Abstract:
Grain amaranth is an emerging crop that produces seeds having high quality protein with balanced amino-acid content. However, production is restricted by agronomic limitations that result in yields that are lower than those normally produced by cereals. In this work, the use of five different rhizobacteria were explored as a strategy to promote growth and yields in Amaranthus hypochondriacus cv. Nutrisol and A. cruentus cv. Candil, two commercially important grain amaranth cultivars. The plants were grown in a rich substrate, high in organic matter, nitrogen (N), and phosphorus (P) and under greenhouse conditions. Burkholderia ambifaria Mex-5 and B. caribensis XV proved to be the most efficient strains and significantly promoted growth in both grain amaranth species tested. Increased grain yield and harvest index occurred in combination with chemical fertilization when tested in A. cruentus. Growth-promotion and improved yields correlated with increased N content in all tissues examined. Positive effects on growth also occurred in A. cruentus plants grown in a poor soil, even after N and P fertilization. No correlation between non-structural carbohydrate levels in roots of inoculated plants and growth promotion was observed. Conversely, gene expression assays performed at 3-, 5- and 7-weeks after seed inoculation in plants inoculated with B. caribensis XV identified a tissue-specific induction of several genes involved in photosynthesis, sugar- and N- metabolism and transport. It is concluded that strains of Burkholderia effectively promote growth and increase seed yields in grain amaranth. Growth promotion was particularly noticeable in plants grown in an infertile soil but also occurred in a well fertilized rich substrate. The positive effects observed may be attributed to a bio-fertilization effect that led to increased N levels in roots and shoots. The latter effect correlated with the differential induction of several genes involved in carbon and N metabolism and transport.

Abstract:
A total of 2,700,168 raw reads were obtained from six 454 pyrosequencing runs, which were assembled into 21,207 high quality sequences (20,408 isotigs + 799 contigs). The average sequence length was 1,064 bp and 930 bp for isotigs and contigs, respectively. Only 5,113 singletons were recovered after quality control. Contigs/isotigs were further incorporated into 15,667 isogroups. All unique sequences were queried against the nr, TAIR, UniRef100, UniRef50 and Amaranthaceae EST databases for annotation. Functional GO annotation was performed with all contigs/isotigs that produced significant hits with the TAIR database. Only 8,260 sequences were found to be homologous when the transcriptomes of A. tuberculatus and A. hypochondriacus were compared, most of which were associated with basic house-keeping processes. Digital expression analysis identified 1,971 differentially expressed genes in response to at least one of four stress treatments tested. These included several multiple-stress-inducible genes that could represent potential candidates for use in the engineering of stress-resistant plants. The transcriptomic data generated from pigmented stems shared similarity with findings reported in developing stems of Arabidopsis and black cottonwood (Populus trichocarpa).This study represents the first large-scale transcriptomic analysis of A. hypochondriacus, considered to be a highly nutritious and stress-tolerant crop. Numerous genes were found to be induced in response to (a)biotic stress, many of which could further the understanding of the mechanisms that contribute to multiple stress-resistance in plants, a trait that has potential biotechnological applications in agriculture.The genus Amaranthus L. (Caryophyllales: Amaranthaceae) comprises C4 dicotyledonous herbaceous plants classified into approximately 70 species. It has a worldwide distribution, although most species are found in the warm temperate and tropical regions of the world [1,2]. Many amaranth species

Abstract:
This study was aimed to elucidate the putative causal agents. Healthy and diseased Echinopsis sp. and Opuntia sp. plants were collected from several Mexican nurseries. DNA was extracted from proliferating buds or stems and used in Polymerase Chain Reactions (PCR) to detect phytoplasmas. Two universal phytoplasma primer pairs were tested in nested PCR, initially with primer pair P1/tint followed by primer pair R16F2/R16R2 in a sequential test. The amplified DNA fragments were cloned and sequenced. Two different 16S rDNA partial operons were determined. One of present sequences was always associated to yellow mosaics in Echinopsis while the other to witches-broom syndromes in Opuntia. The comparative analysis of the sequences against the GenBank indicated that they were highly but not 100% homologous to phytoplasmas of group 16SrII. This is of major importance since this is the first report of finding representatives of this group affecting cacti in the Americas; all other reports of this kind of phytoplasmas have been detected in mainly in Asia.

Abstract:
The sample consisted of 179 patients younger than 70 years of age, who were evaluated for chest pain at the emergency department daytime Monday through Friday and judged by a physician to have no organic cause for their chest pain. The study had a cross-sectional design.Emotive coping was related to chest pain intensity (r = 0.17, p = 0.02). Women used emotive coping to a greater extent than did men (p = 0.05). In the multivariate analysis was shown that physical activity decreased emotive coping (OR 0.13, p < 0.0001) while sex, age, sleep, mental strain at work and negative life events increased emotive coping. Twenty-seven percent of the patients had sleep problems 8 to14 nights per month or more. Permanent stress at work during the last year was reported by 18% of the patients and stress at home by 7%. Thirty-five percent of the patients were worried often or almost all the time about being rushed at work and 23% were worried about being unable to keep up with their workload. Concerning total life events, 20% reported that a close relative had had a serious illness and 27% had reasons to be worried about a close relative.Our results indicated that patients with more intense UCP more often apply emotive coping in dealing with their pain. Given that emotive coping was also found to be related to disturbed sleep, negative life events, mental strain at work and physical activity, it may be of value to help these patients to both verbalise their emotions and to become cognizant of the influence of such factors on their pain experience.Chest pain is one of the most common symptoms prompting individuals to seek acute care; however, more than half of the patients will not be judged to have chest pain of a cardiac origin [1,2]. In Sweden, this patient group has increased dramatically during the last fifteen years [3].The unexplained chest pain (UCP) is often experienced for more than three months as was shown in two qualitative studies [4,5] that included 20 subject each.

Abstract:
Gyrokinetic simulations have greatly improved our theoretical understanding of turbulent transport in fusion devices. Most gyrokinetic models in use are delta-f simulations in which the slowly varying radial profiles of density and temperature are assumed to be constant for turbulence saturation times, and only the turbulent electromagnetic fluctuations are calculated. New massive simulations are being built to self-consistently determine the radial profiles of density and temperature. However, these new codes have failed to realize that modern gyrokinetic formulations, composed of a gyrokinetic Fokker-Planck equation and a gyrokinetic quasineutrality equation, are only valid for delta-f simulations that do not reach the longer transport time scales necessary to evolve radial profiles. In tokamaks, due to axisymmetry, the evolution of the axisymmetric radial electric field is a challenging problem requiring substantial modifications to gyrokinetic treatments. In this thesis, I study the effect of turbulence on the global electric field and plasma flows. By studying the current conservation equation, or vorticity equation, I prove that the long wavelength, axisymmetric flow must remain neoclassical and I show that the tokamak is intrinsically ambipolar, i.e., the radial current is zero to a very high order for any long wavelength radial electric field. Intrinsic ambipolarity is the origin of the problems with the modern gyrokinetic approach since the lower order gyrokinetic quasineutrality (if properly evaluated) is effectively independent of the radial electric field. I propose a new gyrokinetic formalism to solve for the global radial electric field.

Abstract:
The dynamics of electrons in ac driven double quantum dots have been extensively analyzed by means of Floquet theory. In these systems, coherent destruction of tunneling has been shown to occur for certain ac field parameters. In the present work we analyze, by means of Floquet theory, the electron dynamics of a triple quantum dot in series attached to electric contacts, where the central dot position oscillates. In particular, we analyze the quasienergy spectrum of this ac driven nanoelectromechanical system, as a function of the intensity and frequency of the ac field and of external dc voltages. For strong driving fields, we derive, by means of perturbation theory, analytical expressions for the quasienergies of the driven oscillator system. From this analysis we discuss the conditions for coherent destruction of tunneling (CDT) to occur as a function of detuning and field parameters. For zero detuning, and from the invariance of the Floquet Hamiltonian under a generalized parity transformation, we find analytical expressions describing the symmetry properties of the Fourier components of the Floquet states under such transformation. By using these expressions, we show that in the vicinity of the CDT condition, the quasienergy spectrum exhibits exact crossings which can be characterized by the parity properties of the corresponding eigenvectors.

Abstract:
Recently, the electrostatic gyrokinetic Hamiltonian and change of coordinates have been computed to order $\epsilon^2$ in general magnetic geometry. Here $\epsilon$ is the gyrokinetic expansion parameter, the gyroradius over the macroscopic scale length. Starting from these results, the long-wavelength limit of the gyrokinetic Fokker-Planck and quasineutrality equations is taken for tokamak geometry. Employing the set of equations derived in the present article, it is possible to calculate the long-wavelength components of the distribution functions and of the poloidal electric field to order $\epsilon^2$. These higher-order pieces contain both neoclassical and turbulent contributions, and constitute one of the necessary ingredients (the other is given by the short-wavelength components up to second order) that will eventually enter a complete model for the radial transport of toroidal angular momentum in a tokamak in the low flow ordering. Finally, we provide an explicit and detailed proof that the system consisting of second-order gyrokinetic Fokker-Planck and quasineutrality equations leaves the long-wavelength radial electric field undetermined; that is, the turbulent tokamak is intrinsically ambipolar.

Abstract:
The radial flux of toroidal angular momentum is needed to determine tokamak intrinsic rotation profiles. Its computation requires knowledge of the gyrokinetic distribution functions and turbulent electrostatic potential to second-order in $\epsilon = \rho/L$, where $\rho$ is the ion Larmor radius and $L$ is the variation length of the magnetic field. In this article, a complete set of equations to calculate the radial transport of toroidal angular momentum in any tokamak is presented. In particular, the $O(\epsilon^2)$ equations for the turbulent components of the distribution functions and electrostatic potential are given for the first time without assuming that the poloidal magnetic field over the magnetic field strength is small.

Abstract:
Gyrokinetic theory is based on an asymptotic expansion in the small parameter $\epsilon$, defined as the ratio of the gyroradius and the characteristic length of variation of the magnetic field. In this article, this ordering is strictly implemented to compute the electrostatic gyrokinetic phase-space Lagrangian in general magnetic geometry to order $\epsilon^2$. In particular, a new expression for the complete second-order gyrokinetic Hamiltonian is provided, showing that in a rigorous treatment of gyrokinetic theory magnetic geometry and turbulence cannot be dealt with independently. The new phase-space gyrokinetic Lagrangian gives a Vlasov equation accurate to order $\epsilon^2$ and a Poisson equation accurate to order $\epsilon$. The final expressions are explicit and can be implemented into any simulation without further computations.

Abstract:
Self-consistent equations for intrinsic rotation in tokamaks with small poloidal magnetic field $B_p$ compared to the total magnetic field $B$ are derived. The model gives the momentum redistribution due to turbulence, collisional transport and energy injection. Intrinsic rotation is determined by the balance between the momentum redistribution and the turbulent diffusion and convection. Two different turbulence regimes are considered: turbulence with characteristic perpendicular lengths of the order of the ion gyroradius, $\rho_i$, and turbulence with characteristic lengths of the order of the poloidal gyroradius, $(B/B_p) \rho_i$. Intrinsic rotation driven by gyroradius scale turbulence is mainly due to the effect of neoclassical corrections and of finite orbit widths on turbulent momentum transport, whereas for the intrinsic rotation driven by poloidal gyroradius scale turbulence, the slow variation of turbulence characteristics in the radial and poloidal directions and the turbulent particle acceleration can be become as important as the neoclassical and finite orbit width effects. The magnetic drift is shown to be indispensable for the intrinsic rotation driven by the slow variation of turbulence characteristics and the turbulent particle acceleration. The equations are written in a form conducive to implementation in a flux tube code, and the effect of the radial variation of the turbulence is included in a novel way that does not require a global gyrokinetic formalism.