Track reconstruction in the LHCb experiment

see thesi

Mitochondrial DNA signature for range-wide populations of Bicyclus anynana suggests a rapid expansion from recent refugia

This study investigates the genetic diversity, population structure and demographic history of the afrotropical butterfly Bicyclus anynana using mitochondrial DNA (mtDNA). Samples from six wild populations covering most of the species range from Uganda to South Africa were compared for the cytochrome c oxidase subunit gene (COI). Molecular diversity indices show overall high mtDNA diversity for the populations, but low nucleotide divergence between haplotypes. Our results indicate relatively little geographic population structure among the southern populations, especially given the extensive distributional range and an expectation of limited gene flow between populations. We implemented neutrality tests to assess signatures of recent historical demographic events. Tajima's D test and Fu's FS test both suggested recent population growth for the populations. The results were only significant for the southernmost populations when applying Tajima's D, but Fu's FS indicated significant deviations from neutrality for all populations except the one closest to the equator. Based on our own findings and those from pollen and vegetation studies, we hypothesize that the species range of B. anynana was reduced to equatorial refugia during the last glacial period, and that the species expanded southwards during the past 10.000 years. These results provide crucial background information for studies of phenotypic and molecular adaptation in wild populations of B. anynan

Semi-flexible polymers near interfaces : equilibrium aspects and adsorption kinetics

The first chapter is about semi-flexible polymers at a liquid-liquid interface: self-consistent-field calculations. The adsorption of semi-flexible polymers at a liquid-liquid interface largely differs from that at a solid surface. The width of the interface is an additional length scale in the problem, making the system behaviour particularly rich. We consider two phase-separating monomeric liquids, C and D, and a polymer A N which dissolves equally well in both liquids. We study this system in a self-consistent-field model in the dilute regime. The stiffness of the polymer is controlled by the use of a rotational isomeric state approach. We show that the interfacial width(determined by the interaction parameter between the two solvents), the persistence length q, and the chain length N are relevant parameters in the adsorption behaviour.A key observation is that, while keeping N 1/2/constant, the adsorbed amount goes through a minimum with increasing q/. An initial increase of q/(q/1) effectively leads to a larger coil size, leading to a decrease of the adsorbed amount. However, when q/1, alignment of parts of the polymer within the interfacial region occurs due to the lack of entropic penalties. This alignment process induces an increase of the adsorbed amount. These observations also have implications for the ongoing discussion about the preferential adsorption in a mixture of flexible and stiff polymers. In this discussion one should consider the effects of the finite size of the interfacial region.The second chapter is about wetting by polymers of a liquid-liquid interface: effects of short-range interactions and of chain stiffness. The behaviour of both flexible and semi-flexible polymers near a liquid-liquid interface is investigated with the aid of the self-consistent-field theory as developed by Scheutjens and Fleer. Aternary system (A/B N C) is studied near the wetting transition. In a symmetric system, i.e.χ AB = χ BC = χ, a change in the interaction parameterχintroduces a wetting transition. The ratio of the interfacial widthof the binary A/C system and the coil size of the polymer determines the order of this transition. Beyond a certain chain length N C (at fixed) the wetting transition is of first order, whereas it is of second order for NC . The characteristics of the prewetting line, including the prewetting critical point, are discussed in some detail. The non-trivial N-dependence of the position of this critical point is analysed in terms of a crude thermodynamic model. For a semi-flexible polymer an increase of the chain stiffness at a certain value ofχis sufficient to introduce a wetting transition.Chapter 3 is about adsorption kinetics of the polysaccharide xanthan on ZrO 2 . The adsorption kinetics of the polysaccharide xanthan from aqueous solution on zirconium oxide were studied as a function of pH and ionic strength. The adsorption was monitored by reflectometry in astagnation-point flow setup. At intermediate pH and ionic strength, xanthan is present in a helical form and it can be viewed as a semi-flexible polymer under these conditions. By lowering the salt concentration or increasing the pH a helix-coil transition takes place. This transition is caused by the mutual electrostatic repulsion of the short side chains of xanthan. The so-formed coil can be considered as a Gaussian chain, with a large radius of gyration. The conformation of the polysaccharide is roughly reflected in its adsorption behaviour.It is, however, deduced that the electrostatic interaction between polymer and surface influences the stability ofthe helix. The adsorption process can be divided in two regimes. At low surface coverage the rate of adsorption is transport-limited, which in a stagnation-point flow leads to a linear time dependence of the adsorbed amount. The adsorption rate in this regime hardly changes with ionic strength or pH. The time range over which it holds, however, does, which can be understood in terms of electrostatic effects. At higher surface coverage two types of behaviour are observed. At low ionic strength and on a highly charged surface the adsorbed amount saturates abruptly. This kind of kinetics resemble those of flexible polymers. In this case the xanthan presumably adsorbs in a coil-like conformation, because the helix becomes unstable in the vicinity of the surface. At higher ionic strength and on a weakly charged surface, the adsorbed amount increases gradually over very long times. Under these conditions, the helix conformation is more stable so that we ascribe this slow process to tentatively rearrangement and alignment processes of the stiff chains on the surface.Chapter 4 is about the competition between transport and spreading in protein adsorption kinetics. The saturation adsorbed amount of polymers on solid surfaces is mostlyfound to be independent of the polymer transport rate, or flux J, to the surface. In most cases this is because the experimental rate of transport strongly deviates from the relaxation rate in the polymer layer. We studied the adsorption of both immunoglobulin G and savinase on SiO 2 from aqueous solution and found that the transport rate is an important parameter in the adsorption kinetics. The adsorption process can be viewed as an attachment to, followed by the spreading over the surface of a polymer molecule. In this way the adsorbed amount strongly depends on J if the time for transport to the surface is in the same range as the spreading time. Using an analytical "growing disk" model for the polymer adsorption, we are able to, at least qualitatively, describe the adsorption kinetics.Chapter 5 is about adsorption and spreading of polymers at plane interfaces; theory and molecular dynamics simulations. Nonequilibrium processes play a key role in the adsorption kinetics of macromolecules. It is expected that the competition between transport of polymer towards an interface and its subsequent spreading has a significant influence on the adsorbed amount. An increase of the transport rate can lead to an increase of the adsorbed amount, especially when the polymer has too little time to spread at the interface. In this study we present both molecular dynamics simulations and analytical calculations to describe some aspects of the adsorption kinetics. From MD simulations on a poly(ethylene oxide) chain in vacuum near a graphite surface, we conclude that the spreading process can, in first approximation, be described by either a simple exponential function or by first-order reaction kinetics. Combining these spreading models with the transport equations for two different geometries (stagnation-point flow and overflowing cylinder)we are able to derive analytical equations for the adsorption kinetics of polymers at solid-liquid and at liquid-fluid interfaces.</p

Expression of the Inhibitory CD200 Receptor Is Associated with Alternative Macrophage Activation

Classical macrophage activation is inhibited by the CD200 receptor (CD200R). Here, we show that CD200R expression was specifically induced on human in vitro polarized macrophages of the alternatively activated M2a subtype, generated by incubation with IL-4 or IL-13. In mice, peritoneal M2 macrophages, elicited during infection with the parasites Taenia crassiceps or Tryponosoma brucei brucei, expressed increased CD200R levels compared to those derived from uninfected mice. However, in vitro stimulation of mouse peritoneal macrophages and T crassiceps infection in IL-4-/- and IL-4R-/- mice showed that, in contrast to humans, induction of CD200R in mice was not IL-4 or IL-13 dependent. Our data identify CD200R as a suitable marker for alternatively activated macrophages in humans and corroborate observations of distinct species- and/or site-specific mechanisms regulating macrophage polarization in mouse and man. Copyright (C) 2009 S. Karger AG, Base

Friendship during patients' stable and unstable phases of incurable cancer:a qualitative interview study

Objectives:Little is known about the added value of friendship during the care of intensive cancer disease trajectories. Friends, however, can play an important (caring-)role to increase their friends' (mental) well-being. We explored the experiences and desires of friends while their ill friends were-most of the time-in a stable phase of incurable cancer. Design:Qualitative study in the Netherlands based on 14 in-depth interviews with friends of patients living with incurable cancer. Interviews were performed at the home setting or the friend's office. Data gathering was inspired by grounded theory and analysed with a thematic analysis. Setting:The home setting/friend's office. Results:Friends reported to experience difficulties in how and how often they wanted to approach their ill friends. They emphasised the ever-present knowledge of cancer inside their friends' body as a time bomb'. They seemed to balance between the wish to take care for their ill friend, having a good time and not knowing what their ill friend desired at specific times. Some friends felt burdened with or forced to provide more care than they could, although they acknowledged that this relationship provided space to reflect about their own life. Conclusions:Friends are constantly negotiating and renegotiating their relationship depending on the severity of the disease, transparency of patients about their illness, their previous experiences and personal circumstances in life. Although a decrease in friendship may impact a patient's quality of life, friends also need to be protected against providing more care than they are willing or able to give. Healthcare professionals, being aware of this phenomenon, can assist in this.</p