RNA secondary structure prediction using large margin methods

The secondary structure of RNA is essential for its biological role. Recently, Do, Woods, Batzoglou, (ISMB 2006) proposed a probabilistic approach that generalizes SCFGs using conditional maximum likelihood to estimate the model parameters. We propose an alternative approach to parameter estimation which is based on an SVM-like large margin method

Almost-stationary motions and gauge conditions in General Relativity

An almost-stationary gauge condition is proposed with a view to Numerical Relativity applications. The time lines are defined as the integral curves of the timelike solutions of the harmonic almost-Killing equation. This vector equation is derived by a variational principle, by minimizing the deviations from isometry. The corresponding almost-stationary gauge condition allows one to put the field equations in hyperbolic form, both in the free-evolution ADM and in the Z4 formalisms.Comment: Talk presented at the Spanish Relativity Meeting, September 6-10 2005 Revised versio

The Generalized Dirichlet to Neumann map for the KdV equation on the half-line

For the two versions of the KdV equation on the positive half-line an initial-boundary value problem is well posed if one prescribes an initial condition plus either one boundary condition if $q_{t}$ and $q_{xxx}$ have the same sign (KdVI) or two boundary conditions if $q_{t}$ and $q_{xxx}$ have opposite sign (KdVII). Constructing the generalized Dirichlet to Neumann map for the above problems means characterizing the unknown boundary values in terms of the given initial and boundary conditions. For example, if $\{q(x,0),q(0,t) \}$ and $\{q(x,0),q(0,t),q_{x}(0,t) \}$ are given for the KdVI and KdVII equations, respectively, then one must construct the unknown boundary values $\{q_{x}(0,t),q_{xx}(0,t) \}$ and $\{q_{xx}(0,t) \}$, respectively. We show that this can be achieved without solving for $q(x,t)$ by analysing a certain ``global relation'' which couples the given initial and boundary conditions with the unknown boundary values, as well as with the function $\Phi^{(t)}(t,k)$, where $\Phi^{(t)}$ satisifies the $t$-part of the associated Lax pair evaluated at $x=0$. Indeed, by employing a Gelfand--Levitan--Marchenko triangular representation for $\Phi^{(t)}$, the global relation can be solved \emph{explicitly} for the unknown boundary values in terms of the given initial and boundary conditions and the function $\Phi^{(t)}$. This yields the unknown boundary values in terms of a nonlinear Volterra integral equation.Comment: 21 pages, 3 figure

Percepções dos pesquisadores de uma empresa pública brasileira de pesquisa científica em relação ao teletrabalho.

Abstract: The space-time flexibilization of work became common in private and public Brazilian companies after the advent of the COVID-19 pandemic. The objective of this study was to analyze, through a survey questionnaire, the researchers? perceptions at the Brazilian Agricultural Research Corporation (Embrapa) about work, social, and labor productivity characteristics related to the teleworking adopted over the course of a year in the company. The target audience of the study included 487 scientific researchers (master, doctor and post-doc level) from the public company located in 32 cities, widely distributed throughout the Brazilian territory. The perceptions of the research participants were highly positive in relation to teleworking, with reflections on labor productivity enhancement and gains related to work autonomy and quality of life. Also, the future expectations about teleworking reveal the desire of a majority of the Embrapa researchers to maintain a flexible working arrangement, particularly based on a hybrid model Resumen: La flexibilización espacio-temporal del trabajo se hizo común en las empresas públicas y privadas brasileñas con el advenimiento de la pandemia COVID-19. El presente estudio tuvo como objetivo analizar, mediante la aplicación de un cuestionario de encuesta, las percepciones de los investigadores de Empresa Brasileira de Pesquisa Agropecuária (Embrapa), luego de un año de trabajo en régimen de teletrabajo, en relación a las características laborales, sociales, productivas y del contexto laboral, así como los beneficios, desafíos y expectativas futuras asociadas a este modelo de trabajo. El público objetivo del estudio incluyó a 487 investigadores científicos (con maestrías, doctorados y postdoctorados) de la empresa pública ubicados en 32 ciudades ampliamente distribuidas en el territorio brasileño. Las percepciones de los participantes de la investigación en relación con el teletrabajo fueron altamente positivas, reflejando un aumento en la productividad laboral y beneficios en la autonomía laboral y la calidad de vida. Las expectativas revelan el deseo de la mayoría de los investigadores de Embrapa de mantener el régimen de trabajo flexible, especialmente en la modalidad híbrida

Emissão de N2O por sistemas de manejo de solo em Passo Fundo, RS.

Orientador: Anderson Santi

Carbono acumulado por sistemas de manejo do solo em experimento de longa duração, em Passo Fundo, RS.

Orientador: Fabiano Daniel De Bona

Monitoring two small catchments to evaluate effects of no-tillage agricultural management in São Paulo state, Brazil.

In recent years, declines in water and soil quality have been observed in areas of Brazil where no-till agriculture had been previously implemented. Poor soil management associated with the absence of public policies has caused soil erosion, because many farmers are moving back from no-till to traditional cultivation for faster economic gains. A research project ? SoloVivo Project - leaded by Embrapa (Brazilian Agricultural Research Corporation) in partnership with Itaipu Binacional aims to develop and validate, in a participatory way, tools to evaluate the technical performance of soil and water management at the rural properties that practice notill agriculture. In this context we have selected two paired small (< 100 ha) catchments in the Paranapanema region, São Paulo State, where no-till management is practiced at two different degrees of effectiveness. In the figure bellow it can be seen a scene of one of the two studied catchments. For monitoring rainfall, soil solution and stream water, each catchment will be equipped with a programmable datalogger (with cell phone communication for data collection) linked to: a high intensity tipping bucket rain gage; a reflectometer to monitor soil volumetric water content, bulk electric conductivity and temperature; a radar water level sensor; a turbidity sensor; and an electric conductivity-temperature probe. We expect that stream flow and sediment generation, besides water quality (measured by conductivity) may serve as indicators of the benefits of no-tillage agriculture done more or less well. The results of this study will be used to stimulate discussions at workshops with the farmers who participate in a rural producers association in the region. In addition this and other results can be used to help the Brazilian National Water Agency (ANA) decide about applying no-till agricultural management systems in its programs of payment for environmental services

Functional traits reveal coastal vegetation assembly patterns in a short edaphic gradient in southern Brazil

The relationship between plant functional traits and soil variables is useful for understanding plant community composition and circumscribing plant functional groups to highlight their adaptations to environmental conditions. The principal aim of this study was to explain assembly patterns of coastal vegetation using functional traits along a short edaphic gradient. The work was carried out on the pioneer zone in the coastal lowland vegetation (foredune) in southern Brazil. We selected 40 functional traits related to the morphology and anatomy of leaves, stems and roots for 60 species recorded in 25 vegetation plots positioned along three transects from the shoreline to slacks. In each plot, floristic and soil data were collected, and functional traits measured. We analysed the relationships between species functional traits and soil factors through RLQ and fourth-corner analyses. Salinity and organic matter content were the most significant edaphic factors in the differentiation of foredune vegetation, while the most significant traits to explain plant adaptations to coastal environments were plant height, sclerenchyma, spongy parenchyma and reserves of inulin in the root. Two functional groups of plants were circumscribed: a conservative group formed by trees and shrubs dominated the Woody Community, with low values of SLA (specific leaf area), thick cuticles, high frequencies of phenolic compounds and crystals, woody stems and great plant heights, which tended to invest in permanent aerial organs; and a more heterogeneous group of herbaceous plants (found in Beach Community, Non-floodable, and Wet Communities) with acquisitive characteristics (high SLA values) or conservative strategy (rhizome and xylopodium). Finally, our results suggested that root and stem functional traits, which are infrequently taken into consideration, were useful to differentiate subtropical coastal plants and, in general, to study plant adaptations to environmental conditions in depth

Symmetric Hyperbolic System in the Self-dual Teleparallel Gravity

In order to discuss the well-posed initial value formulation of the teleparallel gravity and apply it to numerical relativity a symmetric hyperbolic system in the self-dual teleparallel gravity which is equivalent to the Ashtekar formulation is posed. This system is different from the ones in other works by that the reality condition of the spatial metric is included in the symmetric hyperbolicity and then is no longer an independent condition. In addition the constraint equations of this system are rather simpler than the ones in other works.Comment: 8 pages, no figure

Global well-posedness of the KP-I initial-value problem in the energy space

We prove that the KP-I initial value problem is globally well-posed in the natural energy space of the equation