Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal Frustration" when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14249-14255). Similarly, repeats and structural mosaics may be fundamentally related to landscapes with multiple embedded funnels. Here we present analytical tools to detect and compare structural repetitions in protein molecules. By an exhaustive analysis of the distribution of structural repeats using a robust metric we define those portions of a protein molecule that best describe the overall structure as a tessellation of basic units. The patterns produced by such tessellations provide intuitive representations of the repeating regions and their association towards higher order arrangements. We find that some protein architectures can be described as nearly periodic, while in others clear separations between repetitions exist. Since the method is independent of amino acid sequence information we can identify structural units that can be encoded by a variety of distinct amino acid sequences

COLA. III. Radio Detection of Active Galactic Nucleus in Compact Moderate Luminosity Infrared Galaxies

We present results from 4.8 GHz Very Large Array (VLA) and global very long baseline interferometry (VLBI) observations of the northern half of the moderate FIR luminosity (median L_(IR) = 10^(11.01) L_☉) COLA sample of star-forming galaxies. VLBI sources are detected in a high fraction (20/90) of the galaxies observed. The radio luminosities of these cores (~10^(21) W Hz^(–1)) are too large to be explained by radio supernovae or supernova remnants and we argue that they are instead powered by active galactic nuclei (AGNs). These sub-parsec scale radio cores are preferentially detected toward galaxies whose VLA maps show bright 100-500 parsec scale nuclear radio components. Since these latter structures tightly follow the FIR to radio-continuum correlation for star formation, we conclude that the AGN-powered VLBI sources are associated with compact nuclear starburst environments. The implications for possible starburst-AGN connections are discussed. The detected VLBI sources have a relatively narrow range of radio luminosity consistent with models in which intense compact Eddington-limited starbursts regulate the gas supply onto a central supermassive black hole. The high incidence of AGN radio cores in compact starbursts suggests little or no delay between the starburst phase and the onset of AGN activity

Ion-scale turbulence in MAST: anomalous transport, subcritical transitions, and comparison to BES measurements

We investigate the effect of varying the ion temperature gradient (ITG) and toroidal equilibrium scale sheared flow on ion-scale turbulence in the outer core of MAST by means of local gyrokinetic simulations. We show that nonlinear simulations reproduce the experimental ion heat flux and that the experimentally measured values of the ITG and the flow shear lie close to the turbulence threshold. We demonstrate that the system is subcritical in the presence of flow shear, i.e., the system is formally stable to small perturbations, but transitions to a turbulent state given a large enough initial perturbation. We propose that the transition to subcritical turbulence occurs via an intermediate state dominated by low number of coherent long-lived structures, close to threshold, which increase in number as the system is taken away from the threshold into the more strongly turbulent regime, until they fill the domain and a more conventional turbulence emerges. We show that the properties of turbulence are effectively functions of the distance to threshold, as quantified by the ion heat flux. We make quantitative comparisons of correlation lengths, times, and amplitudes between our simulations and experimental measurements using the MAST BES diagnostic. We find reasonable agreement of the correlation properties, most notably of the correlation time, for which significant discrepancies were found in previous numerical studies of MAST turbulence.Comment: 67 pages, 37 figures. Submitted to PPC

Adolescent Reactions to Maternal Responsiveness and Internalizing Symptomatology: A Daily Diary Investigation

A daily diary methodology was employed to gather teens’ perceptions of maternal responsiveness to daily stressful events and teens’ reactions to maternal responsiveness in a diverse sample (792 entries from 104 teens; 81% African American, mean age 13.7 years). Additionally, parents and teens completed baseline reports of internalizing symptoms. Diary findings were congruent with prior studies employing self-report measures of global maternal responses to emotion (e.g., higher probability of Accepting reactions to supportive responses, higher probabilities of Attack, Avoid-Withdraw reactions to non-supportive responses). Elevated baseline internalizing symptoms were related to perception of elevated Punish and Magnify responses during the week, and more Avoidant (Avoid-Withdraw and Avoid-Protect) reactions to responsiveness. Results are discussed in the context of reciprocal emotion socialization processes

Perpendicular momentum injection by lower hybrid wave in a tokamak

The injection of lower hybrid waves for current drive into a tokamak affects the profile of intrinsic rotation. In this article, the momentum deposition by the lower hybrid wave on the electrons is studied. Due to the increase in the poloidal momentum of the wave as it propagates into the tokamak, the parallel momentum of the wave increases considerably. The change of the perpendicular momentum of the wave is such that the toroidal angular momentum of the wave is conserved. If the perpendicular momentum transfer via electron Landau damping is ignored, the transfer of the toroidal angular momentum to the plasma will be larger than the injected toroidal angular momentum. A proper quasilinear treatment proves that both perpendicular and parallel momentum are transferred to the electrons. The toroidal angular momentum of the electrons is then transferred to the ions via different mechanisms for the parallel and perpendicular momentum. The perpendicular momentum is transferred to ions through an outward radial electron pinch, while the parallel momentum is transferred through collisions.Comment: 22 pages, 4 figure

Analysis of Modified Mechanical Properties in the Repair by SMAW Welding of Plow Discs in Andean Agricultural Areas

The objective of this contribution is to analyze the results of the technical studies of mechanical properties in standard plow discs, after their repair by manual arc welding with a SMAW coated electrode, commonly used in tillage tasks in Andean agricultural areas. For the repair process, the available, convenient, and easily acquired resources are implemented, such as consumables, equipment, and accessories necessary for the procedure. The nature of the base material was initially determined, by means of a spark spectrometry study for the case of worn plow discs, in such a way that the characteristic alloying elements of AISI-SAE 1340 steel are evident. The base of the original material allows defining and implementing essential and non-essential variables of the SMAW welding process according to AWS D1.1 and D14.3; therefore, the lap joint is designed, comprising of a worn disc plus similar sacrificial metals of identical conditions. As a conventional part of the welding processes, the quality control of the welds is carried out by means of penetrating inks under the ASTM E-165 standard, the respective measurements of the mechanical properties achieved, maintain analog factory hardness values of 37 HRC and increases the hardenability of the lap-type weld bead. Finally, it is concluded that the repair process contributes to a sustainable and efficient alternative that preserves the average hardness and improves hardenability, which are necessary to withstand the operational context that induces the typical premature wear of clayey and humid soils. Keywords: Hardness, hardenability, plow disc, welding, agricultural soil. Resumen El presente aporte tiene el objetivo de analizar los resultados de los estudios técnicos de propiedades mecánicas en discos de arado estándar, posterior a su reparación por soldadura de arco manual con electrodo revestido SMAW, de uso común en labores de labranza de zonas agrícolas andinas. Para el proceso de la reparación, se implementan los recursos disponibles, convenientes y de fácil adquisición, como consumibles, equipos y accesorios necesarios para el procedimiento. Se determina inicialmente la naturaleza del material base, mediante un estudio de espectrometría de chispa para el caso de discos de arado desgastados, de tal manera se evidencia los elementos aleantes característicos del acero AISI-SAE 1340. La base del material original permite definir e implementar variables esenciales y no esenciales del proceso de soldadura SMAW según AWS D1.1 y D14.3, por lo tanto, se diseña la junta de traslape, que comprende de un disco desgastado más metales similares de sacrificio de condiciones idénticas. Como parte convencional de los procesos de soldadura se realiza el control de calidad de las soldaduras mediante tintas penetrantes bajo la normativa ASTM E-165, las respectivas mediciones de las propiedades mecánicas conseguidas, mantienen valores de dureza de fábrica 37 HRC análogos y la templabilidad aumenta en el cordón de soldadura de tipo traslape. Finalmente, se concluye que el proceso de reparación contribuye con una alternativa sustentable y eficiente que conserva la dureza promedio y mejora la templabilidad, necesaria para soportar el contexto operacional que induce el desgaste prematuro típico de terrenos arcillosos y húmedos. Palabras Clave: Dureza, templabilidad, disco de arado, soldadura, suelo agrícola

Combined microbiological test to assess changes in an organic matrix used to avoid agricultural soil contamination, exposed to an insecticide

Combined microbiological test (Biolog Ecoplate, denaturing gradient gel electrophoresis (DGGE) and Real Time PCR (qPCR)) were developed to evaluate the impact of repeated diazinon (DZN) applications at high concentration (40 mg kg-1) on microbial communities in a microcosm simulating the organic matrix (straw (50%): peat (25%): soil (25%) vv-1) of an pesticide biopurification system (PBS). Moreover, pesticide dissipation was also evaluated. After three successive exposition of DZN, dissipation efficiency was high; achieved 87%, 93% and 96% after each application, respectively showing a clear accelerated dissipation of this pesticide in the organic matrix. The results obtained with Biolog Ecoplate showed that community level physiological profiles were no affected by the addition of DZN. On the other hand, molecular assays (DGGE and QPCR) demonstrated that the microbial structure (bacteria and fungi) remained relatively stable over time with high DZN doses compared to control. Therefore, the results of the present study, clearly, demonstrate the high dissipation capacity of this biomixture and highlight the microbiological robustness of this biological system.Fil: Tortella, G. R.. Universidad de la Frontera. Nucleo Cientifico y Tecnologico En Recursos Naturales (bioren-ufro). Departamento de Ciencias Quimicas y Recursos Naturales; ChileFil: Salgado, E.. Universidad de la Frontera. Nucleo Cientifico y Tecnológico En Recursos Naturales; ChileFil: Cuozzo, Sergio Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Planta Piloto de Procesos Industriales Microbiológicos (i); ArgentinaFil: Mella Herrera, R. A.. Universidad de la Frontera. Nucleo Cientifico y Tecnológico En Recursos Naturales; ChileFil: Parra, L.. Universidad de la Frontera. Núcleo Científico y Tecnológico en Recursos Naturales; ChileFil: Diez, M. C.. Universidad de la Frontera. Nucleo Cientifico y Tecnológico En Recursos Naturales; ChileFil: Rubilar, O.. Universidad de la Frontera. Nucleo Cientifico y Tecnológico En Recursos Naturales; Chil