of the olecranon on both sides of the chest

Homozygosity and risk of childhood death due to invasive bacterial disease.

BACKGROUND: Genetic heterozygosity is increasingly being shown to be a key predictor of fitness in natural populations, both through inbreeding depression, inbred individuals having low heterozygosity, and also through chance linkage between a marker and a gene under balancing selection. One important component of fitness that is often highlighted is resistance to parasites and other pathogens. However, the significance of equivalent loci in human populations remains unclear. Consequently, we performed a case-control study of fatal invasive bacterial disease in Kenyan children using a genome-wide screen with microsatellite markers. METHODS: 148 cases, comprising children aged <13 years who died of invasive bacterial disease, (variously, bacteraemia, bacterial meningitis or neonatal sepsis) and 137 age-matched, healthy children were sampled in a prospective study conducted at Kilifi District Hospital, Kenya. Samples were genotyped for 134 microsatellite markers using the ABI LD20 marker set and analysed for an association between homozygosity and mortality. RESULTS: At five markers homozygosity was strongly associated with mortality (odds ratio range 4.7 - 12.2) with evidence of interactions between some markers. Mortality was associated with different non-overlapping marker groups in Gram positive and Gram negative bacterial disease. Homozygosity at susceptibility markers was common (prevalence 19-49%) and, with the large effect sizes, this suggests that bacterial disease mortality may be strongly genetically determined. CONCLUSION: Balanced polymorphisms appear to be more widespread in humans than previously appreciated and play a critical role in modulating susceptibility to infectious disease. The effect sizes we report, coupled with the stochasticity of exposure to pathogens suggests that infection and mortality are far from random due to a strong genetic basis

Homozygosity and risk of childhood death due to invasive bacterial disease

BACKGROUND: Genetic heterozygosity is increasingly being shown to be a key predictor of fitness in natural populations, both through inbreeding depression, inbred individuals having low heterozygosity, and also through chance linkage between a marker and a gene under balancing selection. One important component of fitness that is often highlighted is resistance to parasites and other pathogens. However, the significance of equivalent loci in human populations remains unclear. Consequently, we performed a case-control study of fatal invasive bacterial disease in Kenyan children using a genome-wide screen with microsatellite markers. METHODS: 148 cases, comprising children aged <13 years who died of invasive bacterial disease, (variously, bacteraemia, bacterial meningitis or neonatal sepsis) and 137 age-matched, healthy children were sampled in a prospective study conducted at Kilifi District Hospital, Kenya. Samples were genotyped for 134 microsatellite markers using the ABI LD20 marker set and analysed for an association between homozygosity and mortality. RESULTS: At five markers homozygosity was strongly associated with mortality (odds ratio range 4.7 - 12.2) with evidence of interactions between some markers. Mortality was associated with different non-overlapping marker groups in Gram positive and Gram negative bacterial disease. Homozygosity at susceptibility markers was common (prevalence 19-49%) and, with the large effect sizes, this suggests that bacterial disease mortality may be strongly genetically determined. CONCLUSION: Balanced polymorphisms appear to be more widespread in humans than previously appreciated and play a critical role in modulating susceptibility to infectious disease. The effect sizes we report, coupled with the stochasticity of exposure to pathogens suggests that infection and mortality are far from random due to a strong genetic basis

Risk of pneumococcal bacteremia in Kenyan children with glucose-6-phosphate dehydrogenase deficiency

Abstract Background Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme deficiency state in humans. The clinical phenotype is variable and includes asymptomatic individuals, episodic hemolysis induced by oxidative stress, and chronic hemolysis. G6PD deficiency is common in malaria-endemic regions, an observation hypothesized to be due to balancing selection at the G6PD locus driven by malaria. G6PD deficiency increases risk of severe malarial anemia, a key determinant of invasive bacterial disease in malaria-endemic settings. The pneumococcus is a leading cause of invasive bacterial infection and death in African children. The effect of G6PD deficiency on risk of pneumococcal disease is undefined. We hypothesized that G6PD deficiency increases pneumococcal disease risk and that this effect is dependent upon malaria. Methods We performed a genetic case-control study of pneumococcal bacteremia in Kenyan children stratified across a period of falling malaria transmission between 1998 and 2010. Results Four hundred twenty-nine Kenyan children with pneumococcal bacteremia and 2677 control children were included in the study. Among control children, G6PD deficiency, secondary to the rs1050828 G>A mutation, was common, with 11.2% (n = 301 of 2677) being hemi- or homozygotes and 33.3% (n = 442 of 1329) of girls being heterozygotes. We found that G6PD deficiency increased the risk of pneumococcal bacteremia, but only during a period of high malaria transmission (P = 0.014; OR 2.33, 95% CI 1.19–4.57). We estimate that the population attributable fraction of G6PD deficiency on risk of pneumococcal bacteremia in areas under high malaria transmission is 0.129. Conclusions Our data demonstrate that G6PD deficiency increases risk of pneumococcal bacteremia in a manner dependent on malaria. At the population level, the impact of G6PD deficiency on invasive pneumococcal disease risk in malaria-endemic regions is substantial. Our study highlights the infection-associated morbidity and mortality conferred by G6PD deficiency in malaria-endemic settings and adds to our understanding of the potential indirect health benefits of improved malaria control

Energy Transfer and Spectra in Simulations of Two-dimensional Compressible Turbulence

We present results of high-resolution numerical simulations of compressible 2D turbulence forced at intermediate spatial scales with a solenoidal white-in-time external acceleration. A case with an isothermal equation of state, low energy injection rate, and turbulent Mach number $M\approx0.34$ without energy condensate is studied in detail. Analysis of energy spectra and fluxes shows that the classical dual-cascade picture familiar from the incompressible case is substantially modified by compressibility effects. While the small-scale direct enstrophy cascade remains largely intact, a large-scale energy flux loop forms with the direct acoustic energy cascade compensating for the inverse transfer of solenoidal kinetic energy. At small scales, the direct enstrophy and acoustic energy cascades are fully decoupled at small Mach numbers and hence the corresponding spectral energy slopes comply with theoretical predictions, as expected. At large scales, dispersion of acoustic waves on vortices softens the dilatational velocity spectrum, while the pseudo-sound component of the potential energy associated with coherent vortices steepens the potential energy spectrum.Comment: 10 pages, 6 figures. To appear in: Turbulence in Complex Conditions, Proc. Euromech/Ercoftac Colloquium 589, ed. M. Gorokhovski, Springer, 201

The CoQ oxidoreductase FSP1 acts parallel to GPX4 to inhibit ferroptosis.

Ferroptosis is a form of regulated cell death that is caused by the iron-dependent peroxidation of lipids1,2. The glutathione-dependent lipid hydroperoxidase glutathione peroxidase 4 (GPX4) prevents ferroptosis by converting lipid hydroperoxides into non-toxic lipid alcohols3,4. Ferroptosis has previously been implicated in the cell death that underlies several degenerative conditions2, and induction of ferroptosis by the inhibition of GPX4 has emerged as a therapeutic strategy to trigger cancer cell death5. However, sensitivity to GPX4 inhibitors varies greatly across cancer cell lines6, which suggests that additional factors govern resistance to ferroptosis. Here, using a synthetic lethal CRISPR-Cas9 screen, we identify ferroptosis suppressor protein 1 (FSP1) (previously known as apoptosis-inducing factor mitochondrial 2 (AIFM2)) as a potent ferroptosis-resistance factor. Our data indicate that myristoylation recruits FSP1 to the plasma membrane where it functions as an oxidoreductase that reduces coenzyme Q10 (CoQ) (also known as ubiquinone-10), which acts as a lipophilic radical-trapping antioxidant that halts the propagation of lipid peroxides. We further find that FSP1 expression positively correlates with ferroptosis resistance across hundreds of cancer cell lines, and that FSP1 mediates resistance to ferroptosis in lung cancer cells in culture and in mouse tumour xenografts. Thus, our data identify FSP1 as a key component of a non-mitochondrial CoQ antioxidant system that acts in parallel to the canonical glutathione-based GPX4 pathway. These findings define a ferroptosis suppression pathway and indicate that pharmacological inhibition of FSP1 may provide an effective strategy to sensitize cancer cells to ferroptosis-inducing chemotherapeutic agents

Quantum Point Contacts and Coherent Electron Focusing

I. Introduction II. Electrons at the Fermi level III. Conductance quantization of a quantum point contact IV. Optical analogue of the conductance quantization V. Classical electron focusing VI. Electron focusing as a transmission problem VII. Coherent electron focusing (Experiment, Skipping orbits and magnetic edge states, Mode-interference and coherent electron focusing) VIII. Other mode-interference phenomenaComment: #3 of a series of 4 legacy reviews on QPC'