Grammar-Guided Evolutionary Construction of Bayesian networks

This paper proposes the EvoBANE system. EvoBANE automatically generates Bayesian networks for solving special-purpose problems. EvoBANE evolves a population of individuals that codify Bayesian networks until it finds near optimal individual that solves a given classification problem. EvoBANE has the flexibility to modify the constraints that condition the solution search space, self-adapting to the specifications of the problem to be solved. The system extends the GGEAS architecture. GGEAS is a general-purpose grammar-guided evolutionary automatic system, whose modular structure favors its application to the automatic construction of intelligent systems. EvoBANE has been applied to two classification benchmark datasets belonging to different application domains, and statistically compared with a genetic algorithm performing the same tasks. Results show that the proposed system performed better, as it manages different complexity constraints in order to find the simplest solution that best solves every problem.

Integration versus segregation in functional brain networks

We propose a new methodology to evaluate the balance between segregation and integration in functional brain networks by using singular value decomposition techniques. By means of magnetoencephalography, we obtain the brain activity of a control group of 19 individuals during a memory task. Next, we project the node-to-node correlations into a complex network that is analyzed from the perspective of its modular structure encoded in the contribution matrix. In this way, we are able to study the role that nodes play I/O its community and to identify connector and local hubs. At the mesoscale level, the analysis of the contribution matrix allows us to measure the degree of overlapping between communities and quantify how far the functional networks are from the configuration that better balances the integrated and segregated activity

Purification and cDNA Cloning of Maize Poly(ADP)-Ribose Polymerase

Poly(ADP)-ribose polymerase (PADPRP) has been purified to apparent homogeneity from suspension cultures of the maize (Zea mays) callus line. The purified enzyme is a single polypeptide of approximately 115 kD, which appears to dimerize through an S-S linkage. The catalytic properties of the maize enzyme are very similar to those of its animal counterpart. The amino acid sequences of three tryptic peptides were obtained by microsequencing. Antibodies raised against peptides from maize PADPRP cross-reacted specifically with the maize enzyme but not with the enzyme from human cells, and vice versa. We have also characterized a 3.45-kb expressed-sequence-tag clone that contains a full-length cDNA for maize PADPRP. An open reading frame of 2943 bp within this clone encodes a protein of 980 amino acids. The deduced amino acid sequence of the maize PADPRP shows 40% to 42% identity and about 50% similarity to the known vertebrate PADPRP sequences. All important features of the modular structure of the PADPRP molecule, such as two zinc fingers, a putative nuclear localization signal, the automodification domain, and the NAD+-binding domain, are conserved in the maize enzyme. Northern-blot analysis indicated that the cDNA probe hybridizes to a message of about 4 kb.

Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain.

A long-term goal in the field of restriction-modification enzymes has been to generate restriction endonucleases with novel sequence specificities by mutating or engineering existing enzymes. This will avoid the increasingly arduous task of extensive screening of bacteria and other microorganisms for new enzymes. Here, we report the deliberate creation of novel site-specific endonucleases by linking two different zinc finger proteins to the cleavage domain of Fok I endonuclease. Both fusion proteins are active and under optimal conditions cleave DNA in a sequence-specific manner. Thus, the modular structure of Fok I endonuclease and the zinc finger motifs makes it possible to create "artificial" nucleases that will cut DNA near a predetermined site. This opens the way to generate many new enzymes with tailor-made sequence specificities desirable for various applications.

A Knowledge-based System for Intelligent Support in Pharmacogenomics Evidence Assessment: Ontology-driven Evidence Representation, Retrieval, Classification and Interpretation

Thesis (Ph.D.)--University of Washington, 2016-06

The correspondence framework for 3D surface matching algorithms

Beyond the inherent technical challenges, current research into the three dimensional surface correspondence problem is hampered by a lack of uniform terminology, an abundance of application specific algorithms, and the absence of a consistent model for comparing existing approaches and developing new ones. This paper addresses these challenges by presenting a framework for analysing, comparing, developing, and implementing surface correspondence algorithms. The framework uses five distinct stages to establish correspondence between surfaces. It is general, encompassing a wide variety of existing techniques, and flexible, facilitating the synthesis of new correspondence algorithms. This paper presents a review of existing surface correspondence algorithms, and shows how they fit into the correspondence framework. It also shows how the framework can be used to analyse and compare existing algorithms and develop new algorithms using the framework's modular structure. Six algorithms, four existing and two new, are implemented using the framework. Each implemented algorithm is used to match a number of surface pairs. Results demonstrate that the correspondence framework implementations are faithful implementations of existing algorithms, and that powerful new surface correspondence algorithms can be created. (C) 2004 Elsevier Inc. All rights reserved.

A methodology for the generation and evaluation of biorefinery process chains, in order to identify the most promising biorefineries for the EU

The topic of bioenergy, biofuels and bioproducts remains at the top of the current political and research agenda. Identification of the optimum processing routes for biomass, in terms of efficiency, cost, environment and socio-economics is vital as concern grows over the remaining fossil fuel resources, climate change and energy security. It is known that the only renewable way of producing conventional hydrocarbon fuels and organic chemicals is from biomass, but the problem remains of identifying the best product mix and the most efficient way of processing biomass to products. The aim is to move Europe towards a biobased economy and it is widely accepted that biorefineries are key to this development. A methodology was required for the generation and evaluation of biorefinery process chains for converting biomass into one or more valuable products that properly considers performance, cost, environment, socio-economics and other factors that influence the commercial viability of a process. In this thesis a methodology to achieve this objective is described. The completed methodology includes process chain generation, process modelling and subsequent analysis and comparison of results in order to evaluate alternative process routes. A modular structure was chosen to allow greater flexibility and allowing the user to generate a large number of different biorefinery configurations The significance of the approach is that the methodology is defined and is thus rigorous and consistent and may be readily re-examined if circumstances change. There was the requirement for consistency in structure and use, particularly for multiple analyses. It was important that analyses could be quickly and easily carried out to consider, for example, different scales, configurations and product portfolios and so that previous outcomes could be readily reconsidered. The result of the completed methodology is the identification of the most promising biorefinery chains from those considered as part of the European Biosynergy Project.

The dawn of the RNA World:toward functional complexity through ligation of random RNA oligomers

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation- based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered. Copyright © 2009 RNA Society.

Layoutgenerierung und Geometrieberechnung für die systematische Planung manuell bedienter Lagersysteme

Im vorliegenden Beitrag wird ein Modell für die Beschreibung und Berechnung der Geometrie manuell bedienter Lagersysteme entwickelt und validiert, welches die Grundlage für eine rechnergestützte Planungssystematik bildet. Der modulare Aufbau des Modells ermöglicht durch entsprechende Erweiterungen die Berechnung des Lagerplatzbedarfs unter Berücksichtigung von Lagerstrategien. Auch die Betrachtung von Speziallösungen wie der Verwendung unterschiedlich hoher Lagerplätze ist möglich. Abschließend wird das vorgestellte Modell auf seine Anwendbarkeit zur systematischen Erzeugung verschiedener Layouts als Lösungsalternativen untersucht.

Los proyectos interdisciplinares de módulo: una experiencia innovadora en el Grado de Educación Social de la UPV/EHU

[ES]En este artículo se presenta una experiencia de innovación que se ha articulado, en el seno de un diseño curricular a través de módulos, al objeto de mejorar los procesos de enseñanza-aprendizaje que se están desarrollando en la Facultad de Fª y Ciencias de la Educación de la UPV/EHU. El marco de innovación aprovecha la oportunidad surgida con la configuración de los nuevos planes de estudio para su convergencia en el Espacio Europeo de Educación Superior. El contexto más amplio en el que se enmarca esta experiencia, es el de los cambios organizativos, curriculares y culturales, que está suponiendo la realización de un diseño modular de las nuevas titulaciones de grado (Pedagogía y Educación Social), trabajando en equipos docentes coordinados y contando con el apoyo institucional de la UPV/EHU. La innovación concreta que se presenta, describe minuciosamente uno de los siete módulos que componen la nueva titulación del Grado en Educación Social, y subraya la labor desplegada por el equipo docente que imparte las cinco materias que conforman el módulo en las dos lenguas oficiales: euskara y castellano, al planificar, desarrollar y evaluar la actividad interdisciplinar que les compete de manera coordinada. En este trabajo se reflexiona respecto a las posibilidades que la estructura modular ofrece para acometer un cambio real en la cultura de la práctica docente, y a cómo gestionar factores clave que garanticen el tránsito a un modelo docente activo, participativo y colaborativo. // This paper presents an innovative approach to improving teacher quality that is being developed at the Faculty of Philosophy and Educational Sciences of the UPV / EHU, taking the opportunity arose with the configuration of the new curricula for their convergence in the European Higher Education Area. It is framed in the broader context of organizational change, curriculum and cultural, that is assuming the implementation of a modular design of the new degree (Education and Social Education), working in teams coordinated and with the institutional support of the UPV. The concrete innovation is presented, describes one of the seven modules of the new degree of Social Education, and underlines the work done by the faculty team who teach the five subjects that make up the module in the two official languages: Basque and Spanish, because they must plan, develop and evaluate the interdisciplinary activity in a coordinated manner. We reflect in this paper on the potential that the modular structure offers to undertake real change in the culture of teaching practice, and how to manage key factors to ensure the transition to a teaching model active, participatory and collaborative.

Conceção de produtos de design de malhas sustentáveis e inovadores

Dissertação para obtenção do grau de Mestre em Design de Moda, apresentada na Universidade de Lisboa - Faculdade de Arquitetura.

A study of brain functional connectivity and cognitive processes in long COVID-19 patients

In this work, a prospective study conducted at the IRCCS Istituto delle Scienze Neurologiche di Bologna is presented. The aim was to investigate the brain functional connectivity of a cohort of patients (N=23) suffering from persistent olfactory dysfunction after SARS-CoV-2 infection (Post-COVID-19 syndrome), as compared to a matching group of healthy controls (N=26). In particular, starting from individual resting state functional-MRI data, different analytical approaches were adopted in order to find potential alterations in the connectivity patterns of patients’ brains. Analyses were conducted both at a whole-brain level and with a special focus on brain regions involved in the processing of olfactory stimuli (Olfactory Network). Statistical correlations between functional connectivity alterations and the results of olfactory and neuropsychological tests were investigated, to explore the associations with cognitive processes. The three approaches implemented for the analysis were the seed-based correlation analysis, the group-level Independent Component analysis and a graph-theoretical analysis of brain connectivity. Due to the relative novelty of such approaches, many implementation details and methodologies are not standardized yet and represent active research fields. Seed-based and group-ICA analyses’ results showed no statistically significant differences between groups, while relevant alterations emerged from those of the graph-based analysis. In particular, patients’ olfactory sub-graph appeared to have a less pronounced modular structure compared to the control group; locally, a hyper-connectivity of the right thalamus was observed in patients, with significant involvement of the right insula and hippocampus. Results of an exploratory correlation analysis showed a positive correlation between the graphs global modularity and the scores obtained in olfactory tests and negative correlations between the thalamus hyper-connectivity and memory tests scores.

Optimization of the Modular Educational Program Structure

Optimized structure of the educational program consisting of a set of the interconnected educational objects is offered by means of problem solution of optimum partition of the acyclic weighed graph. The condition of acyclicity preservation for subgraphs is formulated and the quantitative assessment of decision options is executed. The original algorithm of search of quasioptimum partition using the genetic algorithm scheme with coding chromosomes by permutation is offered. Object-oriented realization of algorithm in language C++ is described and results of numerical experiments are presented.

Modular catalyst: from the tiling of a water plane to the design of a floating structure

La tesi nasce dalla volontà di agire sull’area della Darsena di Ravenna, strategica in quanto via d’acqua navigabile che congiunge il mare con il centro città ma dal potenziale ancora poco sfruttato. Il progetto è studiato per essere inserito come catalizzatore urbano, creando spazi di interazione attraverso elementi modulari galleggianti e riconfigurabili per adattarsi a programmi d’uso flessibili; tali elementi si aggregano formando un sistema che ristruttura lo spazio dell’attuale banchina, cambiandone la percezione da barriera a waterfront urbano. La necessità di ottenere una struttura con capacità di crescita e flessibilità programmatica sfocia in un approccio modulare seguendo il principio massima variazione/minimo numero di elementi i cui principi aggregativi si basano sulla tassellazione “Cairo”. Vengono studiate le possibilità di incorporare variazione ed eterogeneità all’interno del sistema senza comprometterne la modularità fino ad integrare percorsi multilivello. La definizione delle morfologie delle parti che compongono i moduli si basano sullo studio dei principi di galleggiamento, stabilità e yacht design: a partire dalla forma dello scafo adatta ai principi di tiling definiti in precedenza, tutte le parti che compongono le varie tipologie di modulo sono progettate cercando continuità e integrazione tettonica (geometrica, strutturale, funzionale e percettiva). Vengono proposte soluzioni integrate sia per le problematiche tipiche delle strutture galleggianti sia per l’inserimento di attività all’interno della soluzione architettonica. Vengono prototipati di una serie di moduli, scelti in modo da dimostrare i principi di ricombinazione, continuità, modularità e tiling.

The Missing Part of Seed Dispersal Networks: Structure and Robustness of Bat-Fruit Interactions

Mutualistic networks are crucial to the maintenance of ecosystem services. Unfortunately, what we know about seed dispersal networks is based only on bird-fruit interactions. Therefore, we aimed at filling part of this gap by investigating bat-fruit networks. It is known from population studies that: (i) some bat species depend more on fruits than others, and (ii) that some specialized frugivorous bats prefer particular plant genera. We tested whether those preferences affected the structure and robustness of the whole network and the functional roles of species. Nine bat-fruit datasets from the literature were analyzed and all networks showed lower complementary specialization (H(2)' = 0.3760.10, mean 6 SD) and similar nestedness (NODF = 0.5660.12) than pollination networks. All networks were modular (M=0.32 +/- 0.07), and had on average four cohesive subgroups (modules) of tightly connected bats and plants. The composition of those modules followed the genus-genus associations observed at population level (Artibeus-Ficus, Carollia-Piper, and Sturnira-Solanum), although a few of those plant genera were dispersed also by other bats. Bat-fruit networks showed high robustness to simulated cumulative removals of both bats (R = 0.55 +/- 0.10) and plants (R = 0.68 +/- 0.09). Primary frugivores interacted with a larger proportion of the plants available and also occupied more central positions; furthermore, their extinction caused larger changes in network structure. We conclude that bat-fruit networks are highly cohesive and robust mutualistic systems, in which redundancy is high within modules, although modules are complementary to each other. Dietary specialization seems to be an important structuring factor that affects the topology, the guild structure and functional roles in bat-fruit networks.