Erythrocyte complement receptor 1 (CR1) expression level is not associated with polymorphisms in the promoter or 3' untranslated regions of the CR1 gene

Complement receptor 1 (CR1) expression level on erythrocytes is genetically determined and is associated with high (H) and low (L) expression alleles identified by a HindIII restriction fragment-length polymorphism (RFLP) in intron 27 of the CR1 gene. The L allele confers protection against severe malaria in Papua New Guinea, probably because erythrocytes with low CR1 expression, are less able to form pathogenic rosettes with Plasmodium falciparum-infected erythrocytes. Despite the biological importance of erythrocyte CR1, the genetic mutation controlling CR1 expression level remains unknown. We investigated the possibility that mutations in the upstream or 3′ untranslated regions of the CR1 gene could control erythrocyte CR1 level. We identified several novel polymorphisms; however, the mutations did not segregate with erythrocyte CR1 expression level or the H and L alleles. Therefore, high and low erythrocyte CR1 levels cannot be explained by polymorphisms in transcriptional control elements in the upstream or 3′ untranslated regions of the CR1 gene

Simulating Turbulence Using the Astrophysical Discontinuous Galerkin Code TENET

In astrophysics, the two main methods traditionally in use for solving the Euler equations of ideal fluid dynamics are smoothed particle hydrodynamics and finite volume discretization on a stationary mesh. However, the goal to efficiently make use of future exascale machines with their ever higher degree of parallel concurrency motivates the search for more efficient and more accurate techniques for computing hydrodynamics. Discontinuous Galerkin (DG) methods represent a promising class of methods in this regard, as they can be straightforwardly extended to arbitrarily high order while requiring only small stencils. Especially for applications involving comparatively smooth problems, higher-order approaches promise significant gains in computational speed for reaching a desired target accuracy. Here, we introduce our new astrophysical DG code TENET designed for applications in cosmology, and discuss our first results for 3D simulations of subsonic turbulence. We show that our new DG implementation provides accurate results for subsonic turbulence, at considerably reduced computational cost compared with traditional finite volume methods. In particular, we find that DG needs about 1.8 times fewer degrees of freedom to achieve the same accuracy and at the same time is more than 1.5 times faster, confirming its substantial promise for astrophysical applications.Comment: 21 pages, 7 figures, to appear in Proceedings of the SPPEXA symposium, Lecture Notes in Computational Science and Engineering (LNCSE), Springe

Historical roots of Agile methods: where did “Agile thinking” come from?

The appearance of Agile methods has been the most noticeable change to software process thinking in the last fifteen years [16], but in fact many of the “Agile ideas” have been around since 70’s or even before. Many studies and reviews have been conducted about Agile methods which ascribe their emergence as a reaction against traditional methods. In this paper, we argue that although Agile methods are new as a whole, they have strong roots in the history of software engineering. In addition to the iterative and incremental approaches that have been in use since 1957 [21], people who criticised the traditional methods suggested alternative approaches which were actually Agile ideas such as the response to change, customer involvement, and working software over documentation. The authors of this paper believe that education about the history of Agile thinking will help to develop better understanding as well as promoting the use of Agile methods. We therefore present and discuss the reasons behind the development and introduction of Agile methods, as a reaction to traditional methods, as a result of people's experience, and in particular focusing on reusing ideas from histor

Phase coherence in quasicondensate experiments: an ab initio analysis via the stochastic Gross-Pitaevskii equation

We perform an ab initio analysis of the temperature dependence of the phase coherence length of finite temperature, quasi-one-dimensional Bose gases measured in the experiments of Richard et al. (Phys. Rev. Lett. 91, 010405 (2003)) and Hugbart et al. (Eur. Phys. J. D 35, 155-163 (2005)), finding very good agreement across the entire observed temperature range ($0.8<T/T_{\phi}<28$). Our analysis is based on the one-dimensional stochastic Gross-Pitaevskii equation, modified to self-consistently account for transverse, quasi-one-dimensional effects, thus making it a valid model in the regime $\mu ~ few \hbar \omega_\perp$. We also numerically implement an alternative identification of $T_{\phi}$, based on direct analysis of the distribution of phases in a stochastic treatment.Comment: Amended manuscript with improved agreement to experiment, following some additional clarifications by Mathilde Hugbart and Fabrice Gerbier and useful comments by the reviewer; accepted for publication in Physical Review

Quantitative study of quasi-one-dimensional Bose gas experiments via the stochastic Gross-Pitaevskii equation

The stochastic Gross-Pitaevskii equation is shown to be an excellent model for quasi-one-dimensional Bose gas experiments, accurately reproducing the in situ density profiles recently obtained in the experiments of Trebbia et al. [Phys. Rev. Lett. 97, 250403 (2006)] and van Amerongen et al. [Phys. Rev. Lett. 100, 090402 (2008)], and the density fluctuation data reported by Armijo et al. [Phys. Rev. Lett. 105, 230402 (2010)]. To facilitate such agreement, we propose and implement a quasi-one-dimensional stochastic equation for the low-energy, axial modes, while atoms in excited transverse modes are treated as independent ideal Bose gases.Comment: 10 pages, 5 figures; updated figures with experimental dat

Matter-wave dark solitons: stochastic vs. analytical results

The dynamics of dark matter-wave solitons in elongated atomic condensates are discussed at finite temperatures. Simulations with the stochastic Gross-Pitaevskii equation reveal a noticeable, experimentally observable spread in individual soliton trajectories, attributed to inherent fluctuations in both phase and density of the underlying medium. Averaging over a number of such trajectories (as done in experiments) washes out such background fluctuations, revealing a well-defined temperature-dependent temporal growth in the oscillation amplitude. The average soliton dynamics is well captured by the simpler dissipative Gross-Pitaevskii equation, both numerically and via an analytically-derived equation for the soliton center based on perturbation theory for dark solitons.Comment: 4 pages, 3 figures. Added several reference

Routine administration of oral polio vaccine in a subtropical area. Factors possibly influencing sero-conversion rates

Poliomyelitis is an important problem of public health in warm-climate countries. Studies of serological responses to vaccination in these countries have given conflicting results but in many investigations the rates have been considerably less than in countries with temperate climates. In this study three possible factors influencing sero-conversion were investigated - the season of the year when vaccine was given, the social status of the mother (as indicated by the number of years of schooling) and the presence of non-poliomyelitis viruses (NPV) in the gut when vaccine was given. Over 200 children about 2 months of age were included in the study. Each was given three doses of trivalent vaccine at 6-week intervals. The sero-conversion rates of the groups fed in winter were excellent but were slightly less good in summer. The differences were greatest in children in the lower socio-economic groups and in children excreting other enteroviruses. The conclusions are that, provided a potent vaccine is used, the factors which diminish the effectiveness of immunization in warm-climate countries can be overcome: (1) by giving three doses of trivalent vaccine; (2) by beginning vaccination at the earliest possible age (when enteroviruses are fewest); (3) by concentrating special attention on the lower socio-economic groups and if necessary by giving a reinforcing dose several months after the third dose has been given - preferably in the colder month

Discontinuous Galerkin method for multifluid Euler equations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106454/1/AIAA2013-2595.pd

Agile methods for agile universities

We explore a term, Agile, that is being used in various workplace settings, including the management of universities. The term may have several related but slightly different meanings. Agile is often used in the context of facilitating more creative problem-solving and advocating for the adoption, design, tailoring and continual updating of more innovative organizational processes. We consider a particular set of meanings of the term from the world of software development. Agile methods were created to address certain problems with the software development process. Many of those problems have interesting analogues in the context of universities, so a reflection on agile methods may be a useful heuristic for generating ideas for enabling universities to be more creative