Modeling microbes: New methods for integrated metabolic and regulatory network reconstruction

PhD Thesis in Bioengineering

Self-narrative reconstruction after dilemma-focused therapy for depression: a comparison of good and poor outcome cases

Objective: The aim of this study is to improve the understanding of self-changes after an intervention for depression focused on implicative dilemmas, a type of cognitive conflict related to identity. As recent research has highlighted the relevance of identity-related dilemmas in clients with depression, we sought to assess the way in which clients resolve such inner conflicts after a tailored dilemma-focused intervention and how this is reflected in the clients’ self-narratives. Method: We used three instruments to observe differences between good (n = 5) and poor (n = 5) outcome cases: (i) the Repertory Grid Technique to track the resolution of dilemmas, (ii) the Change Interview to compile clients’ accounts of changes at posttreatment, and (iii) the Innovative Moments Coding System to examine the emergence of clients’ novelties at the Change Interview. Results: Groups did not differ in terms of the number and relevance of client-identified significantly helpful events. However, between-group differences were found for the resolution of dilemmas and for the proportion of high-level innovative moment (IM) types. Furthermore, a greater self-narrative reconstruction was associated with higher levels of symptom improvement. Conclusions: Good outcome cases seem to be associated with the resolution of conflicts and high-level IMs.

Rational approximations of sectional category and Poincaré duality

Félix, Halperin, and Lemaire have shown that the rational module category Mcat and the rational Toomer invariant coincide for simply connected Poincaré duality complexes. We establish an analogue of this result for the sectional category of a fibration.

Rational manipulation of mRNA folding free energy allows rheostat control of pneumolysin production by Streptococcus pneumoniae

Rational manipulation of mRNA folding free energy allows rheostat control of pneumolysin production by Streptococcus pneumoniae

Assessment of the effects of the expansion of the city of Estarreja on the rational land use

The management of urban environment, together with the preservation of the natural environment and the creation of a sustainable built environment, is a complex challenge for contemporary societies. In the name of progress, cities are contributing for the degradation of all surrounding ecosystems. Therefore there is an arising demand for developing new strategies and a new urban development paradigm settled in the search for the equilibrium between natural and built environments and efficient use of resources. The objective of this paper is to analyse how the urban expansion of the city of Estarreja took place in relation to the land use, based on the land capability classification maps of the area. Based in the results some sustainable development strategies that might be applied to the city are discussed. The obtained results demonstrate that the city has been growing faster then its population, consuming vast portions of land, since its growth as been occurring in a linear form. Despite this fact, results show that most of this expansion took place towards a territory of lower agricultural potential, when comparing to the location of its original settlement.

Dynamic three-dimensional reconstruction of the heart by transesophageal echocardiography

OBJECTIVE: To evaluate echocardiography accuracy in performing and obtaining images for dynamical three-dimensional (3D) reconstruction. METHODS: Three-dimensional (3D) image reconstruction was obtained in 20 consecutive patients who underwent transesophageal echocardiography. A multiplanar 5 MHz transducer was used for 3D reconstruction. RESULTS: Twenty patients were studied consecutively. The following cardiac diseases were present: valvar prostheses-6 (2 mitral, 2 aortic and 2 mitral and aortic); mitral valve prolapse- 3; mitral and aortic disease - 2; aortic valve disease- 5; congenital heart disease- 3 (2 atrial septal defect- ASD - and 1 transposition of the great arteries -TGA); arteriovenous fistula- 1. In 7 patients, color Doppler was also obtained and used for 3D flow reconstruction. Twenty five cardiac structures were acquired and 60 reconstructions generated (28 of mitral valves, 14 of aortic valves, 4 of mitral prostheses, 7 of aortic prostheses and 7 of the ASD). Fifty five of 60 (91.6%) reconstructions were considered of good quality by 2 independent observers. The 11 reconstructed mitral valves/prostheses and the 2 reconstructed ASDs provided more anatomical information than two dimensional echocardiography (2DE) alone. CONCLUSION: 3D echocardiography using a transesophageal transducer is a feasible technique, which improves detection of anatomical details of cardiac structures, particularly of the mitral valve and atrial septum.

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2016.00275

A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.

Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

Terapéutica racional, mediante indicadores de eficacia antimicrobiana, de la mastitis caprina utilizando marbofloxacina y cefquinoma. Rational therapeutics, indicators of antimicrobial efficiency in the mastitis goats using marbofloxacine and cefquinome

La producción de leche de cabra es considerada en nuestro país, y en la provincia de Córdoba, una alternativa productiva para el desarrollo sustentable y socio – económico de la población. Por otra parte, existe una mayor demanda del mercado nacional e internacional de esta leche, por lo que los productores deben garantizar la seguridad y calidad de la misma de acuerdo a las normas vigentes. Es por ello que el control y tratamiento de las diferentes enfermedades es de vital importancia tanto para maximizar la producción del hato como para cumplir con los cánones de seguridad exigidos. En este contexto la mastitis caprina es una de las enfermedades que afecta la productividad del sector, y para controlarla una de las medidas a emplear es la terapéutica con antimicrobianos. Se trabajará en este proyecto con marbofloxacina y cefquinoma, estableciendo pautas racionales (eficaces y seguras) para su empleo en la afección a nivel regional. Los indicadores de eficacia estarán fijados de acuerdo a los parámetros integrados de farmacocinética (FC) y farmacodinamia (FD). Estos últimos (FD) serán calculados a través de la determinación concentraciones inhibitorias mínimas de cepas bacterianas aisladas de mastitis caprinas en Córdoba. Se establecerán los parámetros farmacocinéticos a dosis únicas y múltiples para la marbofloxacina (5 mg/kg IV, IM) y cefquinoma (2 mg/kg IV, IM e IMM) a partir de muestras de suero y leche de cabras Anglo Nubian (n = 6 por antimicrobiano; diseño cruzado en función de la ruta de administración). Se determinarán sus concentraciones en dichos fluidos, por cromatografía líquida de alta precisión. Los resultados FC/FD para ambos medicamentos se compararán con parámetros recomendados por expertos para cada tipo de antimicrobiano y se utilizarán como medida para recomendar una terapéutica racional, fundamental para optimizar la posología, garantizar la eficacia clínica, y reducir al mínimo la selección y propagación de cepas resistentes de agentes patógenos. The production of milk of goat is considered the province of Cordoba, a productive alternative for the sustainable development and partner - economically of the population. There is a major demand of the domestic and international market of this milk, for what the producers must guarantee the safety and quality of the same one of agreement to the in force procedure. It is for it that the control and treatment of the different diseases performs vital importance so much to maximize the production of the herd as to expire with the safety demanded. In this context the mastitis goat is one of the diseases that affect the productivity of the sector, and to control her one of the measures to using is the therapeutics with antimicrobial. One will be employed at this project with marbofloxacine and cefquinome, establishing rational guidelines (effective and sure) for his employment in the affection to regional level. The indicators of efficiency will be fixed in agreement to the integrated parameters of pharmacokinetics (PK) and pharmacodinamics (PD). The latter (PK) will be calculated across the determination inhibitory minimal concentrations of bacterial strains isolated of mastitis goat in Córdoba. The parameters will be established pharmacokinetics to the only and multiple doses for the marbofloxacine (5 mg/kg the IV, IM) and cefquinome (2 mg/kg the IVth, IM and IMM), From samples of whey and milk of goats Anglo Nubian (n = 6 for antimicrobial; design crossed depending on the route of administration). Its concentrations will decide in the above mentioned fluids, for liquid chromatography of high precision. The results PK/PD for both antimicrobial will be compared with parameters recommended by experts for every type of antimicrobial and will be in use as measure for recommending a rational, fundamental therapeutics for optimizing the dosage, for guaranteeing the clinical efficiency, and to reduce to the minimum the selection and spread of resistant of pathogenic agents.

Problemáticas de la interacción discursiva en la enseñanza y el aprendizaje de las Ciencias Naturales. Aportes didácticos. Interaction discoursive issues in teaching and learning Natural Sciences. Didactic contributions

Las didácticas específicas de las ciencias naturales revelan diferentes problemáticas en su enseñanza y aprendizaje en los diferentes niveles del sistema educativo. En particular, en las clases de ciencias la interacción discursiva docente alumnos adquiere relevancia, ya que el proceso de comunicación del conocimiento es uno de los pilares didácticos, junto a la trasposición del mismo. Especificamente, en este proyecto nos abocamos a aquellas intervenciones de docentes y alumnos que se relacionan con la construcción del conocimiento biológico y químico. El proyecto se enmarca en una actual linea de trabajo que indaga sobre las dificultades en los abordajes del conocimiento científico en las aulas, las características del discurso entre docentes y alumnos, las habilidades y dificultades en la comprensión de los enunciados de problemas y las características de los textos que se utilizan en las clases. Se focaliza este estudio en casos que intentan dar respuesta a tres temáticas, agrupadas en un conjunto de situaciones de investigación relacionadas con la interacción discursiva docente-alumno, retomando el rol del docente al hablar, guiar o diseñar las situaciones de referencia para el aprendizaje de los alumnos. Los casos son: 1- En cuanto a las concepciones sobre diversidad biológica en estudiantes de escuela secundaria y en textos académicos, atendemos a cómo la escuela presenta los contenidos ecológicos como un conjunto de dogmas y conceptos estáticos. Además suelen simplificarse conceptualmente y presentarse poco actualizados. Es por ello que se planea estudiar las concepciones y actitudes de los alumnos de secundaria sobre la biodiversidad, cómo estas dificultan su comprensión y los textos usados en relación a la promoción de la transposición didáctica. 2- En relación a cómo se elabora el patrón temático del tema célula en clases de Biología, se analizarán las diferentes estrategias de significados y de desarrollo temático, que se emplean en la comunicación aulica. Se intentará establecer si hay cambios en el desarrollo temático a medida que se avanza en la escolaridad. Esto es porque se puede apreciar que muchos de los problemas de aprendizaje del alumnado se deben a un desconocimiento tanto del patrón temático como del patrón estructural de la ciencia, siendo preciso evocar los patrones temáticos que se quieren utilizar, para construir un conocimiento compartido. 3-Finalmente, en los enunciados de problemas de Química, se analizarán las dificultades de comprensión lectora de alumnos de Ingeniería. Los docentes frecuentemente atribuyen los problemas a deficiencias en la instrucción recibida, sin considerarse los conocimientos previos del alumno, los obstáculos conceptuales originados en el tema, las deficiencias en la habilidad lectora, el tipo textual predominante en la consigna, el formato en el que se escribió la consigna y los factores personales, etc., siendo que la comprensión del enunciado de una consigna de trabajo condiciona fuertemente la posibilidad de su resolución. Los tres casos utilizarán metodologías cualitaritas que incluyan análisis de contenido en discursos orales y escritos. Los datos se registrarán desde observación no participante, registro etnográfico y con grabaciones de audio. Se espera contribuir al conocimiento, realizando aportes a la formación docente en tanto las estrategias discursivas que se emplean en el aula, en forma oral y en la escrita, conocer concepciones que dificultan o favoren la construcción del conocimiento científico, entre otras. Los productos de estos estudios estarán integrados por nuevos desarrollos para la formación docente, publicaciones científicas de impacto nacional e internacional, presentaciones a congresos, materiales didácticos y divulgativos, dictado de seminarios y/o cursos, redacción de informes a las escuelas intervinientes.. The specific Natural Sciences didactics show different problems in teaching and learning along the school system. In particular, the discourse used to communicate knowledge in Science lessons becomes important. With this project we will focus on the teachers and students actions regarding the construction of biological and chemical knowledge. This project attempts to answer these issues and brings together a range of research situations related to teacher-student interaction, through discourse, taking up the role of the teacher to speak, to plan and to guide student learning. We will study the ideas and attitudes of high school students about biodiversity that make difficult its understanding and the textbooks used in relation to promotion of the didactic transposition. In addition, regarding how the thematic pattern in biology classes is costructed, it will be analyzed the different meaning and thematic development strategies that are used in communication. We will attempt to establish whether there are any changes in the thematic development throughout high school education. Finally, we will analyze the reading comprehension problems in engineering students. Teachers frequently attribute these issues to deficiencies in prior education, without considering the students background, the conceptual obstacles arising in the field, the format in which the prompt is written, personal factors, etc., keeping in mind that the outcome of an activity is strictly dependant con the prompt understanding. We expect to make contributions to the teacher education in both the discourse strategies used in the classroom, orally and in writing, to learn about the conceptions that hinder or favor the knowledge construction, among others. The products of this study will be national and international impact scientific publications, conference presentations, popular science publications, seminars courses and reports to the schools involeved.

Controlled resolution reconstruction of one-dimensional permittivity profiles

Electromagnetic scattering inverse problems, microwave imaging, reconstruction of dielectric media, remote sensing, tomography

Ehrhart polynomials, successive minima, and an Ehrhart theory for rational dilates of a rational polytope

Magdeburg, Univ., Fak. für Mathematik, Diss., 2011

3-D surface reconstruction using spatial frequency-based approaches under influence of perspective distortion

Magdeburg, Univ., Fak. für Elektrotechnik und Informationstechnik, Diss., 2008