<p>The aim of the project was to identify biologically relevant novel gene clusters by using combined genomic data instead of using only gene expression data in isolation. The clustering algorithm based on self-organizing maps (Kasturi et al., 2005) was extended and implemented in order to use gene location data together with the gene expression and the motif occurrence data for gene clustering. A distance function was defined to be used with gene location data. The algorithm was also extended in order to use vector angle distance for gene expression data. <em>Arabidopsis thaliana</em> is chosen as a data source to evaluate the developed algorithm. A test data set was created by using 100 Arabidopsis genes that have gene expression data with seven different time points during cold stress condition, motif occurrence data which indicates the occurrence frequency of 614 different motifs and the chromosomal location data of each gene. Gene Ontology (http://www.geneontology.org) and TAIR (http://arabidopsis.org) databases were used to find the <em>molecular function</em> and <em>biological process</em> information of each gene in order to examine the biological accuracy of newly discovered clusters after using combined genomic data. The biological evaluation of the results showed that using combined genomic data to cluster genes resulted in new biologically relevant clusters.</p>

Small failures should only disrupt a small part of a network. One wayto do this is by marking the surrounding area as untrustworthy ---circumscribing the failure. This can be done with a distributedalgorithm using hierarchical clustering and neighbor relations, andthe resulting circumscription is near-optimal for convex failures.

This dissertation comprises three articles that propose explanations for the eventual extinction of Neanderthals in Europe after a period of several thousand years of coexistence with anatomically modern humans (AMH). I propose that bioenergetic differences between Neanderthals and AMH favored the persistence of AMH. This difference in energetic efficiency was augmented by any behavior that was advantageous to AMH. Consequently, such behaviors directly impacted the rate of Neanderthal extinction. The first article proposes a mathematical model that reconstructs Neanderthal and AMH energetic budgets to predict how using fire for cooking might have affected the success of each species. I first use the model to establish that energetic differences alone result in Neanderthal extinction when Neanderthals and AMH occupy the same landscape. I then establish that cooking meat increases its caloric value, and incorporate that parameter into the model. The outcome indicates that differential fire use by Neanderthals and AMH significantly affects the rate of Neanderthal extinction. The second article analyzes the evidence for marrow and bone grease extraction from reindeer carcasses by Neanderthals and AMH during cold climate phases. I analyze two assemblages produced by Neanderthals and three produced by AMH to determine how each group exploited these crucial nutritional resources. Results indicate that marrow processing intensity correlates with site function rather than with human species while bone grease may have been more intensively processed by AMH. In the third article, I integrate these studies within a new theoretical framework combining self-organizing criticality (SOC) and resilience thinking (RT). I explore Neanderthal extinction across multiple scales. SOC explores how interactions at the scale of the individual can combine to cause events such as an extinction. RT provides a systems-level framework for understanding how patterns of change among Neanderthals, AMH, prey populations, and the landscapes they inhabit may lead to instability and collapse. I identify the arrival of AMH into a landscape occupied by Neanderthals as a threshold point that set the process of Neanderthal demise in motion. I then use SOC and RT together to explain Neanderthal extinction as a slow and patchy process, rather than a sudden extinction.

BEZERRA, Italo Pereira. Auto-organização de aglomerados finitos de dipolos magnéticos carregados. 2009. 65 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2009. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-05-04T18:22:34Z No. of bitstreams: 1 2009_dis_ipbezerra.pdf: 8023171 bytes, checksum: e47ba0b7e87905fb3b10ff887cc2f1f8 (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-05-07T16:51:22Z (GMT) No. of bitstreams: 1 2009_dis_ipbezerra.pdf: 8023171 bytes, checksum: e47ba0b7e87905fb3b10ff887cc2f1f8 (MD5) / Made available in DSpace on 2015-05-07T16:51:22Z (GMT). No. of bitstreams: 1 2009_dis_ipbezerra.pdf: 8023171 bytes, checksum: e47ba0b7e87905fb3b10ff887cc2f1f8 (MD5) Previous issue date: 2009 / It is studied at this thesis a two-dimensional cluster of magnetic particles, with surface charge, confined by a circular parabolic potential. The particles have the same magnitude of magnetic dipole moment and the same amount and sign of surface charge. The goal of the present study is the characterization of the ground state configurations and the normal mode spectra of the cluster. The numerical study of the system is based on the Monte Carlo simulation technique, using the Metropolis Algorithm. It was also used the called Newton Method technique to reach the ground state configurations . The present study is divided in two parts: i) In the first one, the dependence of the equilibrium configurations and the normal modes is analyzed considering the presence or not of a external magnetic field. The magnetic dipole moment is taken as constant. ii) In the second one, the surface charge and the magnetic dipole moment are taken as constant, and the ground state configurations and the normal modes are studied as function the the external magnetic field intensity. At this part, it is also calculated the magnetization of the system as function of the external magnetic field. It was observed a great number of different ground state configurations, like concentric rings, and chains. The vibrational normal mode frequencies spectra was obtained by using the harmonic approximation. Due to the non-spatial symmetry of the magnetic dipole interaction, the normal modes must show an extra rotational component. It can be noted that due to surface charge of the particles the frequencies spectra can present elevated variation on the intensity. It can also be noted that some properties of the first case system also occurs on the second case system, and these properties are independent of the applied magnetic field, and in the second case system it can be noted that there are less different ground state configurations as compared with the first one. / Estuda-se, neste trabalho, aglomerados bidimensionais de partículas dipolares magnéticas, com carga elétrica superficial, confinadas em um potencial parabólico circular. As partículas possuem mesmo módulo de momento de dipolo magnético, assim como mesmos módulo e sinal de carga superficial. O objetivo do presente estudo é a caracterização das configurações do estado fundamental e do espectro dos modos normais do aglomerado. O sistema é estudado numericamente através de simulações Monte Carlo, utilizando o algoritmo de Metropolis. Utilizou-se ainda o chamado Método de Newton Modificado para auxiliar a obtenção das configurações de mínima energia. O estudo é dividido em duas partes: i) Na primeira, a dependência das configurações de equilíbrio e modos normais é analisada em função da carga superficial, na presença e ausência de campo magnético externo, considerando-se o momento de dipolo magnético constante. ii) Na segunda, a carga superficial e o momento de dipolo magnético são fixados e as configurações de equilíbrio e os modos normais são estudados em função da intensidade do campo magnético externo. Nesta parte, calcula-se ainda a magnetização do sistema em função do campo externo. O espectro de frequências dos modos normais de vibração foram obtidos através da técnica de aproximação harmônica. Devido à não-simetria espacial da interação magnética dipolar, os modos normais devem apresentar um componente extra de rotação. Observa-se que para um intervalo característico da carga superficial das partículas, o espectro de frequências sofre uma grande variação de intensidade. Observa-se que no caso dependente da carga, o sistema apresenta características que independem do campo magnético aplicado. Observa-se, no caso dependente do campo aplicado, uma menor variedade de configurações de equilíbrio deste tipo de sistema em relação ao dependente da carga.

Abstract Phospholipids are the main components of cell membranes, lipoproteins and other membrane structures in living organisms. Properties of lipid molecules are important to the overall behaviour and interactions of membranes. Furthermore, characteristics of the biological membranes act as important regulators of membrane functions. Molecular dynamics (MD) simulations were applied in this thesis to study properties of biological membranes. A certain degree of acyl chain polyunsaturation is essential for the proper functioning of membranes, but earlier MD simulations had not addressed the effects of polyunsaturation. Therefore a solvated all-atom bilayer model consisting of diunsaturated 1-palmitoyl-2-linoleoyl-3-phosphatidylcholine (PLPC) molecules was simulated. The analysis of the simulation data was focused on the effects of double bonds on a membrane structure. Self-organising neural networks were applied to the analysis of the conformational data from the 1-ns simulation of PLPC membrane. Mapping of 1.44 million molecular conformations to a two-dimensional array of neurons revealed, without human intervention or requirement of a priori knowledge, the main conformational features. This method provides a powerful tool for gaining insight into the main molecular conformations of any simulated molecular assembly. Furthermore, an application of MD simulations in the comparative analysis of the effects of lipid hydrolysis products on the membrane structure was introduced. The hydrolysis products of the phospholipase A2 (PLA2) enzyme are known to have a role in a variety of physiological processes and the membrane itself acts as an important regulator of this enzyme. The simulations revealed differences in the bilayer properties between the original and hydrolysed phospholipid membranes. This study provides further evidence that MD simulations on biomembranes are able to provide information on the properties of biologically and biochemically important lipid systems at the molecular level.

M.Ing. / This project investigates the use of Self-Organizing Maps (SOM) for feature recognition and analysis in 3D objects. Object data was generated to simulate data obtained from 3D scanning and trained using SOM. The trained data was analysed using speci cally developed software. The feature recognition and analysis process can be summarized as follows: a 3D object le is converted to a pure 3D data le, this data le is trained using the SOM algorithm after which the output is analyzed using a 3D object viewer and SOM data display.

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Considering the commonality of breast cancer among women in the United States and the increasing popularity of precision medicine and data analytics in healthcare, the aim of this study was to use self-organizing maps (SOM) to profile and make decisions about breast cancer patients. Breast cancer mass measurements were combined with nine non-medical attributes—family income, history of cancer, level of education, preference of probability level, presence of dependents, employment status, marital status, age, and location—that were randomly generated based on recent population statistics and fed into a SOM. The SOM’s accuracy was evaluated at around 80%. To show the decision-making capabilities of the SOM, a subset of the patients were treated as new patients and placed on the map. Profiles of these clusters were created to show how decisions made about patients’ diagnosis, delivery, and treatment differed based on the cluster to which they belonged.

<p> Connectionist models of language acquisition typically have difficulty with systematicity, or the ability for the network to generalize its limited experience with language to novel utterances. In this way, connectionist systems learning grammar from a set of example sentences tend to store a set of specific instances, rather than a generalized abstract knowledge of the process of grammatical combination. Further, recent models that do show limited systematicity do so at the expense of simultaneously storing explicit lexical knowledge, and also make use of both developmentally-implausible training data and biologically-implausible learning rules. Consequently, this research program develops a novel unsupervised neural network architecture, and applies this architecture to the problem of systematicity in language models.</p> <p> In the first of several studies, a connectionist architecture capable of simultaneously storing explicit and separate representations of both conceptual and grammatical information is developed, where this architecture is a hybrid of both a self-organizing map and an intra-layer Hebbian associative network. Over the course of several studies, this architecture's capacity to acquire linguistic grammar is evaluated, where the architecture is progressively refined until it is capable of acquiring a benchmark grammar consisting of several difficult clausal sentence structures - though it must acquire this grammar at the level of grammatical category, rather than the lexical level.</p> <p> The final study bridges the gap between the lexical and grammatical category levels, and develops an activation function based on a semantic feature co-occurrence metric. In concert with developmentally-plausible sensorimotor grounded conceptual representations, it is shown that a network using this metric is able to undertake a process of semantic bootstrapping, and successfully acquire separate explicit representations at the level of the concept, part-of-speech category, and grammatical sequence. This network demonstrates broadly systematic behaviour on a difficult test of systematicity, and extends its knowledge of grammar to novel sensorimotor-grounded words.</p> / Thesis / Doctor of Philosophy (PhD)

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