Design of polyzinc finger peptides with structured linkers

Zinc finger domains are perhaps the most versatile of all known DNA binding domains. By fusing up to six zinc finger modules, which normally recognize up to 18 bp of DNA, designer transcription factors can be produced to target unique sequences within large genomes. However, not all continuous DNA sequences make good zinc finger binding sites. To avoid having to target unfavorable DNA sequences, we designed multizinc finger peptides with linkers capable of spanning long stretches of nonbound DNA. Two three-finger domains were fused by using either transcription factor IIIA for the Xenopus 5S RNA gene (TFIIIA) finger 4 or a non-sequence-specific zinc finger as a “structured” linker. Our gel-shift results demonstrate that these peptides are able to bind with picomolar affinities to target sequences containing 0–10 bp of nonbound DNA. Furthermore, these peptides display greater sequence selectivity and bind with higher affinity than similar six-finger peptides containing long, flexible linkers. These peptides are likely to be of use in understanding the behavior of polydactyl proteins in nature and in the targeting of human, animal, or plant genomes for numerous applications. We also suggest that in certain polydactyl peptides an individual finger can “flip” out of the major groove to allow its neighbors to bind shorter, nontarget DNA sequences.

Patterns of variance in stage-structured populations: Evolutionary predictions and ecological implications

Variability in population growth rate is thought to have negative consequences for organism fitness. Theory for matrix population models predicts that variance in population growth rate should be the sum of the variance in each matrix entry times the squared sensitivity term for that matrix entry. I analyzed the stage-specific demography of 30 field populations from 17 published studies for pattern between the variance of a demographic term and its contribution to population growth. There were no instances in which a matrix entry both was highly variable and had a large effect on population growth rate; instead, correlations between estimates of temporal variance in a term and contribution to population growth (sensitivity or elasticity) were overwhelmingly negative. In addition, survivorship or growth sensitivities or elasticities always exceeded those of fecundity, implying that the former two terms always contributed more to population growth rate. These results suggest that variable life history stages tend to contribute relatively little to population growth rates because natural selection may alter life histories to minimize stages with both high sensitivity and high variation.

Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming.

We present a general approach to forming structure-activity relationships (SARs). This approach is based on representing chemical structure by atoms and their bond connectivities in combination with the inductive logic programming (ILP) algorithm PROGOL. Existing SAR methods describe chemical structure by using attributes which are general properties of an object. It is not possible to map chemical structure directly to attribute-based descriptions, as such descriptions have no internal organization. A more natural and general way to describe chemical structure is to use a relational description, where the internal construction of the description maps that of the object described. Our atom and bond connectivities representation is a relational description. ILP algorithms can form SARs with relational descriptions. We have tested the relational approach by investigating the SARs of 230 aromatic and heteroaromatic nitro compounds. These compounds had been split previously into two subsets, 188 compounds that were amenable to regression and 42 that were not. For the 188 compounds, a SAR was found that was as accurate as the best statistical or neural network-generated SARs. The PROGOL SAR has the advantages that it did not need the use of any indicator variables handcrafted by an expert, and the generated rules were easily comprehensible. For the 42 compounds, PROGOL formed a SAR that was significantly (P < 0.025) more accurate than linear regression, quadratic regression, and back-propagation. This SAR is based on an automatically generated structural alert for mutagenicity.

Interaction of GroEL with a highly structured folding intermediate: iterative binding cycles do not involve unfolding.

The GroE proteins are molecular chaperones involved in protein folding. The general mechanism by which they facilitate folding is still enigmatic. One of the central open questions is the conformation of the GroEL-bound nonnative protein. Several suggestions have been made concerning the folding stage at which a protein can interact with GroEL. Furthermore, the possibility exists that binding of the nonnative protein to GroEL results in its unfolding. We have addressed these issues that are basic for understanding the GroE-mediated folding cycle by using folding intermediates of an Fab antibody fragment as molecular probes to define the binding properties of GroEL. We show that, in addition to binding to an early folding intermediate, GroEL is able to recognize and interact with a late quaternary-structured folding intermediate (Dc) without measurably unfolding it. Thus, the prerequisite for binding is not a certain folding stage of a nonnative protein. In contrast, general surface properties of nonnative proteins seem to be crucial for binding. Furthermore, unfolding of a highly structured intermediate does not necessarily occur upon binding to GroEL. Folding of Dc in the presence of GroEL and ATP involves cycles of binding and release. Because in this system no off-pathway reactions or kinetic traps are involved, a quantitative analysis of the reactivation kinetics observed is possible. Our results indicate that the association reaction of Dc and GroEL in the presence of ATP is rather slow, whereas in the absence of ATP association is several orders of magnitude more efficient. Therefore, it seems that ATP functions by inhibiting reassociation rather than promoting release of the bound substrate.

Método multigrid algébrico: reutilização das estruturas multigrid no transporte de contaminantes

A necessidade de obter solução de grandes sistemas lineares resultantes de processos de discretização de equações diferenciais parciais provenientes da modelagem de diferentes fenômenos físicos conduz à busca de técnicas numéricas escaláveis. Métodos multigrid são classificados como algoritmos escaláveis.Um estimador de erros deve estar associado à solução numérica do problema discreto de modo a propiciar a adequada avaliação da solução obtida pelo processo de aproximação. Nesse contexto, a presente tese caracteriza-se pela proposta de reutilização das estruturas matriciais hierárquicas de operadores de transferência e restrição dos métodos multigrid algébricos para acelerar o tempo de solução dos sistemas lineares associados à equação do transporte de contaminantes em meio poroso saturado. Adicionalmente, caracteriza-se pela implementação das estimativas residuais para os problemas que envolvem dados constantes ou não constantes, os regimes de pequena ou grande advecção e pela proposta de utilização das estimativas residuais associadas ao termo de fonte e à condição inicial para construir procedimentos adaptativos para os dados do problema. O desenvolvimento dos códigos do método de elementos finitos, do estimador residual e dos procedimentos adaptativos foram baseados no projeto FEniCS, utilizando a linguagem de programação PYTHONR e desenvolvidos na plataforma Eclipse. A implementação dos métodos multigrid algébricos com reutilização considera a biblioteca PyAMG. Baseado na reutilização das estruturas hierárquicas, os métodos multigrid com reutilização com parâmetro fixo e automática são propostos, e esses conceitos são estendidos para os métodos iterativos não-estacionários tais como GMRES e BICGSTAB. Os resultados numéricos mostraram que o estimador residual captura o comportamento do erro real da solução numérica, e fornece algoritmos adaptativos para os dados cuja malha retornada produz uma solução numérica similar à uma malha uniforme com mais elementos. Adicionalmente, os métodos com reutilização são mais rápidos que os métodos que não empregam o processo de reutilização de estruturas. Além disso, a eficiência dos métodos com reutilização também pode ser observada na solução do problema auxiliar, o qual é necessário para obtenção das estimativas residuais para o regime de grande advecção. Esses resultados englobam tanto os métodos multigrid algébricos do tipo SA quanto os métodos pré-condicionados por métodos multigrid algébrico SA, e envolvem o transporte de contaminantes em regime de pequena e grande advecção, malhas estruturadas e não estruturadas, problemas bidimensionais, problemas tridimensionais e domínios com diferentes escalas.

Electoral Systems and Ethnic Conciliation: A Structured, Focused Analysis of Vote-Pooling in Northern Ireland Elections 1998-2011

This research project examines the role of electoral system rules in affecting the extent of conciliatory behavior and cross-ethnic coalition making in Northern Ireland. It focuses on the role of the Single Transferable Vote (STV) electoral system in shaping party and voter incentives in a post-conflict divided society. The research uses a structured, focused comparison of the four electoral cycles since the Belfast Agreement of 1998. This enables a systematic examination of each electoral cycle using a common set of criteria focused on conciliation and cross-ethnic coalition making. Whilst preference voting is assumed to benefit moderate candidates, in Northern Ireland centrist and multi-ethnic parties outside of the dominant ethnic communities have received little electoral success. In Northern Ireland the primary effect of STV has not been to encourage inter-communal voting but to facilitate intra-community and intra-party moderation. STV has encouraged the moderation of the historically extreme political parties in each of the ethnic bloc. Patterns across electoral cycles suggest that party elites from the Democratic Unionist Party (DUP) and Sinn Fein have moderated their policy positions due to the electoral system rules. Therefore they have pursued lower-preference votes from within their ethnic bloc but in doing so have marginalized parties of a multi-ethnic or non-ethnic orientation.

A Transdiagnostic Social Skills Intervention; Using a Structured Story to Teach Children How to Ask a Friend to Play

An (independent samples comparison) controlled study was conducted to assess the efficacy of a novel approach to social skills training for children in a local socialization group at Knippenberg, Patterson & Associates (KPA). The treatment condition involved the combination of a Structured Story (i.e., novel bibliotherapy technique for children with social skills deficits), and a behavioral rehearsal (or role-play) segment, where the children practiced the target social skill featured in the Structure Story. The control group did not receive the Structured Story nor the behavioral rehearsal. Children in both groups engaged in ten-minutes of free play that was videorecorded for later observation and scoring by the principal investigator. Two target behaviors were assessed; asking a friend to play, and duration of joint play between two or more peers. The results did not show significant differences for either target variable between the group that received the novel intervention and the control group. Limitations of the current study and implications for further research are discussed.

Estratégias de comercialização e investimento, com ênfase em energias renováveis, suportadas por modelos de otimização especializados para avaliação estocástica de risco x retorno.

A comercialização de energia elétrica de fontes renováveis, ordinariamente, constitui-se uma atividade em que as operações são estruturadas sob condições de incerteza, por exemplo, em relação ao preço \"spot\" no mercado de curto prazo e a geração de energia dos empreendimentos. Deriva desse fato a busca dos agentes pela formulação de estratégias e utilização de ferramentais para auxiliá-los em suas tomadas de decisão, visando não somente o retorno financeiro, mas também à mitigação dos riscos envolvidos. Análises de investimentos em fontes renováveis compartilham de desafios similares. Na literatura, o estudo da tomada de decisão considerada ótima sob condições de incerteza se dá por meio da aplicação de técnicas de programação estocástica, que viabiliza a modelagem de problemas com variáveis randômicas e a obtenção de soluções racionais, de interesse para o investidor. Esses modelos permitem a incorporação de métricas de risco, como por exemplo, o Conditional Value-at-Risk, a fim de se obter soluções ótimas que ponderem a expectativa de resultado financeiro e o risco associado da operação, onde a aversão ao risco do agente torna-se um condicionante fundamental. O objetivo principal da Tese - sob a ótica dos agentes geradores, consumidores e comercializadores - é: (i) desenvolver e implementar modelos de otimização em programação linear estocástica com métrica CVaR associada, customizados para cada um desses agentes; e (ii) aplicá-los na análise estratégica de operações como forma de apresentar alternativas factíveis à gestão das atividades desses agentes e contribuir com a proposição de um instrumento conceitualmente robusto e amigável ao usuário, para utilização por parte das empresas. Nesse contexto, como antes frisado, dá-se ênfase na análise do risco financeiro dessas operações por meio da aplicação do CVaR e com base na aversão ao risco do agente. Considera-se as fontes renováveis hídrica e eólica como opções de ativos de geração, de forma a estudar o efeito de complementaridade entre fontes distintas e entre sites distintos da mesma fonte, avaliando-se os rebatimentos nas operações.

Broadening the Scope of Ethnic Identity: A Social Sustainability Solution for Pan African Communities through Ethnically Relevant Educational Programming

This conceptual study explores ethnic identity development theory in order to argue that ethnic identity development education is a means of developing broad senses of community in the African Diaspora that expand beyond a tribal, local, familial level. This study suggests that the broadening of community understanding would contribute to establishing social sustainability on regional, national and international levels within the Pan African community. Establishing such social sustainability would have direct effects on the areas of economic and environmental sustainability. One of the goals of this project is to offer suggestions for ethnically relevant education that can develop social sustainability in several places throughout the Diaspora, such as in Nigeria where ethnic conflicts are a contemporary concern.

3D plane-based egomotion for SLAM on semi-structured environment

Several works deal with 3D data in SLAM problem. Data come from a 3D laser sweeping unit or a stereo camera, both providing a huge amount of data. In this paper, we detail an efficient method to extract planar patches from 3D raw data. Then, we use these patches in an ICP-like method in order to address the SLAM problem. Using ICP with planes is not a trivial task. It needs some adaptation from the original ICP. Some promising results are shown for outdoor environment.

Robust linear semi-infinite programming duality under uncertainty

In this paper, we propose a duality theory for semi-infinite linear programming problems under uncertainty in the constraint functions, the objective function, or both, within the framework of robust optimization. We present robust duality by establishing strong duality between the robust counterpart of an uncertain semi-infinite linear program and the optimistic counterpart of its uncertain Lagrangian dual. We show that robust duality holds whenever a robust moment cone is closed and convex. We then establish that the closed-convex robust moment cone condition in the case of constraint-wise uncertainty is in fact necessary and sufficient for robust duality. In other words, the robust moment cone is closed and convex if and only if robust duality holds for every linear objective function of the program. In the case of uncertain problems with affinely parameterized data uncertainty, we establish that robust duality is easily satisfied under a Slater type constraint qualification. Consequently, we derive robust forms of the Farkas lemma for systems of uncertain semi-infinite linear inequalities.

Integration of modular process simulators under the Generalized Disjunctive Programming framework for the structural flowsheet optimization

The optimization of chemical processes where the flowsheet topology is not kept fixed is a challenging discrete-continuous optimization problem. Usually, this task has been performed through equation based models. This approach presents several problems, as tedious and complicated component properties estimation or the handling of huge problems (with thousands of equations and variables). We propose a GDP approach as an alternative to the MINLP models coupled with a flowsheet program. The novelty of this approach relies on using a commercial modular process simulator where the superstructure is drawn directly on the graphical use interface of the simulator. This methodology takes advantage of modular process simulators (specially tailored numerical methods, reliability, and robustness) and the flexibility of the GDP formulation for the modeling and solution. The optimization tool proposed is successfully applied to the synthesis of a methanol plant where different alternatives are available for the streams, equipment and process conditions.