Exploiting Chordality in Optimization Algorithms for Model Predictive Control

In this chapter we show that chordal structure can be used to devise efficient optimization methods for many common model predictive control problems. The chordal structure is used both for computing search directions efficiently as well as for distributing all the other computations in an interior-point method for solving the problem. The chordal structure can stem both from the sequential nature of the problem as well as from distributed formulations of the problem related to scenario trees or other formulations. The framework enables efficient parallel computations.Comment: arXiv admin note: text overlap with arXiv:1502.0638

Runway Safety Analysis for 2015 to 2017

Reducing the risk of runway incursions or excursions in order to meet future aviation growth can be achieved two fold: by preventing and by limiting the level of damage. In order to reach an As Low As Reasonably Practicable (ALARP) level of runway safety is insight in the cost of runway safety events as well as in their mitigations required. Aircraft and Aerodrome operators could get this insight by combining the likelihood of future occurrences with their cumulative costs. On top of already existing prevention measures, new additional restrictions could face financial limits as indicated by the law of diminishing returns. That implies that either accepting the risk ‘as is’ and thus accepting higher levels of runway incursions and excursions or find cost-effective mitigations postponing the financial limits to safety. ; thus a cost-benefit approach. A method of estimating the costs of runway related an occurrence has recently been published. Combining this method with a model capable of predicting the likelihood of runway incursions or excursions tailor-made per aircraft or aerodrome operator and their mitigations opens the possibility of a cost benefit approach. Runway incidents and accidents in the period 2015-2017 are analyzed and their costs estimated at $ 11 Billion, corrected for purchasing power. Veer-offs are shown to be by far the most costly events, followed by overruns. Runway incursion analysis has showed to be the least cost event compared with the two aforementioned events. The number and severity of veer-offs are expected to rise. The costs of future veer-offs should be weighed against the costs of prevention and the cost of reducing the levels of damage. Damage reduction is the main objective of the runway strip (RESA for overruns). It appears that the level of damage and costs rise considerably when a runway strip or RESA is inadequate or inappropriate for the moment (e.g. bearing strength). A cost driven, flexible risk based system is recommended in order to reduce the risks and costs associated with runway excursions with emphasis on veer-offs and overruns. Concrete actions include a three step approach for aircraft and aerodrome operators

Domain structure of human complement C4b extends with increasing NaCl concentration: implications for its regulatory mechanism

During the activation of complement C4 to C4b, the exposure of its thioester domain (TED) is crucial for the attachment of C4b to activator surfaces. In the C4b crystal structure, TED forms an Arg(104)-Glu(1032) salt bridge to tether its neighbouring macroglobulin (MG1) domain. Here, we examined the C4b domain structure to test whether this salt bridge affects its conformation. Dual polarisation interferometry of C4b immobilised at a sensor surface showed that the maximum thickness of C4b increased by 0.46 nm with increase in NaCl concentration from 50 mM to 175 mM NaCl. Analytical ultracentrifugation showed that the sedimentation coefficient s20, w of monomeric C4b of 8.41 S in 50 mM NaCl buffer decreased to 7.98 S in 137 mM NaCl buffer, indicating that C4b became more extended. Small angle X-ray scattering reported similar RG values of 4.89-4.90 nm for C4b in 137-250 mM NaCl. Atomistic scattering modelling of the C4b conformation showed that TED and the MG1 domain were separated by 4.7 nm in 137-250 mM NaCl, this being greater than that of 4.0 nm in the C4b crystal structure. Our data reveal that in low NaCl concentrations, both at surfaces and in solution, C4b forms compact TED-MG1 structures. In solution, physiologically-relevant NaCl concentrations lead to the separation of the TED and MG1 domain, making C4b less able to bind to its complement regulators. These conformational changes are similar to those seen previously for complement C3b, confirming the importance of this salt bridge for regulating both C4b and C3b

Mesangial cells are key contributors to the fibrotic damage seen in the lupus nephritis glomerulus.

Background: Lupus nephritis (LN) affects up to 80% of juvenile-onset systemic lupus erythematosus patients. Mesangial cells (MCs) comprise a third of the glomerular cells and are key contributors to fibrotic changes within the kidney. This project aims to identify the roles of MCs in an in vitro model of LN. Methods: Conditionally immortalised MCs were treated with pro-inflammatory cytokines or with patient sera in an in vitro model of LN and assessed for their roles in inflammation and fibrosis. Results: MCs were shown to produce pro-inflammatory cytokines in response to a model of the inflammatory environment in LN. Further the cells expressed increased levels of mRNA for extracellular matrix (ECM) proteins (COL1A1, COL1A2, COL4A1 and LAMB1), matrix metalloproteinase enzymes (MMP9) and tissue inhibitors of matrix metalloproteinases (TIMP1). Treatment of MCs with serum from patients with active LN was able to induce a similar, albeit milder phenotype. Treatment of MCs with cytokines or patient sera was able to induce secretion of TGF-β1, a known inducer of fibrotic changes. Inhibition of TGF-β1 actions through SB-431542 (an activin A receptor type II-like kinase (ALK5) inhibitor) was able to reduce these responses suggesting that the release of TGF-β1 plays a role in these changes. Conclusions: MCs contribute to the inflammatory environment in LN by producing cytokines involved in leukocyte recruitment, activation and maturation. Further the cells remodel the ECM via protein deposition and enzymatic degradation. This occurs through the actions of TGF-β1 on its receptor, ALK5. This may represent a potential therapeutic target for treatment of LN-associated fibrosis

Non-linearity of the collagen triple helix in solution and implications for collagen function

Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly)n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units. In addition, one unblocked peptide, (POG)10unblocked, was compared with the blocked (POG)10 as a control for the significance of end effects. Complementary analytical ultracentrifugation and synchrotron small angle X-ray scattering data showed that the conformations of the longer triple helical peptides were not well explained by a linear structure derived from crystallography. To interpret these data, molecular dynamics simulations were used to generate 50 000 physically realistic collagen structures for each of the helices. These structures were fitted against their respective scattering data to reveal the best fitting structures from this large ensemble of possible helix structures. This curve fitting confirmed a small degree of non-linearity to exist in these best fit triple helices, with the degree of bending approximated as 4–17° from linearity. Our results open the way for further studies of other collagen triple helices with different sequences and stabilities in order to clarify the role of molecular rigidity and flexibility in collagen extracellular and immune function and disease

Chandra observations of Cygnus OB2

Cygnus OB2 is the nearest example of a massive star forming region, containing over 50 O-type stars and hundreds of B-type stars. We have analyzed two Chandra pointings in Cyg OB2, detecting ~1700 X-ray sources, of which ~1450 are thought to be members of the association. Optical and near-IR photometry has been obtained for ~90% of these sources from recent deep Galactic plane surveys. We have performed isochrone fits to the near-IR color-magnitude diagram, deriving ages of 3.5(+0.75,-1.0) and 5.25(+1.5,-1.0) Myrs for sources in the two fields, both with considerable spreads around the pre-MS isochrones. The presence of a second population in the region, somewhat older than the present-day O-type stars, has been suggested by other authors and fits with the ages derived here. The fraction of sources with inner circumstellar disks (as traced by the K-band excess) is found to be very low, but appropriate for a population of age ~5 Myrs. We measure the stellar mass functions and find a power-law slope of Gamma = -1.09 +/- 0.13, in good agreement with the global mean value estimated by Kroupa. A steepening of the mass function at high masses is observed and we suggest this is due to the presence of the previous generation of stars that have lost their most massive members. Finally, combining our mass function and an estimate of the radial density profile of the association suggests a total mass of Cyg OB2 of ~30,000 Msun, similar to that of many of our Galaxy's most massive star forming regions.Comment: 6 pages, 4 figures, conference proceedings for JENAM 2010: Star Clusters in the Era of Large Surveys, Editors: A.Moitinho and J. Alve

An improved model for joint segmentation and registration based on linear curvature smoother

Image segmentation and registration are two of the most challenging tasks in medical imaging. They are closely related because both tasks are often required simultaneously. In this article, we present an improved variational model for a joint segmentation and registration based on active contour without edges and the linear curvature model. The proposed model allows large deformation to occur by solving in this way the difficulties other jointly performed segmentation and registration models have in case of encountering multiple objects into an image or their highly dependence on the initialisation or the need for a pre-registration step, which has an impact on the segmentation results. Through different numerical results, we show that the proposed model gives correct registration results when there are different features inside the object to be segmented or features that have clear boundaries but without fine details in which the old model would not be able to cope. </jats:p

A phase 1 trial dose-escalation study of tipifarnib on a week-on, week-off schedule in relapsed, refractory or high-risk myeloid leukemia.

Inhibition of farnesyltransferase (FT) activity has been associated with in vitro and in vivo anti-leukemia activity. We report the results of a phase 1 dose-escalation study of tipifarnib, an oral FT inhibitor, in patients with relapsed, refractory or newly diagnosed (if over age 70) acute myelogenous leukemia (AML), on a week-on, week-off schedule. Forty-four patients were enrolled, two patients were newly diagnosed, and the rest were relapsed or refractory to previous treatment, with a median age of 61 (range 33-79). The maximum tolerated dose was determined to be 1200 mg given orally twice daily (b.i.d.) on this schedule. Cycle 1 dose-limiting toxicities were hepatic and renal. There were three complete remissions seen, two at the 1200 mg b.i.d. dose and one at the 1000 mg b.i.d. dose, with minor responses seen at the 1400 mg b.i.d. dose level. Pharmacokinetic studies performed at doses of 1400 mg b.i.d. showed linear behavior with minimal accumulation between days 1-5. Tipifarnib administered on a week-on, week-off schedule shows activity at higher doses, and represents an option for future clinical trials in AML

Dual HLA B*42 and B*81-reactive T cell receptors recognize more diverse HIV-1 Gag escape variants

Closely related HLA alleles presenting similar HIV-1 epitopes can be associated with variable clinical outcome. Here the authors report their findings on CD8+ T cell responses to the HIV-1 Gag-p24 TL9 immunodominant epitope in the context of closely related protective and less protective HLA alleles, and their differential effect on viral contro

First Steps towards Underdominant Genetic Transformation of Insect Populations

The idea of introducing genetic modifications into wild populations of insects to stop them from spreading diseases is more than 40 years old. Synthetic disease refractory genes have been successfully generated for mosquito vectors of dengue fever and human malaria. Equally important is the development of population transformation systems to drive and maintain disease refractory genes at high frequency in populations. We demonstrate an underdominant population transformation system in Drosophila melanogaster that has the property of being both spatially self-limiting and reversible to the original genetic state. Both population transformation and its reversal can be largely achieved within as few as 5 generations. The described genetic construct {Ud} is composed of two genes; (1) a UAS-RpL14.dsRNA targeting RNAi to a haploinsufficient gene RpL14 and (2) an RNAi insensitive RpL14 rescue. In this proof-of-principle system the UAS-RpL14.dsRNA knock-down gene is placed under the control of an Actin5c-GAL4 driver located on a different chromosome to the {Ud} insert. This configuration would not be effective in wild populations without incorporating the Actin5c-GAL4 driver as part of the {Ud} construct (or replacing the UAS promoter with an appropriate direct promoter). It is however anticipated that the approach that underlies this underdominant system could potentially be applied to a number of species. Figure