A Decomposition of the Pure Parsimony Problem

We partially order a collection of genotypes so that we can represent the problem of inferring the least number of haplotypes in terms of substructures we call g-lattices. This representation allows us to prove that if the genotypes partition into chains with certain structure, then the NP-Hard problem can be solved efficiently. Even without the specified structure, the decomposition shows how to separate the underlying integer programming model into smaller models

The Impact of Halo Properties, Energy Feedback and Projection Effects on the Mass-SZ Flux Relation

We present a detailed analysis of the intrinsic scatter in the integrated SZ effect - cluster mass (Y-M) relation, using semi-analytic and simulated cluster samples. Specifically, we investigate the impact on the Y-M relation of energy feedback, variations in the host halo concentration and substructure populations, and projection effects due to unresolved clusters along the line of sight (the SZ background). Furthermore, we investigate at what radius (or overdensity) one should measure the integrated SZE and define cluster mass so as to achieve the tightest possible scaling. We find that the measure of Y with the least scatter is always obtained within a smaller radius than that at which the mass is defined; e.g. for M_{200} (M_{500}) the scatter is least for Y_{500} (Y_{1100}). The inclusion of energy feedback in the gas model significantly increases the intrinsic scatter in the Y-M relation due to larger variations in the gas mass fraction compared to models without feedback. We also find that variations in halo concentration for clusters of a given mass may partly explain why the integrated SZE provides a better mass proxy than the central decrement. Substructure is found to account for approximately 20% of the observed scatter in the Y-M relation. Above M_{200} = 2x10^{14} h^{-1} msun, the SZ background does not significantly effect cluster mass measurements; below this mass, variations in the background signal reduce the optimal angular radius within which one should measure Y to achieve the tightest scaling with M_{200}.Comment: 12 pages, 6 figures, to be submitted to Ap

Multistable setups combining magnetic shape memory alloys with reluctance counterforces

Systems with the ability to hold a given position without consumption of energy, i.e. multistability, can be employed in a variety of applications. Apart from the most commonly frictionbased systems, smart materials are an option to create multistability. Here, the ability to create a multistable system from magnetic shape memory alloy (MSM) in a magnetic field, combined with a reluctance counterforce is discussed. For the approach the necessary design process is described, as well as the experimental characterization of a demonstrator system. With the multistable range of the stroke at 0.82 mm and an average resistance to disturbance of ±10 N, two key parameters of the multistable properties are determined. As an outlook, potential applications in the design of adaptable interfaces is discussed

Measuring galaxy cluster masses with CMB lensing using a Maximum Likelihood estimator: Statistical and systematic error budgets for future experiments

We develop a Maximum Likelihood estimator (MLE) to measure the masses of galaxy clusters through the impact of gravitational lensing on the temperature and polarization anisotropies of the cosmic microwave background (CMB). We show that, at low noise levels in temperature, this optimal estimator outperforms the standard quadratic estimator by a factor of two. For polarization, we show that the Stokes Q/U maps can be used instead of the traditional E- and B-mode maps without losing information. We test and quantify the bias in the recovered lensing mass for a comprehensive list of potential systematic errors. Using realistic simulations, we examine the cluster mass uncertainties from CMB-cluster lensing as a function of an experiment's beam size and noise level. We predict the cluster mass uncertainties will be 3 - 6% for SPT-3G, AdvACT, and Simons Array experiments with 10,000 clusters and less than 1% for the CMB-S4 experiment with a sample containing 100,000 clusters. The mass constraints from CMB polarization are very sensitive to the experimental beam size and map noise level: for a factor of three reduction in either the beam size or noise level, the lensing signal-to-noise improves by roughly a factor of two.Comment: 28 pages, 5 figures: figs 2, 3 updated, references added: accepted for publication in JCA

Targeted disruption of py235ebp-1: Invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein

Plasmodium yoelii YM asexual blood stage parasites express multiple members of the py235 gene family, part of the super-family of genes including those coding for Plasmodium vivax reticulocyte binding proteins and Plasmodium falciparum RH proteins. We previously identified a Py235 erythrocyte binding protein (Py235EBP-1, encoded by the PY01365 gene) that is recognized by protective mAb 25.77. Proteins recognized by a second protective mAb 25.37 have been identified by mass spectrometry and are encoded by two genes, PY01185 and PY05995/PY03534. We deleted the PY01365 gene and examined the phenotype. The expression of the members of the py235 family in both the WT and gene deletion parasites was measured by quantitative RT-PCR and RNA-Seq. py235ebp-1 expression was undetectable in the knockout parasite, but transcription of other members of the family was essentially unaffected. The knockout parasites continued to react with mAb 25.77; and the 25.77-binding proteins in these parasites were the PY01185 and PY05995/PY03534 products. The PY01185 product was also identified as erythrocyte binding. There was no clear change in erythrocyte invasion profile suggesting that the PY01185 gene product (designated PY235EBP-2) is able to fulfill the role of EBP-1 by serving as an invasion ligand although the molecular details of its interaction with erythrocytes have not been examined. The PY01365, PY01185, and PY05995/PY03534 genes are part of a distinct subset of the py235 family. In P. falciparum, the RH protein genes are under epigenetic control and expression correlates with binding to distinct erythrocyte receptors and specific invasion pathways, whereas in P. yoelii YM all the genes are expressed and deletion of one does not result in upregulation of another. We propose that simultaneous expression of multiple Py235 ligands enables invasion of a wide range of host erythrocytes even in the presence of antibodies to one or more of the proteins and that this functional redundancy at the protein level gives the parasite phenotypic plasticity in the absence of differences in gene expression

Recombinant canine single chain insulin analogues: Insulin receptor binding capacity and ability to stimulate glucose uptake

Virtually all diabetic dogs require exogenous insulin therapy to control their hyperglycaemia. In the UK, the only licensed insulin product currently available is a purified porcine insulin preparation. Recombinant insulin is somewhat problematic in terms of its manufacture, since the gene product (preproinsulin) undergoes substantial post-translational modification in pancreatic β cells before it becomes biologically active. The aim of the present study was to develop recombinant canine single chain insulin (SCI) analogues that could be produced in a prokaryotic expression system and which would require minimal processing. Three recombinant SCI constructs were developed in a prokaryotic expression vector, by replacing the insulin C-peptide sequence with one encoding a synthetic peptide (GGGPGKR), or with one of two insulin-like growth factor (IGF)-2 C-peptide coding sequences (human: SRVSRRSR; canine: SRVTRRSSR). Recombinant proteins were expressed in the periplasmic fraction of Escherichia coli and assessed for their ability to bind to the insulin and IGF-1 receptors, and to stimulate glucose uptake in 3T3-L1 adipocytes. All three recombinant SCI analogues demonstrated preferential binding to the insulin receptor compared to the IGF-1 receptor, with increased binding compared to recombinant canine proinsulin. The recombinant SCI analogues stimulated glucose uptake in 3T3-L1 adipocytes compared to negligible uptake using recombinant canine proinsulin, with the canine insulin/cIGF-2 chimaeric SCI analogue demonstrating the greatest effect. Thus, biologically-active recombinant canine SCI analogues can be produced relatively easily in bacteria, which could potentially be used for treatment of diabetic dogs

A brief glimpse of blue : examining the participation and political effects of 21st-century election reform in North Carolina

This study examines registration, voting and election results in the presidential elections from 1992 to 2012. During this period, North Carolina introduced a series of election reforms which were designed to increase political participation by making registration and voting more widely accessible. These reforms included making One Stop early voting and absentee voting by mail universally available, and making it possible to register and vote in a single step at an early voting site. This study examines the implementation of these reforms by county boards of elections, and the effects which they have had on voter participation and on election results. The study finds that election reform has coincided with an increase in voter turnout, and produced a short-term advantage for the Democratic Party