Antikaon production in nucleon-nucleon reactions near threshold

The antikaon production cross section from nucleon-nucleon reactions near threshold is studied in a meson exchange model. We include both pion and kaon exchange, but neglect the interference between the amplitudes. In case of pion exchange the antikaon production cross section can be expressed in terms of the antikaon production cross section from a pion-nucleon interaction, which we take from the experimental data if available. Otherwise, a $K^*$-resonance exchange model is introduced to relate the different reaction cross sections. In case of kaon exchange the antikaon production cross section is related to the elastic $KN$ and $\bar KN$ cross sections, which are again taken from experimental measurements. We find that the one-meson exchange model gives a satisfactory fit to the available data for the $NN\to NNK\bar K$ cross section at high energies. We compare our predictions for the cross section near threshold with an earlier empirical parameterization and that from phase space models.Comment: 16 pages, LaTeX, 5 postscript figures included, submitted to Z. Phys.

Holographic Superconductor/Insulator Transition with logarithmic electromagnetic field in Gauss-Bonnet gravity

The behaviors of the holographic superconductors/insulator transition are studied by introducing a charged scalar field coupled with a logarithmic electromagnetic field in both the Einstein-Gauss-Bonnet AdS black hole and soliton. For the Einstein-Gauss-Bonnet AdS black hole, we find that: i) the larger coupling parameter of logarithmic electrodynamic field $b$ makes it easier for the scalar hair to be condensated; ii) the ratio of the gap frequency in conductivity $\omega_g$ to the critical temperature $T_c$ depends on both $b$ and the Gauss-Bonnet constant $\alpha$; and iii) the critical exponents are independent of the $b$ and $\alpha$. For the Einstein-Gauss-Bonnet AdS Soliton, we show that the system is the insulator phase when the chemical potential $\mu$ is small, but there is a phase transition and the AdS soliton reaches the superconductor (or superfluid) phase when $\mu$ larger than critical chemical potential. A special property should be noted is that the critical chemical potential is not changed by the coupling parameter $b$ but depends on $\alpha$.Comment: 15 pages, 7 figures, 3 tables, accepted for publication in Phys. Lett.

Holographic Superconductors with Power-Maxwell field

With the Sturm-Liouville analytical and numerical methods, we investigate the behaviors of the holographic superconductors by introducing a complex charged scalar field coupled with a Power-Maxwell field in the background of $d$-dimensional Schwarzschild AdS black hole. We note that the Power-Maxwell field takes the special asymptotical solution near boundary which is different from all known cases. We find that the larger power parameter $q$ for the Power-Maxwell field makes it harder for the scalar hair to be condensated. We also find that, for different $q$, the critical exponent of the system is still 1/2, which seems to be an universal property for various nonlinear electrodynamics if the scalar field takes the form of this paper.Comment: 14 pages, 1 figure, and 2 table

The holographic superconductors in higher-dimensional AdS soliton

We explore the behaviors of the holographic superconductors at zero temperature for a charged scalar field coupled to a Maxwell field in higher-dimensional AdS soliton spacetime via analytical way. In the probe limit, we obtain the critical chemical potentials increase linearly as a total dimension $d$ grows up. We find that the critical exponent for condensation operator is obtained as 1/2 independently of $d$, and the charge density is linearly related to the chemical potential near the critical point. Furthermore, we consider a slightly generalized setup the Einstein-Power-Maxwell field theory, and find that the critical exponent for condensation operator is given as $1/(4-2n)$ in terms of a power parameter $n$ of the Power-Maxwell field, and the charge density is proportional to the chemical potential to the power of $1/(2-n)$.Comment: LaTeX, 16 pages, 5 figures, typos corrected, one reference added, version to appear in European Physical Journal

Interpol: An R package for preprocessing of protein sequences

<p>Abstract</p> <p>Background</p> <p>Most machine learning techniques currently applied in the literature need a fixed dimensionality of input data. However, this requirement is frequently violated by real input data, such as DNA and protein sequences, that often differ in length due to insertions and deletions. It is also notable that performance in classification and regression is often improved by numerical encoding of amino acids, compared to the commonly used sparse encoding.</p> <p>Results</p> <p>The software "Interpol" encodes amino acid sequences as numerical descriptor vectors using a database of currently 532 descriptors (mainly from AAindex), and normalizes sequences to uniform length with one of five linear or non-linear interpolation algorithms. Interpol is distributed with open source as platform independent R-package. It is typically used for preprocessing of amino acid sequences for classification or regression.</p> <p>Conclusions</p> <p>The functionality of Interpol widens the spectrum of machine learning methods that can be applied to biological sequences, and it will in many cases improve their performance in classification and regression.</p

A New Method To Determine In Vivo Interactomes Reveals Binding of the Legionella pneumophila Effector PieE to Multiple Rab GTPases

This project was supported by grants from the Wellcome Trust and the Medical Research Council UK (G.F.). J.S.C. and L.Y. are supported by the Wellcome Trust (079643/Z/06/Z)

Activated Ion Electron Capture Dissociation (AI ECD) of proteins: synchronization of infrared and electron irradiation with ion magnetron motion.

Here, we show that to perform activated ion electron capture dissociation (AI-ECD) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a CO(2) laser, it is necessary to synchronize both infrared irradiation and electron capture dissociation with ion magnetron motion. This requirement is essential for instruments in which the infrared laser is angled off-axis, such as the Thermo Finnigan LTQ FT. Generally, the electron irradiation time required for proteins is much shorter (ms) than that required for peptides (tens of ms), and the modulation of ECD, AI ECD, and infrared multiphoton dissociation (IRMPD) with ion magnetron motion is more pronounced. We have optimized AI ECD for ubiquitin, cytochrome c, and myoglobin; however the results can be extended to other proteins. We demonstrate that pre-ECD and post-ECD activation are physically different and display different kinetics. We also demonstrate how, by use of appropriate AI ECD time sequences and normalization, the kinetics of protein gas-phase refolding can be deconvoluted from the diffusion of the ion cloud and measured on the time scale longer than the period of ion magnetron motion

Exhaustion of Activated CD8 T Cells Predicts Disease Progression in Primary HIV-1 Infection

The rate at which HIV-1 infected individuals progress to AIDS is highly variable and impacted by T cell immunity. CD8 T cell inhibitory molecules are up-regulated in HIV-1 infection and associate with immune dysfunction. We evaluated participants (n = 122) recruited to the SPARTAC randomised clinical trial to determine whether CD8 T cell exhaustion markers PD-1, Lag-3 and Tim-3 were associated with immune activation and disease progression. Expression of PD-1, Tim-3, Lag-3 and CD38 on CD8 T cells from the closest pre-therapy time-point to seroconversion was measured by flow cytometry, and correlated with surrogate markers of HIV-1 disease (HIV-1 plasma viral load (pVL) and CD4 T cell count) and the trial endpoint (time to CD4 count <350 cells/μl or initiation of antiretroviral therapy). To explore the functional significance of these markers, co-expression of Eomes, T-bet and CD39 was assessed. Expression of PD-1 on CD8 and CD38 CD8 T cells correlated with pVL and CD4 count at baseline, and predicted time to the trial endpoint. Lag-3 expression was associated with pVL but not CD4 count. For all exhaustion markers, expression of CD38 on CD8 T cells increased the strength of associations. In Cox models, progression to the trial endpoint was most marked for PD-1/CD38 co-expressing cells, with evidence for a stronger effect within 12 weeks from confirmed diagnosis of PHI. The effect of PD-1 and Lag-3 expression on CD8 T cells retained statistical significance in Cox proportional hazards models including antiretroviral therapy and CD4 count, but not pVL as co-variants. Expression of 'exhaustion' or 'immune checkpoint' markers in early HIV-1 infection is associated with clinical progression and is impacted by immune activation and the duration of infection. New markers to identify exhausted T cells and novel interventions to reverse exhaustion may inform the development of novel immunotherapeutic approaches

Flammable biomes dominated by eucalypts originated at the Cretaceous-Palaeogene boundary

Fire is a major modifier of communities, but the evolutionary origins of its prevalent role in shaping current biomes are uncertain. Australia is among the most fire-prone continents, with most of the landmass occupied by the fire-dependent sclerophyll and savanna biomes. In contrast to biomes with similar climates in other continents, Australia has a tree flora dominated by a single genus, Eucalyptus, and related Myrtaceae. A unique mechanism in Myrtaceae for enduring and recovering from fire damage likely resulted in this dominance. Here, we find a conserved phylogenetic relationship between post-fire resprouting (epicormic) anatomy and biome evolution, dating from 60 to 62 Ma, in the earliest Palaeogene. Thus, fire-dependent communities likely existed 50 million years earlier than previously thought. We predict that epicormic resprouting could make eucalypt forests and woodlands an excellent long-term carbon bank for reducing atmospheric CO2 compared with biomes with similar fire regimes in other continents

Modelling food security: Bridging the gap between the micro and the macro scale

Achieving food and nutrition security for all in a changing and globalized world remains a critical challenge of utmost importance. The development of solutions benefits from insights derived from modelling and simulating the complex interactions of the agri-food system, which range from global to household scales and transcend disciplinary boundaries. A wide range of models based on various methodologies (from food trade equilibrium to agent-based) seek to integrate direct and indirect drivers of change in land use, environment and socio-economic conditions at different scales. However, modelling such interaction poses fundamental challenges, especially for representing non-linear dynamics and adaptive behaviours. We identify key pieces of the fragmented landscape of food security modelling, and organize achievements and gaps into different contextual domains of food security (production, trade, and consumption) at different spatial scales. Building on in-depth reflection on three core issues of food security – volatility, technology, and transformation – we identify methodological challenges and promising strategies for advancement. We emphasize particular requirements related to the multifaceted and multiscale nature of food security. They include the explicit representation of transient dynamics to allow for path dependency and irreversible consequences, and of household heterogeneity to incorporate inequality issues. To illustrate ways forward we provide good practice examples using meta-modelling techniques, non-equilibrium approaches and behavioural-based modelling endeavours. We argue that further integration of different model types is required to better account for both multi-level agency and cross-scale feedbacks within the food system.</p