Data assurance in opaque computations

The chess endgame is increasingly being seen through the lens of, and therefore effectively defined by, a data ‘model’ of itself. It is vital that such models are clearly faithful to the reality they purport to represent. This paper examines that issue and systems engineering responses to it, using the chess endgame as the exemplar scenario. A structured survey has been carried out of the intrinsic challenges and complexity of creating endgame data by reviewing the past pattern of errors during work in progress, surfacing in publications and occurring after the data was generated. Specific measures are proposed to counter observed classes of error-risk, including a preliminary survey of techniques for using state-of-the-art verification tools to generate EGTs that are correct by construction. The approach may be applied generically beyond the game domain

Holonomy of Einstein Lorentzian manifolds

The classification of all possible holonomy algebras of Einstein and vacuum Einstein Lorentzian manifolds is obtained. It is shown that each such algebra appears as the holonomy algebra of an Einstein (resp., vacuum Einstein) Lorentzian manifold, the direct constructions are given. Also the holonomy algebras of totally Ricci-isotropic Lorentzian manifolds are classified. The classification of the holonomy algebras of Lorentzian manifolds is reviewed and a complete description of the spaces of curvature tensors for these holonomies is given.Comment: Dedicated to to Mark Volfovich Losik on his 75th birthday. This version is an extended part of the previous version; another part of the previous version is extended and submitted as arXiv:1001.444

Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix

Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Like Chain (ssWLC) model, which is known to capture the folding properties of supercoiled DNA, and provide a detailed explanation of a standard MC simulation method. On the other hand, we explain how to extend this ssWLC model to include structural transitions of the helix.Comment: Book chapter to appear in The Bacterial Nucleoid, Methods and Protocols, Springer serie

Transforming phylogenetic networks: Moving beyond tree space

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks

Functional significance may underlie the taxonomic utility of single amino acid substitutions in conserved proteins

We hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of ß-tubulin. Our analysis identified one amino acid substitution—ß-tubulin F224—which was highly lineage specific. Investigation of ß-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the ß-tubulin Neighbor-Net and demonstrated a fundamental division between core ß-tubulins (plant-like) and divergent ß-tubulins (animal and fungal). F224 was almost completely restricted to the core ß-tubulins, while divergent ß-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of ß-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core ß-tubulins and Y-type, divergent ß-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins

Composite Fermion Description of Correlated Electrons in Quantum Dots: Low Zeeman Energy Limit

We study the applicability of composite fermion theory to electrons in two-dimensional parabolically-confined quantum dots in a strong perpendicular magnetic field in the limit of low Zeeman energy. The non-interacting composite fermion spectrum correctly specifies the primary features of this system. Additional features are relatively small, indicating that the residual interaction between the composite fermions is weak. \footnote{Published in Phys. Rev. B {\bf 52}, 2798 (1995).}Comment: 15 pages, 7 postscript figure

Are 12^{12}CO lines good indicators of the star formation rate in galaxies?

In this paper, we investigate the relevance of using the $^{12}$CO line emissions as indicators of star formation rates (SFR). For the first time, we present this study for a relatively large number of $^{12}$CO transitions (12) as well as over a large interval in redshift (from z$\sim$0 to z$\sim$6). For the nearby sources (D$\leq$10 Mpc), we have used homogeneous sample of $^{12}$CO data provided by Bayet et al. (2004, 2006), mixing observational and modelled line intensities. For higher-z sources (z $\geq$ 1), we have collected $^{12}$CO observations from various papers and have completed the data set of line intensities with model predictions which we also present in this paper. Finally, for increasing the statistics, we have included recent $^{12}$CO(1-0) and $^{12}$CO(3-2) observations of intermediate-z sources. Linear regressions have been calculated for identifying the tightest SFR-$^{12}$CO line luminosity relationships. We show that the \emph{total} $^{12}$CO, the $^{12}$CO(5-4), the $^{12}$CO(6-5) and the $^{12}$CO(7-6) luminosities are the best indicators of SFR (as measured by the far-infrared luminosity). Comparisons with theoretical approaches from Krumholz and Thompson (2007) and Narayanan et al. (2008) are also performed in this paper. Although in general agreement, the predictions made by these authors and the observational results we present here show small and interesting discrepancies. In particular, the slope of the linear regressions, for J$_{upper}\geq$ 4 $^{12}$CO lines are not similar between theoretical studies and observations. On one hand, a larger high-J $^{12}$CO data set of observations might help to better agree with models, increasing the statistics. On the other hand, theoretical studies extended to high redshift sources might also reduce such discrepancies.Comment: 10 pages, 3 figures and 4 tables, Accepted in MNRA

Patent Human Infections with the Whipworm, Trichuris trichiura, Are Not Associated with Alterations in the Faecal Microbiota

Background: The soil-transmitted helminth (STH), Trichuris trichiura colonises the human large intestine where it may modify inflammatory responses, an effect possibly mediated through alterations in the intestinal microbiota. We hypothesised that patent T. trichiura infections would be associated with altered faecal microbiota and that anthelmintic treatment would induce a microbiota resembling more closely that observed in uninfected individuals. Materials and Methods: School children in Ecuador were screened for STH infections and allocated to 3 groups: uninfected, T. trichiura only, and mixed infections with T. trichiura and Ascaris lumbricoides. A sample of uninfected children and those with T. trichiura infections only were given anthelmintic treatment. Bacterial community profiles in faecal samples were studied by 454 pyrosequencing of 16 S rRNA genes. Results: Microbiota analyses of faeces were done for 97 children: 30 were uninfected, 17 were infected with T. trichiura, and 50 with T. trichiura and A. lumbricoides. Post-treatment samples were analyzed for 14 children initially infected with T. trichiura alone and for 21 uninfected children. Treatment resulted in 100% cure of STH infections. Comparisons of the microbiota at different taxonomic levels showed no statistically significant differences in composition between uninfected children and those with T. trichiura infections. We observed a decreased proportional abundance of a few bacterial genera from the Clostridia class of Firmicutes and a reduced bacterial diversity among children with mixed infections compared to the other two groups, indicating a possible specific effect of A. lumbricoides infection. Anthelmintic treatment of children with T. trichiura did not alter faecal microbiota composition. Discussion: Our data indicate that patent human infections with T. trichiura may have no effect on faecal microbiota but that A. lumbricoides colonisation might be associated with a disturbed microbiota. Our results also catalogue the microbiota of rural Ecuadorians and indicate differences with individuals from more urban industrialised societies

An interdisciplinary intervention for older Taiwanese patients after surgery for hip fracture improves health-related quality of life

Abstract Background The effects of intervention programs on health-related quality of life (HRQOL) of patients with hip fracture have not been well studied. We hypothesized that older patients with hip fracture who received our interdisciplinary intervention program would have better HRQOL than those who did not. Methods A randomized experimental design was used. Older patients with hip fracture (N = 162), 60 to 98 years old, from a medical center in northern Taiwan were randomly assigned to an experimental (n = 80) or control (n = 82) group. HRQOL was measured by the SF-36 Taiwan version at 1, 3, 6, and 12 months after discharge. Results The experimental group had significantly better overall outcomes in bodily pain (β = 9.38, p = 0.002), vitality (β = 9.40, p < 0.001), mental health (β = 8.16, p = 0.004), physical function (β = 16.01, p < 0.001), and role physical (β = 22.66, p < 0.001) than the control group at any time point during the first year after discharge. Physical-related health outcomes (physical functioning, role physical, and vitality) had larger treatment effects than emotional/mental- and social functioning-related health outcomes. Conclusions This interdisciplinary intervention program may improve health outcomes of elders with hip fracture. Our results may provide a reference for health care providers in countries using similar programs with Chinese/Taiwanese immigrant populations. Trial registration NCT01052636http://deepblue.lib.umich.edu/bitstream/2027.42/78259/1/1471-2474-11-225.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78259/2/1471-2474-11-225.pdfPeer Reviewe

BRCA2-dependent homologous recombination is required for repair of Arsenite-induced replication lesions in mammalian cells

Arsenic exposure constitutes one of the most widespread environmental carcinogens, and is associated with increased risk of many different types of cancers. Here we report that arsenite (As[III]) can induce both replication-dependent DNA double-strand breaks (DSB) and homologous recombination (HR) at doses as low as 5 µM (0.65 mg/l), which are within the typical doses often found in drinking water in contaminated areas. We show that the production of DSBs is dependent on active replication and is likely to be the result of conversion of a DNA single-strand break (SSB) into a toxic DSB when encountered by a replication fork. We demonstrate that HR is required for the repair of these breaks and show that a functional HR pathway protects against As[III]-induced cytotoxicity. In addition, BRCA2-deficient cells are sensitive to As[III] and we suggest that As[III] could be exploited as a therapy for HR-deficient tumours such as BRCA1 and BRCA2 mutated breast and ovarian cancers