Walking, hopping and jumping: a model of transcription factor dynamics on DNA

We present a model of how transcription factors scan DNA to find their specific binding sites. Following the classical work of Winter et al. (1981), our model assumes two modes of transcription factor dynamics. Adjacent moves, where the proteins make a single step movement to one side, or short walks where the transcription factors slide along the DNA several binding sites at a time. The purpose of this article is twofold. Firstly, we discuss how such a system can be efficiently modeled computationally. Secondly, we analyse how the mean first binding times of transcription factors to their specific time depends on key parameters of the system

Evolving Biological Systems: Evolutionary Pressure to Inefficiency

The evolution of quantitative details (i.e. “parameter values”) of biological systems is highly under-researched. We use evolutionary algorithms to co-evolve parameters for a generic but biologically plausible topological differential equation model of nutrient uptake. In our model, evolving cells compete for a finite pool of nutrient resources. From our investigations it emerges that the choice of values is very important for the properties of the biological system. Our analysis also shows that clonal populations that are not subject to competition from other species best grow at a very slow rate. However, if there is co-evolutionary pressure, that is, if a population of clones has to compete with other cells, then the fast growth is essential, so as not to leave resources to the competitor. We find that this strategy, while favoured evolutionarily, is inef- ficient from an energetic point of view, that is less growth is achieved per unit of input nutrient. We conclude, that competition can lead to an evolutionary pressure towards inefficiency

Evolving strategies for single-celled organisms in multi-nutrient environments

When micro-organisms are in environments with multiple nutrients, they often preferentially utilise one first. A second is only utilised once the first is exhausted. Such a two-phase growth pattern is known as diauxic growth. Experimentally, this manifests itself through two distinct exponential growth phases separated by a lag phase of arrested growth. The dura- tion of the lag phase can be quite substantial. From an evolu- tionary point of view the existence of a lag phase is somewhat puzzling because it implies a substantial loss of growth op- portunity. Mutants with shorter lag phases would be prone to outcompete those with longer phases. Yet in nature, diauxic growth with lag phases appears to be a robust phenomenon. We introduce a model of the evolution of diauxic growth that captures the basic interactions regulating it in bacteria. We observe its evolution without a lag phase. We conclude that the lag phase is an adaptation that is only beneficial when fit- ness is averaged over a large number of environments

Quasi-periodic pulsations in solar and stellar flares: re-evaluating their nature in the context of power-law flare Fourier spectra

The nature of quasi-periodic pulsations in solar and stellar flares remains debated. Recent work has shown that power-law-like Fourier power spectra, also referred to as 'red' noise processes, are an intrinsic property of solar and stellar flare signals, a property that many previous studies of this phenomenon have not accounted for. Hence a re-evaluation of the existing interpretations and assumptions regarding QPP is needed. Here we adopt a Bayesian method for investigating this phenomenon, fully considering the Fourier power law properties of flare signals. Using data from the PROBA2/LYRA, Fermi/GBM, Nobeyama Radioheliograph and Yohkoh/HXT instruments, we study a selection of flares from the literature identified as QPP events. Additionally we examine optical data from a recent stellar flare that appears to exhibit oscillatory properties. We find that, for all but one event tested, an explicit oscillation is not required in order to explain the observations. Instead, the flare signals are adequately described as a manifestation of a power law in the Fourier power spectrum, rather than a direct signature of oscillating components or structures. However, for the flare of 1998 May 8, strong evidence for the existence of an explicit oscillation with P ~ 14-16 s is found in the 17 GHz radio data and the 13-23 keV Yohkoh HXT data. We conclude that, most likely, many previously analysed events in the literature may be similarly described in terms of power laws in the flare Fourier power spectrum, without the need to invoke a narrowband, oscillatory component. As a result the prevalence of oscillatory signatures in solar and stellar flares may be less than previously believed. The physical mechanism behind the appearance of the observed power laws is discussed.Comment: 11 pages, 7 figures, 1 table. Accepted for publication in The Astrophysical Journa

Women's position and attitudes towards female genital mutilation in Egypt : a secondary analysis of the Egypt demographic and health surveys, 1995-2014

Background: Female genital mutilation (FGM) is still widespread in Egyptian society. It is strongly entrenched in local tradition and culture and has a strong link to the position of women. To eradicate the practice a major attitudinal change is a required for which an improvement in the social position of women is a prerequisite. This study examines the relationship between Egyptian women's social positions and their attitudes towards FGM, and investigates whether the spread of anti-FGM attitudes is related to the observed improvements in the position of women over time. Methods: Changes in attitudes towards FGM are tracked using data from the Egypt Demographic and Health Surveys from 1995 to 2014. Multilevel logistic regressions are used to estimate 1) the effects of indicators of a woman's social position on her attitude towards FGM, and 2) whether these effects change over time. Results: Literate, better educated and employed women are more likely to oppose FGM. Initially growing opposition to FGM was related to the expansion of women's education, but lately opposition to FGM also seems to have spread to other segments of Egyptian society. Conclusions: The improvement of women's social position has certainly contributed to the spread of anti-FGM attitudes in Egyptian society. Better educated and less traditional women were at the heart of this change, and formed the basis from where anti-FGM sentiment has spread over wider segments of Egyptian society

Occupational Health Problem Network : the Exposome

We present a thinking on the concept of relational networks applied to the french national occupational disease surveillance and prevention network (R\'eseau National de Vigilance et de Pr\'evention des Pathologies Professionnelles, RNV3P). This approach consists in searching common exposures to occupational health problems

Size-independence of statistics for boundary collisions of random walks and its implications for spin-polarized gases

A bounded random walk exhibits strong correlations between collisions with a boundary. For an one-dimensional walk, we obtain the full statistical distribution of the number of such collisions in a time t. In the large t limit, the fluctuations in the number of collisions are found to be size-independent (independent of the distance between boundaries). This occurs for any inter-boundary distance, including less and greater than the mean-free-path, and means that this boundary effect does not decay with increasing system-size. As an application, we consider spin-polarized gases, such as 3-Helium, in the three-dimensional diffusive regime. The above results mean that the depolarizing effect of rare magnetic-impurities in the container walls is orders of magnitude larger than a Smoluchowski assumption (to neglect correlations) would imply. This could explain why depolarization is so sensitive to the container's treatment with magnetic fields prior to its use.Comment: 5 page manuscript with extra details in appendices (additional 3 pages

Impact of dopant species on the interfacial trap density and mobility in amorphous In-X-Zn-O solution-processed thin-film transistors

Alloying of In/Zn oxides with various X atoms stabilizes the IXZO structures but generates electron traps in the compounds, degrading the electron mobility. To assess whether the latter is linked to the oxygen affinity or the ionic radius, of the X element, several IXZO samples are synthesized by the sol-gel process, with a large number (14) of X elements. The IXZOs are characterized by XPS, SIMS, DRX, and UV-spectroscopy and used for fabricating thin film transistors. Channel mobility and the interface defect density NST, extracted from the TFT electrical characteristics and low frequency noise, followed an increasing trend and the values of mobility and NST are linked by an exponential relation. The highest mobility (8.5 cm2/Vs) is obtained in In-Ga-Zn-O, and slightly lower value for Sb and Sn-doped IXZOs, with NST is about 2E12 cm2/eV, close to that of the In-Zn-O reference TFT. This is explained by a higher electronegativity of Ga, Sb, and Sn than Zn and In, their ionic radius values being close to that of In and Zn. Consequently, Ga, Sb, and Sn induce weaker perturbations of In-O and Zn-O sequences in the sol-gel process, than the X elements having lower electronegativity and different ionic radius. The TFTs with X = Ca, Al, Ni and Cu exhibited the lowest mobility and NST > 1E13 cm2/eV, most likely because of metallic or oxide clusters formation

Non-Arrhenius conduction due to the interface-trap-induced disorder in X-doped amorphous InXZnO thin-film transistors

Thin film transistors, with channels composed of In-X-Zn oxides, IXZO, with X dopants: Ga, Sb, Be, Mg, Ag, Ca, Al, Ni, and Cu, were fabricated and their I-V characteristics were taken at selected temperatures in the 77K<T<300K range. The low field mobility, mu, and the interface defect density, Nst were extracted from the characteristics for each of the studied IXZOs. At higher T the mobility follows the Arrhenius law with an upward distortion, increasing as T was lowered, gradually transforming into the exp [-(T0/T)1/4] variation. We showed that mu(T, Nst) follows mu0exp[-Eaeff(T,Nst)/kT], with T-dependent effective activation energy Eaeff(T, Nst) accounts for the data, revealing a linear correlation between Eaeff and Nst at higher T. Temperature variation of Eaeff(T, Nst) was evaluated using a model assuming a random distribution of conduction mobility edge Ec values in the oxides, stemming from spatial fluctuations induced by disorder in the interface traps distribution. For a Gaussian distribution of Ec, the activation energy Eaeff(T, Nst) varies linearly with 1/T, which accounts satisfactorily for the data obtained on all the studied IXZOs. The model also shows that Eaeff(T, Nst) is a linear function of Nst at a fixed T, which explains the exponential decrease of mu with NST

Welfare Impacts of Agricultural and Non-Agricultural Trade Reforms

The variability of protection rates within sectors is frequently particularly high in agriculture relative to non-agriculture. Standard aggregation procedures ignore the variability within sectors, and underweight the importance of highly protected sectors. It therefore seems likely that they underestimate the potential benefits of agricultural trade reform relative to non-agricultural reform. This study examines this question using a new procedure for aggregating trade distortions. It finds that the key impact of using better aggregators is to increase the benefits of both agricultural and non-agricultural reform. It finds that using optimal aggregation procedures increases the measured importance of agricultural trade reform relative to non-agricultural reform from a very high initial level, but only by around two percentage points.agricultural trade, nonagricultural trade, trade distortions, tariffs, aggregation, World Trade Organization, WTO, trade reform, Food Security and Poverty, International Relations/Trade, F13, F14, Q13, Q17, Q18,