Using the local gyrokinetic code, GS2, to investigate global ITG modes in tokamaks. (I) s-α{\alpha} model with profile and flow shear effects

This paper combines results from a local gyrokinetic code with analytical theory to reconstruct the global eigenmode structure of the linearly unstable ion-temperature-gradient (ITG) mode with adiabatic electrons. The simulations presented here employ the s-${\alpha}$ tokamak equilibrium model. Local gyrokinetic calculations, using GS2 have been performed over a range of radial surfaces, x, and for ballooning phase angle, p, in the range -${\pi} {\leq} p {\leq\pi}$, to map out the complex local mode frequency, ${\Omega_0(x, p) = \omega_0(x, p) + i\gamma_0(x, p)}$. Assuming a quadratic radial profile for the drive, namely ${\eta_i = L_n/L_T}$, (holding constant all other equilibrium profiles such as safety factor, magnetic shear etc.), ${\Omega_0(x, p)}$ has a stationary point. The reconstructed global mode then sits on the outboard mid plane of the tokamak plasma, and is known as a conventional or isolated mode, with global growth rate, ${\gamma}$ ~ Max[${\gamma_0(x, p)}$], where ${\gamma_0(x, p)}$ is the local growth rate. Taking the radial variation in other equilibrium profiles (e.g safety factor q(x)) into account, removes the stationary point in ${\Omega_0(x, p)}$ and results in a mode that peaks slightly away from the outboard mid-plane with a reduced global growth rate. Finally, the influence of flow shear has also been investigated through a Doppler shift, ${\omega_0 \rightarrow \omega_0 + n\Omega^{\prime}x}$, where n is the toroidal mode number and ${\Omega^{\prime}}$ incorporates the effect of flow shear. The equilibrium profile variation introduces an asymmetry to the growth rate spectrum with respect to the sign of ${\Omega^{\prime}}$, consistent with recent global gyrokinetic calculations.Comment: 10 pages, 8 figures and 1 tabl

Effects of mannose, fructose, and fucose on the structure, stability, and hydration of lysozyme in aqueous solution

The bio-protective properties of monosaccharaides, namely mannose, fructose and fucose, on the stability and dynamical properties of the NMR determined hen egg-white lysozyme structure have been investigated by means of molecular dynamics simulations at room temperature in aqueous solution and in 7 and 13 wt % concentrations of the three sugars. Results are discussed in the framework of the bio-protective phenomena. The three sugars show similar bio-protective behaviours at room temperature (300 K) in the concentration range studied as shown by the small RMSDs of the resulting MD structures from that of starting NMR structure. The effects of sugars on protein conformation are found to be relatively strong in that the conformation of lysozyme is stable after an initial 9 ns equilibration for fucose and mannose and 12 ns equilibration for fructose, respectively, at high concentrations. For mannose the final RMSD is significantly smaller than that of fucose and fructose at the higher concentration, while at the lower concentration the RMSD are essentially the same. The radial distribution function of the water and sugars around lysozyme was used to monito

Impact of Grazing on Soil Seed Bank Replenishment under the Mediterranean Climate of Northern Syria

Rangelands represent 70% of the semi-arid and arid Mediterranean land mass. It is a habitat for millions of people whose livelihood depends on animal husbandry. The revolutionary developments in the animal husbandry and veterinary medicines resulted in exponential increases in livestock and human populations living on and from dry lands. To respond to population growth, expansion on urbanization, transportation and road networks, land reform and rural development policies forced nomads to adopt sedentary lifestyles. The demographic changes coupled with national and international border crossing restrictions escalated opportunistic cultivation, and excessive exploitation of the scarce and slowly renewable vegetation cover of rangelands (Louhaichi, 2011). In an attempt to stop and reverse the degradation process, large-scale re-vegetation programs based on transplanting and reseeding with perennial shrubs, resting and grazing management systems were devised and implemented (Mosallam, 2007; Mourad et al., 2000; Le Houerou, 1981). This study aimed to evaluate the impacts of the rehabilitation programs on the above-ground vegetation cover and soil seed bank replenishment in the Syrian rangelands. The underlying assumption of the rehabilitation program is that with a wellestablished perennial plant cover and proper grazing management, top soil is stabilized, soil moisture, nutrients and seed bank are replenished, organic matter is accumulated and microorganisms’ activity is promoted resulting in greater abundance, species richness and diversity of annuals. To test the above hypothesis, field and controlled environment based studies were carried out with quantitative data collection and processing on plant species abundance, richness and diversity of above-ground vegetation and soil seed bank for fully protected rotationally and continuously grazed areas of 10 rangeland sites in northern Syria for two consecutive seasons based on Russi et al., 1992; Magurran, 2004)

Generalised ballooning theory of two-dimensional tokamak modes

In this work, using solutions from a local gyrokinetic flux-tube code combined with higher order ballooning theory, a new analytical approach is developed to reconstruct the global linear mode structure with associated global mode frequency. In addition to the isolated mode (IM), which usually peaks on the outboard mid-plane, the higher order ballooning theory has also captured other types of less unstable global modes: (a) the weakly asymmetric ballooning theory (WABT) predicts a mixed mode (MM) that undergoes a small poloidal shift away from the outboard mid-plane, (b) a relatively more stable general mode (GM) balloons on the top (or bottom) of the tokamak plasma. In this paper, an analytic approach is developed to combine these disconnected analytical limits into a single generalised ballooning theory. This is used to investigate how an IM behaves under the effect of sheared toroidal flow. For small values of flow an IM initially converts into a MM where the results of WABT are recaptured, and eventually, as the flow increases, the mode asymptotically becomes a GM on the top (or bottom) of the plasma. This may be an ingredient in models for understanding why in some experimental scenarios, instead of large edge localised modes (ELMs), small ELMs are observed. Finally, our theory can have other important consequences, especially for calculations involving Reynolds stress driven intrinsic rotation through the radial asymmetry in the global mode structures. Understanding the intrinsic rotation is significant because external torque in a plasma the size of ITER is expected to be relatively low

Spin-dependent effective interactions for halo nuclei

We discuss the spin-dependence of the effective two-body interactions appropriate for three-body computations. The only reasonable choice seems to be the fine and hyperfine interactions known for atomic electrons interacting with the nucleus. One exception is the nucleon-nucleon interaction imposing a different type of symmetry. We use the two-neutron halo nucleus 11Li as illustration. We demonstrate that models with the wrong spin-dependence are basically without predictive power. The Pauli forbidden core and valence states must be consistently treated.Comment: TeX file, 6 pages, 3 postscript figure

Positron-molecule interactions: resonant attachment, annihilation, and bound states

This article presents an overview of current understanding of the interaction of low-energy positrons with molecules with emphasis on resonances, positron attachment and annihilation. Annihilation rates measured as a function of positron energy reveal the presence of vibrational Feshbach resonances (VFR) for many polyatomic molecules. These resonances lead to strong enhancement of the annihilation rates. They also provide evidence that positrons bind to many molecular species. A quantitative theory of VFR-mediated attachment to small molecules is presented. It is tested successfully for selected molecules (e.g., methyl halides and methanol) where all modes couple to the positron continuum. Combination and overtone resonances are observed and their role is elucidated. In larger molecules, annihilation rates from VFR far exceed those explicable on the basis of single-mode resonances. These enhancements increase rapidly with the number of vibrational degrees of freedom. While the details are as yet unclear, intramolecular vibrational energy redistribution to states that do not couple directly to the positron continuum appears to be responsible for these enhanced annihilation rates. Downshifts of the VFR from the vibrational mode energies have provided binding energies for thirty species. Their dependence upon molecular parameters and their relationship to positron-atom and positron-molecule binding energy calculations are discussed. Feshbach resonances and positron binding to molecules are compared with the analogous electron-molecule (negative ion) cases. The relationship of VFR-mediated annihilation to other phenomena such as Doppler-broadening of the gamma-ray annihilation spectra, annihilation of thermalized positrons in gases, and annihilation-induced fragmentation of molecules is discussed.Comment: 50 pages, 40 figure

Detection, identification and characterization of extended-spectrum beta-lactamases producing Enterobacteriaceae in wastewater and salads marketed in Ouagadougou, Burkina Faso

Extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-PE) represent a threat for failure of empirical antibiotic therapy and are associated with high mortality, morbidity and expenses. The aims of this study was to determine the prevalence of ESBL-PE and multidrug resistant enterobacteria (MDR), enterobacteria profil, investigate the associated resistance in wastewater and salads. After wastewater and salad sampling, enterobacteria was isoled on (EMB + 4μg / L cefotaxim). The stains of Enterobacteriaceae were identified by using biochemical methods and confirmed as ESBL by double-disc synergy test (amoxicillin/clavulanic acid with cefotaxime 30 μg, ceftazidime 30 μg and ceftriaxone 30 μg). Finally, the associated resistance was investigated by testing the susceptibility of the strains by the disc diffusion method. Global prevalence of ESBL-PE was 53.92% (95% CI: 48,2-59,5) (153/293), 61.11% from wastewater and 42.47% from salads. Major ESBL-E was Escherichia coli (73.44%), followed by Klebsiella pneumoniae (21.88%). Resistance to the aminoglycoside , fluroquinolonones and sulfonamides classes were dominant, observed in 53,83%, 93,86% and 98,95% of the isolates, respectively. The frequence of MDR was hight to channel1 (32,40%) and channel2 (26,26%). This study reports very worrying results. There is an urgent need to develop measures to monitor the spread of these multidrug-resistant strains.Keywords: Wastewater, ESBL-PE, Salads, Ouagadougou

Ecology of Phlebotomine Sand Flies in the Rural Community of Mont Rolland (Thiès Region, Senegal): Area of Transmission of Canine Leishmaniasis

BACKGROUND: Different epidemiological studies previously indicated that canine leishmaniasis is present in the region of Thiès (Senegal). However, the risks to human health, the transmission cycle and particularly the implicated vectors are unknown. METHODOLOGY/PRINCIPAL FINDINGS: To improve our knowledge on the population of phlebotomine sand flies and the potential vectors of canine leishmaniasis, sand flies were collected using sticky traps, light traps and indoor spraying method using pyrethroid insecticides in 16 villages of the rural community of Mont Rolland (Thiès region) between March and July 2005. The 3788 phlebotomine sand flies we collected (2044 males, 1744 females) were distributed among 9 species of which 2 belonged to the genus Phlebotomus: P. duboscqi (vector of cutaneous leishmaniasis in Senegal) and P. rodhaini. The other species belonged to the genus Sergentomyia: S. adleri, S. clydei, S. antennata, S. buxtoni, S. dubia, S. schwetzi and S. magna. The number of individuals and the species composition differed according to the type of trap, suggesting variable, species-related degrees of endophily or exophily. The two species of the genus Phlebotomus were markedly under-represented in comparison to the species of the genus Sergentomyia. This study also shows a heterogeneous spatial distribution within the rural community that could be explained by the different ecosystems and particularly the soil characteristics of this community. Finally, the presence of the S. dubia species appeared to be significantly associated with canine leishmaniasis seroprevalence in dogs. CONCLUSIONS/SIGNIFICANCE: Our data allow us to hypothesize that the species of the genus Sergentomyia and particularly the species S. dubia and S. schwetzi might be capable of transmitting canine leishmaniasis. These results challenge the dogma that leishmaniasis is exclusively transmitted by species of the genus Phlebotomus in the Old World. This hypothesis should be more thoroughly evaluated

Etiology and factors associated with pneumonia in children under 5 years of age in Mali: A prospective case-control study

Background: There are very limited data on children with pneumonia in Mali. The objective was to assess the etiology and factors associated with community-acquired pneumonia in hospitalized children <5 years of age in Mali. Methods: A prospective hospital-based case-control study

Serum Alpha-Fetoprotein Predicts Treatment Outcome in Chronic Hepatitis C Patients Regardless of HCV Genotype

We examined the association between serum alpha-fetoprotein (AFP) level and sustained virological response (SVR) in 93 chronic hepatitis C patients. The SVR rate was much higher among patients with serum AFP levels below rather than above the median value (5.7 ng/ml) (58.7% and 19.2%, respectively; P<0.0001). Serum AFP should be added to the list of factors predictive of treatment response in chronic hepatitis C