Deterministic and stochastic descriptions of gene expression dynamics

A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or implicitly etc. Here we consider simple systems of unregulated (constitutive) gene expression and compare different mathematical descriptions systematically to obtain insight into the errors that are introduced by various common approximations such as describing cell growth and division by an effective protein degradation term. In particular, we show that the population average of protein content of a cell exhibits a subtle dependence on the dynamics of growth and division, the specific model for volume growth and the age structure of the population. Nevertheless, the error made by models with implicit cell growth and division is quite small. Furthermore, we compare various models that are partially stochastic to investigate the impact of different sources of (intrinsic) noise. This comparison indicates that different sources of noise (protein synthesis, partitioning in cell division) contribute comparable amounts of noise if protein synthesis is not or only weakly bursty. If protein synthesis is very bursty, the burstiness is the dominant noise source, independent of other details of the model. Finally, we discuss two sources of extrinsic noise: cell-to-cell variations in protein content due to cells being at different stages in the division cycles, which we show to be small (for the protein concentration and, surprisingly, also for the protein copy number per cell) and fluctuations in the growth rate, which can have a significant impact.Comment: 23 pages, 5 figures; Journal of Statistical physics (2012

Ownership and control in a competitive industry

We study a differentiated product market in which an investor initially owns a controlling stake in one of two competing firms and may acquire a non-controlling or a controlling stake in a competitor, either directly using her own assets, or indirectly via the controlled firm. While industry profits are maximized within a symmetric two product monopoly, the investor attains this only in exceptional cases. Instead, she sometimes acquires a noncontrolling stake. Or she invests asymmetrically rather than pursuing a full takeover if she acquires a controlling one. Generally, she invests indirectly if she only wants to affect the product market outcome, and directly if acquiring shares is profitable per se. --differentiated products,separation of ownership and control,private benefits of control

Decoupling A and B model in open string theory -- Topological adventures in the world of tadpoles

In this paper we analyze the problem of tadpole cancellation in open topological strings. We prove that the inclusion of unorientable worldsheet diagrams guarantees a consistent decoupling of A and B model for open superstring amplitudes at all genera. This is proven by direct microscopic computation in Super Conformal Field Theory. For the B-model we explicitly calculate one loop amplitudes in terms of analytic Ray-Singer torsions of appropriate vector bundles and obtain that the decoupling corresponds to the cancellation of D-brane and orientifold charges. Local tadpole cancellation on the worldsheet then guarantees the decoupling at all loops. The holomorphic anomaly equations for open topological strings at one loop are also obtained and compared with the results of the Quillen formula

Nuclear Alpha-Particle Condensates

The $\alpha$-particle condensate in nuclei is a novel state described by a product state of $\alpha$'s, all with their c.o.m. in the lowest 0S orbit. We demonstrate that a typical $\alpha$-particle condensate is the Hoyle state ($E_{x}=7.65$ MeV, $0^+_2$ state in $^{12}$C), which plays a crucial role for the synthesis of $^{12}$C in the universe. The influence of antisymmentrization in the Hoyle state on the bosonic character of the $\alpha$ particle is discussed in detail. It is shown to be weak. The bosonic aspects in the Hoyle state, therefore, are predominant. It is conjectured that $\alpha$-particle condensate states also exist in heavier $n\alpha$ nuclei, like $^{16}$O, $^{20}$Ne, etc. For instance the $0^+_6$ state of $^{16}$O at $E_{x}=15.1$ MeV is identified from a theoretical analysis as being a strong candidate of a $4\alpha$ condensate. The calculated small width (34 keV) of $0^+_6$, consistent with data, lends credit to the existence of heavier Hoyle-analogue states. In non-self-conjugated nuclei such as $^{11}$B and $^{13}$C, we discuss candidates for the product states of clusters, composed of $\alpha$'s, triton's, and neutrons etc. The relationship of $\alpha$-particle condensation in finite nuclei to quartetting in symmetric nuclear matter is investigated with the help of an in-medium modified four-nucleon equation. A nonlinear order parameter equation for quartet condensation is derived and solved for $\alpha$ particle condensation in infinite nuclear matter. The strong qualitative difference with the pairing case is pointed out.Comment: 71 pages, 41 figures, review article, to be published in "Cluster in Nuclei (Lecture Notes in Physics) - Vol.2 -", ed. by C. Beck, (Springer-Verlag, Berlin, 2011

Height and risk of death among men and women: aetiological implications of associations with cardiorespiratory disease and cancer mortality

OBJECTIVES: Height is inversely associated with cardiovascular disease mortality risk and has shown variable associations with cancer incidence and mortality. The interpretation of findings from previous studies has been constrained by data limitations. Associations between height and specific causes of death were investigated in a large general population cohort of men and women from the West of Scotland. DESIGN: Prospective observational study. SETTING: Renfrew and Paisley, in the West of Scotland. SUBJECTS: 7052 men and 8354 women aged 45-64 were recruited into a study in Renfrew and Paisley, in the West of Scotland, between 1972 and 1976. Detailed assessments of cardiovascular disease risk factors, morbidity and socioeconomic circumstances were made at baseline. MAIN OUTCOME MEASURES: Deaths during 20 years of follow up classified into specific causes. RESULTS: Over the follow up period 3347 men and 2638 women died. Height is inversely associated with all cause, coronary heart disease, stroke, and respiratory disease mortality among men and women. Adjustment for socioeconomic position and cardiovascular risk factors had little influence on these associations. Height is strongly associated with forced expiratory volume in one second (FEV1) and adjustment for FEV1 considerably attenuated the association between height and cardiorespiratory mortality. Smoking related cancer mortality is not associated with height. The risk of deaths from cancer unrelated to smoking tended to increase with height, particularly for haematopoietic, colorectal and prostate cancers. Stomach cancer mortality was inversely associated with height. Adjustment for socioeconomic position had little influence on these associations. CONCLUSION: Height serves partly as an indicator of socioeconomic circumstances and nutritional status in childhood and this may underlie the inverse associations between height and adulthood cardiorespiratory mortality. Much of the association between height and cardiorespiratory mortality was accounted for by lung function, which is also partly determined by exposures acting in childhood. The inverse association between height and stomach cancer mortality probably reflects Helicobacter pylori infection in childhood resulting inor being associated withshorter height. The positive associations between height and several cancers unrelated to smoking could reflect the influence of calorie intake during childhood on the risk of these cancers

Measurement of D*+/- meson production in jets from pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

This paper reports a measurement of D*+/- meson production in jets from proton-proton collisions at a center-of-mass energy of sqrt(s) = 7 TeV at the CERN Large Hadron Collider. The measurement is based on a data sample recorded with the ATLAS detector with an integrated luminosity of 0.30 pb^-1 for jets with transverse momentum between 25 and 70 GeV in the pseudorapidity range |eta| < 2.5. D*+/- mesons found in jets are fully reconstructed in the decay chain: D*+ -> D0pi+, D0 -> K-pi+, and its charge conjugate. The production rate is found to be N(D*+/-)/N(jet) = 0.025 +/- 0.001(stat.) +/- 0.004(syst.) for D*+/- mesons that carry a fraction z of the jet momentum in the range 0.3 < z < 1. Monte Carlo predictions fail to describe the data at small values of z, and this is most marked at low jet transverse momentum.Comment: 10 pages plus author list (22 pages total), 5 figures, 1 table, matches published version in Physical Review

Isometric Sliced Inverse Regression for Nonlinear Manifolds Learning

[[abstract]]Sliced inverse regression (SIR) was developed to find effective linear dimension-reduction directions for exploring the intrinsic structure of the high-dimensional data. In this study, we present isometric SIR for nonlinear dimension reduction, which is a hybrid of the SIR method using the geodesic distance approximation. First, the proposed method computes the isometric distance between data points; the resulting distance matrix is then sliced according to K-means clustering results, and the classical SIR algorithm is applied. We show that the isometric SIR (ISOSIR) can reveal the geometric structure of a nonlinear manifold dataset (e.g., the Swiss roll). We report and discuss this novel method in comparison to several existing dimension-reduction techniques for data visualization and classification problems. The results show that ISOSIR is a promising nonlinear feature extractor for classification applications.[[incitationindex]]SCI[[booktype]]紙本[[booktype]]電子

Equine infectious anemia : prevalence in working equids of livestock herds, in Minas Gerais, Brazil

Estimaram-se, no estado de Minas Gerais, a prevalência e a distribuição espacial da anemia infecciosa eqüina (AIE) em propriedades com eqüídeos de serviço. As amostras de sangue, de 6540 eqüídeos de 1940 rebanhos foram coletadas no período de setembro de 2003 a março de 2004, nos 853 municípios do estado. Utilizaram-se dois testes de laboratório em seqüência: ELISA, usando-se antígeno recombinante gp90, e imunodifusão em gel de ágar (IDGA). As prevalências foram de 5,3% [IC=4,3 a 6,3%] para rebanhos e de 3,1% [IC=2,2 a 3,9%] para animais. O estado de Minas Gerais foi considerado área endêmica para AIE. As mais altas prevalências para rebanhos e para animais foram encontradas na região Norte/Noroeste, seguida pela região Vale do Mucuri/Jequitinhonha. ___________________________________________________________________________________________________________ ABSTRACTThe prevalence and spatial distribution of equine infectious anemia (EIA) were estimated in livestock herds where equids were used as draft power and for transportation in the State of Minas Gerais, Brazil. Serum samples were collected from September/2003 to March/2004 in 853 municipalities of the state. The sample comprised 6,540 equids from 1,940 herds. Two laboratorial tests were performed in sequence: ELISA using a recombinant gp90 protein, following by the AGID. The prevalence in the herds was estimated in 5.3% [CI = 4.3 to 6.3%], and 3.1% [CI = 2.2 to 3.9%] of the animals tested were positive. Minas Gerais was considered an endemic region for EIA. The highest prevalence for herds and animals was found in North/Northwest region (strata) followed by Vale do Mucuri/Jequitinhonha region

Absolute luminosity measurements with the LHCb detector at the LHC

Absolute luminosity measurements are of general interest for colliding-beam experiments at storage rings. These measurements are necessary to determine the absolute cross-sections of reaction processes and are valuable to quantify the performance of the accelerator. Using data taken in 2010, LHCb has applied two methods to determine the absolute scale of its luminosity measurements for proton-proton collisions at the LHC with a centre-of-mass energy of 7 TeV. In addition to the classic "van der Meer scan" method a novel technique has been developed which makes use of direct imaging of the individual beams using beam-gas and beam-beam interactions. This beam imaging method is made possible by the high resolution of the LHCb vertex detector and the close proximity of the detector to the beams, and allows beam parameters such as positions, angles and widths to be determined. The results of the two methods have comparable precision and are in good agreement. Combining the two methods, an overall precision of 3.5% in the absolute luminosity determination is reached. The techniques used to transport the absolute luminosity calibration to the full 2010 data-taking period are presented.Comment: 48 pages, 19 figures. Results unchanged, improved clarity of Table 6, 9 and 10 and corresponding explanation in the tex

Absolute luminosity measurements with the LHCb detector at the LHC

Absolute luminosity measurements are of general interest for colliding-beam experiments at storage rings. These measurements are necessary to determine the absolute cross-sections of reaction processes and are valuable to quantify the performance of the accelerator. Using data taken in 2010, LHCb has applied two methods to determine the absolute scale of its luminosity measurements for proton-proton collisions at the LHC with a centre-of-mass energy of 7 TeV. In addition to the classic "van der Meer scan" method a novel technique has been developed which makes use of direct imaging of the individual beams using beam-gas and beam-beam interactions. This beam imaging method is made possible by the high resolution of the LHCb vertex detector and the close proximity of the detector to the beams, and allows beam parameters such as positions, angles and widths to be determined. The results of the two methods have comparable precision and are in good agreement. Combining the two methods, an overall precision of 3.5% in the absolute luminosity determination is reached. The techniques used to transport the absolute luminosity calibration to the full 2010 data-taking period are presented.Comment: 48 pages, 19 figures. Results unchanged, improved clarity of Table 6, 9 and 10 and corresponding explanation in the tex