Decidability for Sturmian Words

We show that the first-order theory of Sturmian words over Presburger arithmetic is decidable. Using a general adder recognizing addition in Ostrowski numeration systems by Baranwal, Schaeffer and Shallit, we prove that the first-order expansions of Presburger arithmetic by a single Sturmian word are uniformly ?-automatic, and then deduce the decidability of the theory of the class of such structures. Using an implementation of this decision algorithm called Pecan, we automatically reprove classical theorems about Sturmian words in seconds, and are able to obtain new results about antisquares and antipalindromes in characteristic Sturmian words

Meiotic Transmission of Drosophila pseudoobscura Chromosomal Arrangements

Drosophila pseudoobscura harbors a rich gene arrangement polymorphism on the third chromosome generated by a series of overlapping paracentric inversions. The arrangements suppress recombination in heterokaryotypic individuals, which allows for the selective maintenance of coadapted gene complexes. Previous mapping experiments used to determine the degree to which recombination is suppressed in gene arrangement heterozygotes produced non-recombinant progeny in non-Mendelian ratios. The deviations from Mendelian expectations could be the result of viability differences between wild and mutant chromosomes, meiotic drive because of achiasmate pairing of homologues in heterokaryotypic females during meiosis, or a combination of both mechanisms. The possibility that the frequencies of the chromosomal arrangements in natural populations are affected by mechanisms other than adaptive selection led us to consider these hypotheses. We performed reciprocal crosses involving both heterozygous males and females to determine if the frequency of the non-recombinant progeny deviates significantly from Mendelian expectations and if the frequencies deviate between reciprocal crosses. We failed to observe non-Mendelian ratios in multiple crosses, and the frequency of the non-recombinant classes differed in only one of five pairs of reciprocal crosses despite sufficient power to detect these differences in all crosses. Our results indicate that deviations from Mendelian expectations in recombination experiments involving the D. pseudoobscura inversion system are most likely due to fitness differences of gene arrangement karyotypes in different environments

Statistical modelling of growth using a mixed model with orthogonal polynomials

In statistical modelling, the effects of single-nucleotide polymorphisms (SNPs) are often regarded as time-independent. However, for traits recorded repeatedly, it is very interesting to investigate the behaviour of gene effects over time. In the analysis, simulated data from the 13th QTL-MAS Workshop (Wageningen, The Netherlands, April 2009) was used and the major goal was the modelling of genetic effects as time-dependent. For this purpose, a mixed model which describes each effect using the third-order Legendre orthogonal polynomials, in order to account for the correlation between consecutive measurements, is fitted. In this model, SNPs are modelled as fixed, while the environment is modelled as random effects. The maximum likelihood estimates of model parameters are obtained by the expectation–maximisation (EM) algorithm and the significance of the additive SNP effects is based on the likelihood ratio test, with p-values corrected for multiple testing. For each significant SNP, the percentage of the total variance contributed by this SNP is calculated. Moreover, by using a model which simultaneously incorporates effects of all of the SNPs, the prediction of future yields is conducted. As a result, 179 from the total of 453 SNPs covering 16 out of 18 true quantitative trait loci (QTL) were selected. The correlation between predicted and true breeding values was 0.73 for the data set with all SNPs and 0.84 for the data set with selected SNPs. In conclusion, we showed that a longitudinal approach allows for estimating changes of the variance contributed by each SNP over time and demonstrated that, for prediction, the pre-selection of SNPs plays an important role

Three-year tracking of fatty acid composition of plasma phospholipids in healthy children

Objectives: The fatty acid composition of plasma phospholipids reflects the dietary fatty acid intake as well as endogenous turnover. We aimed at investigating the potential tracking of plasma phospholipid fatty acid composition in children that participated in a prospective cohort study. Methods: 26 healthy children participated in a longitudinal study on health risks and had been enrolled after birth. All children were born at term with birth weights appropriate for gestational age. Follow-up took place at ages 24, 36 and 60 months. At each time point a 24-hour dietary recall was obtained, anthropometric parameters were measured and a blood sample for phospholipid fatty acid analysis was taken. Results: Dietary intake of saturated (SFA), monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids at the three time points were not correlated. We found lower values for plasma MUFA and the MUFA/SFA ratio at 60 months compared to 24 months. In contrast, total PUFA, total n-6 and n-6 long-chain polyunsaturated fatty acids (LC-PUFA) were higher at 60 months. Significant averaged correlation coefficients (average of Pearson's R for 24 versus 36 months and 36 versus 60 months) were found for n-6 LC-PUFA (r = 0.67), n-6/n-3 LC-PUFA ratio (r = 0.59) and arachidonic acid/linoleic acid ratio (r = 0.64). Partial tracking was found for the docosahexaenoic acid/alpha-linolenic acid ratio (r = 0.33). Body mass index and sum of skinfolds Z-scores were similar in the three evaluations. Conclusions: A significant tracking of n-6 LC-PUFA, n-6 LC-PUFA/n-3 LC-PUFA ratio, arachidonic acid/ linoleic acid ratio and docosahexaenoic acid/alpha-linolenic acid ratio may reflect an influence of individual endogenous fatty acid metabolism on plasma concentrations of some, but not all, fatty acids. Copyright (c) 2007 S. Karger AG, Basel

Consensus clustering in complex networks

The community structure of complex networks reveals both their organization and hidden relationships among their constituents. Most community detection methods currently available are not deterministic, and their results typically depend on the specific random seeds, initial conditions and tie-break rules adopted for their execution. Consensus clustering is used in data analysis to generate stable results out of a set of partitions delivered by stochastic methods. Here we show that consensus clustering can be combined with any existing method in a self-consistent way, enhancing considerably both the stability and the accuracy of the resulting partitions. This framework is also particularly suitable to monitor the evolution of community structure in temporal networks. An application of consensus clustering to a large citation network of physics papers demonstrates its capability to keep track of the birth, death and diversification of topics.Comment: 11 pages, 12 figures. Published in Scientific Report

The dearth of halo dwarf galaxies: is there power on short scales?

N-body simulations of structure formation with scale-invariant primordial perturbations show significantly more virialized objects of dwarf-galaxy mass in a typical galactic halo than are observed around the Milky Way. We show that the dearth of observed dwarf galaxies could be explained by a dramatic downturn in the power spectrum at small distance scales. This suppression of small-scale power might also help mitigate the disagreement between cuspy simulated halos and smooth observed halos, while remaining consistent with Lyman-alpha-forest constraints on small-scale power. Such a spectrum could arise in inflationary models with broken scale invariance.Comment: 5 pages LaTeX, 3 figure

On the cosmological mass function theory

This paper provides, from one side, a review of the theory of the cosmological mass function from a theoretical point of view, starting from the seminal paper of Press & Shechter (1974) to the last developments (Del Popolo & Gambera (1998, 1999), Sheth & Tormen 1999 (ST), Sheth, Mo & Tormen 2001 (ST1), Jenkins et al. 2001 (J01), Shet & Tormen 2002 (ST2), Del Popolo 2002a, Yagi et al. 2004 (YNY)), and from another side some improvements on the multiplicity function models in literature. ...Comment: Astronomy Reports, in prin

From Weak Lensing to non-Gaussianity via Minkowski Functionals

We present a new harmonic-domain approach for extracting morphological information, in the form of Minkowski Functionals (MFs), from weak lensing (WL) convergence maps. Using a perturbative expansion of the MFs, which is expected to be valid for the range of angular scales probed by most current weak-lensing surveys, we show that the study of three generalized skewness parameters is equivalent to the study of the three MFs defined in two dimensions. We then extend these skewness parameters to three associated skew-spectra which carry more information about the convergence bispectrum than their one-point counterparts. We discuss various issues such as noise and incomplete sky coverage in the context of estimation of these skew-spectra from realistic data. Our technique provides an alternative to the pixel-space approaches typically used in the estimation of MFs, and it can be particularly useful in the presence of masks with non-trivial topology. Analytical modeling of weak lensing statistics relies on an accurate modeling of the statistics of underlying density distribution. We apply three different formalisms to model the underlying dark-matter bispectrum: the hierarchical ansatz, halo model and a fitting function based on numerical simulations; MFs resulting from each of these formalisms are computed and compared. We investigate the extent to witch late-time gravity-induced non-Gaussianity (to which weak lensing is primarily sensitive) can be separated from primordial non-Gaussianity and how this separation depends on source redshift and angular scale.Comment: 22 Pages, 12 Figures. Submitting To MNRA

The Effects of G-CSF on Proliferation of Mouse Myocardial Microvascular Endothelial Cells

This paper explores the effect of granulocyte colony-stimulating factor (G-CSF) on mouse myocardial microvascular endothelial cell (CMECs) proliferation. CMECs were harvested from C57/BL6 mice. CMECs were cultured in medium containing G-CSF (0 ng/mL, 20 ng/mL, 40 ng/mL, 60 ng/mL) for five days. Proliferative activity of CMECs was examined by CCK-8 method. Hypoxia inducible factor-1 (HIF-1) and p53 expression levels was determined from the mRNA obtained by reverse transcription polymerase chain reaction (RT-PCR). Results showed that the purity quotient of the CMECs, which were cultured by the method of modified myocardial tissue explant culture, was higher than 95%. Compared with control untreated cells, the proliferative activity of CMECs and the expression level of HIF-1 mRNA in these cells were enhanced by G-CSF treatment, whereas the expression level of p53 mRNA was markedly reduced. It may be concluded that G-CSF could promote the proliferative activity of CMECs, which might be mediated by upregulation of HIF-1 and downregulation of p53

The superhydrophobicity of polymer surfaces: Recent developments

Superhydrophobicity is the extreme water repellence of highly textured surfaces. The field of superhydrophobicity research has reached a stage where huge numbers of candidate treatments have been proposed and jumps have been made in theoretically describing them. There now seems to be a move to more practical concerns and to considering the demands of individual applications instead of more general cases. With these developments, polymeric surfaces with their huge variety of properties have come to the fore and are fast becoming the material of choice for designing, developing, and producing superhydrophobic surfaces. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1203–1217, 201