Dissertations / Theses on the topic 'Emergent coding'

Purpose – The aim of this thesis is to explore the possibility of text mining social media, for consumer insights from an organizational perspective. Design/methodology/approach – An exploratory, single case embedded case study with inductive approach and partially mixed, concurrent, dominant status mixed method research design. The case study contains three different studies to try to triangulate the research findings and support research objective of using social media for consumer insights for new products, new ideas and helping research and development process of any organization. Findings – Text mining is a useful, novel, flexible and an unobtrusive method to harness the hidden information in social media. By text-mining social media, an organization can find consumer insights from a large data set and this initiative requires an understanding of social media and its building blocks. In addition, a consumer focused product development approach not only drives social media mining but also enriched by using consumer insights from social media. Research limitations/implications – Text mining is a relatively new subject and focus on developing better analytical tool kits would promote the use of this novel method. The researchers in the field of consumer driven new product development can use social media as additional evidence in their research. Practical implications – The consumer insights gained from the text mining of social media within a workable ethical policy are positive implications for any organization. Unlike conventional marketing research methods text mining is social media is cost and time effective. Originality/value –This thesis attempts to use innovatively text-mining tools, which appear, in the field of computer sciences to mine social media for gaining better understanding of consumers thereby enriching the field of marketing research, a cross-industry effort. The ability of consumers to spread the electronic word of mouth (eWOM) using social media is no secret and organizations should now consider social media as a source to supplement if not replace the insights captured using conventional marketing research methods. Keywords – Social media, Web 2.0, Consumer generated content, Text mining, Mixed methods design, Consumer insights, Marketing research, Case study, Analytic coding, Hermeneutics, Asynchronous, Emergent strategy Paper type Master Thesis

Identifying dangerous or rewarding elements in an animal’s surroundings is an important – if not primary – function of sensory systems. This holds particularly true for the mouse olfactory system since odors convey crucial information about predators, mates, kin and food. Thus, the olfactory system needs to effectively determine which odors are present as well as whether each odor has a positive or negative association, termed valence. Currently, we have little knowledge of how reward influences the processing of odors in the olfactory system of behaving mice. My work focuses on two high-level olfactory areas, the posterior piriform cortex (pPC) and olfactory tubercle (OT), that are situated at the intersection of sensory and reward-related brain regions. The pPC receives direct input from early olfactory areas and makes reciprocal connections to cognitive brain regions such as orbitofrontal cortex, limbic structures and the medial temporal lobe. The OT is a part of the ventral striatum which also receives input from early olfactory areas and is heavily interconnected with the reward system. To examine odor and reward coding in these areas, I developed a novel odor categorization task and recorded individual pPC and OT neurons during task performance. Mice successfully learn multiple, novel odor-response associations after only a few repetitions when the contingencies predict reward. I find that an explicit representation for reward category emerges in the OT within minutes of learning a novel odor-response association, whereas the pPC lacks an explicit representation even after more than one month of overtraining. The explicit representation is visible in the first sniff of an odor on each trial, when the motor decision is made, and is not correlated with the trial-to-trial motor decision. Together, these results suggest that decoding of stimulus information required for reward-driven sensorimotor decision making does not occur within olfactory cortex, rather decoding occurs in circuits involving olfactory striatum.
Medical Sciences

During neocortical development, network activity undergoes a dramatic transition from largely synchronized, so-called cluster activity, to a relatively sparse pattern around the time of eye-opening in rodents. Biophysical mechanisms underlying this sparsification phenomenon remain poorly understood. Here, we present a dynamic systems modeling study of a developing neural network that provides the first mechanistic insights into sparsification. We find that the rest state of immature networks is strongly affected by the dynamics of a transient, unstable state hidden in their firing activities, allowing these networks to either be silent or generate large cluster activity. We address how, and which, specific developmental changes in neuronal and synaptic parameters drive sparsification. We also reveal how these changes refine the information processing capabilities of an in vivo developing network, mainly by showing a developmental reduction in the instability of network’s firing activity, an effective availability of inhibition-stabilized states, and an emergence of spontaneous attractors and state transition mechanisms. Furthermore, we demonstrate the key role of GABAergic transmission and depressing glutamatergic synapses in governing the spatiotemporal evolution of cluster activity. These results, by providing a strong link between experimental observations and model behavior, suggest how adult sparse coding networks may emerge developmentally.

During neocortical development, network activity undergoes a dramatic transition from largely synchronized, so-called cluster activity, to a relatively sparse pattern around the time of eye-opening in rodents. Biophysical mechanisms underlying this sparsification phenomenon remain poorly understood. Here, we present a dynamic systems modeling study of a developing neural network that provides the first mechanistic insights into sparsification. We find that the rest state of immature networks is strongly affected by the dynamics of a transient, unstable state hidden in their firing activities, allowing these networks to either be silent or generate large cluster activity. We address how, and which, specific developmental changes in neuronal and synaptic parameters drive sparsification. We also reveal how these changes refine the information processing capabilities of an in vivo developing network, mainly by showing a developmental reduction in the instability of network’s firing activity, an effective availability of inhibition-stabilized states, and an emergence of spontaneous attractors and state transition mechanisms. Furthermore, we demonstrate the key role of GABAergic transmission and depressing glutamatergic synapses in governing the spatiotemporal evolution of cluster activity. These results, by providing a strong link between experimental observations and model behavior, suggest how adult sparse coding networks may emerge developmentally.

Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide. The development and progression of HCC is a multistep process which attributed to the accumulation of genetic alterations. Recently, mounting evidence has suggested the role of non-coding RNAs (ncRNAs) as the master driver of carcinogenesis, through their regulation on different oncogenes and tumor suppressive genes. Deregulation of ncRNAs was frequently observed in multiple types of cancers, including HCC. Herein, we demonstrated the aberrant expression pattern of miRNAs and lncRNAs in human HCC and investigated their functional roles in promoting hepatocarcinogenesis. Deregulation of miRNAs was previously demonstrated as a common event in human HCC, and miR-142-3p and miR-142-5pwereidentified as one of the significantly down-regulated miRNAs in HCC. Down-regulation of miR-142-3p and miR-142-5p was frequently observed in HCC patients and their expressions were progressively decreased along the multi-steps HCC development and progression. Functionally, overexpression of miR-142 has significantly inhibited HCC cell migration and invasion. Ectopic expression of miR-142 also markedly attenuated stress fiber formation and disrupted the cytoskeleton organization of HCC cells. Mature miR-142-3p and miR-142-5p, which derived from the same miRNA precursor were shown to collaboratively inhibited HCC cell migration through targeting different components of the key pathways regulating cell motility. On the other hand, we demonstrated the aberrant expression of lncRNAs in HCC by profiling of 88 well-annotated lncRNAs in 20 pairs of primary HCC and their corresponding non-tumorous liver. HOXA distal transcript antisense RNA (HOTTIP)was identified as the most frequently up-regulated lncRNA in HCC. Functionally, knock down of HOTTIP significantly attenuated cell proliferation in HCC cells and markedly abrogated tumorigenicity in nude mice. Knockdown of HOTTIP had lead to a global reduction in the HOXA genes expression, which are highly expressed in human HCC. Our data suggested that HOTTIP may regulate the expression of its neighboring protein-coding genes and contribute to the development of HCC. We also investigated the up-stream regulation of HOTTIP and identified miR-125b and miR-29a as regulators of HOTTIP in HCC. Clinically, miR-125b and miR-29a exhibited a reverse expression pattern to HOTTIP in HCC. Ectopic expression of miR-125b and miR-29a abolished HOTTIP-coupled luciferase activity and suppressed the endogenous level of HOTTIP. Intriguingly, we also identified a negative feedback relationship between HOTTIP and miR-125b. Taken together, our findings suggested the up-regulation of HOTTIP may be attributed to the down-regulation of miR-125b and miR-29a in HCC, and the sophisticated regulatory network between HOTTIP and miR-125b has further increased the complexity of gene regulation in HCC. In conclusion, we demonstrated the dysregulated expression pattern of miRNAs and lncRNAs in HCC and well illustrated their functional roles in promoting hepatocarcinogenesis. From the studies of miR-142 and lncRNA HOTTIP we appreciated the complex interactions and regulations between different ncRNAs. Taken together, our study has enriched the current knowledge on ncRNAs and their involvements in HCC development.
published_or_final_version
Pathology
Doctoral
Doctor of Philosophy

La codificación de red (NC) ha surgido recientemente como una nueva solución para mejorar el rendimiento de la red en términos de rendimiento y fiabilidad. Sin embargo, la naturaleza multiusuario de NC y su aplicabilidad inherente a la ingeniería de flujo versátil en todas las capas de la pila de protocolos requieren nuevos enfoques de diseño de sistemas inalámbricos. El objetivo de esta tesis es estudiar el diseño de NC como una funcionalidad de red ofrecida a los diseñadores de servicios de comunicación inalámbrica 5G. El diseño facilitaría el control del rendimiento de la red, la confiabilidad y la conectividad a través de redes inalámbricas 5G. Las contribuciones de esta tesis son las siguientes. Primero desarrollamos un diseño de Funcionalidad de codificación de red como una caja de herramientas de dominios de diseño NC y mostramos cómo se puede integrar en las infraestructuras virtualizadas actuales. En segundo lugar, evaluamos el rendimiento de longitud finita de diferentes códigos de red usando matrices aleatorias vs Pascal. Modelamos el proceso de codificación, recodificación y decodificación de diferentes esquemas de codificación en notación de matriz y las correspondientes probabilidades de error. A continuación, proponemos un algoritmo de búsqueda binaria para identificar la velocidad de codificación óptima para algunas tasas de pérdida de paquetes de destino específicas dada una longitud de bloque de codificación predefinida. Nos enfocaremos en los códigos de logro de capacidad y los esquemas de codificación con la programación de escenarios representativos y mostraremos la compensación de la tasa de retardo alcanzable entre los códigos aleatorios y los códigos estructurados con la programación. En la última parte de esta tesis, validamos el diseño de NCF propuesto para un caso de uso completo para mejorar la conectividad de los dispositivos de red móvil ad-hoc (MANET) sobre las redes convergidas de nubes satelitales en aplicaciones de emergencia. La idea clave es que en un escenario de emergencia puede no haber acceso directo a la niebla o la computación en la nube, que luego se proporcionará por satélite y los únicos recursos computacionales locales disponibles son los dispositivos MANET. Para resolver esta situación, definimos un NCF a nivel de paquetes con entradas de objetivos de calidad del servicio de datos, restricciones de computación local y estadísticas por ruta. Las salidas son tasas de codificación centralmente optimizadas que equilibran los recursos computacionales por nodo y la cobertura resultante.
Network coding (NC) has recently emerged as a new solution for improving network performance in terms of throughput and reliability. However, the multi-user nature of NC and its inherent applicability to versatile flow engineering across all layers of the protocol stack, call for novel wireless system design approaches. The goal of this thesis is to study the design of NC as a network functionality offered to the 5G wireless communication service designers. The design would facilitate the control of network throughput, reliability, and connectivity over 5G wireless networks. The contributions of this thesis are the following. We first develop a design of Network Coding Functionality as a toolbox of NC design domains and show how it can be integrated in current virtualized infrastructures. Second, we evaluate the finite-length performance of different network codes using random vs Pascal matrices. We model the encoding, re-encoding, and decoding process of different coding schemes in matrix notation and corresponding error probabilities. We then propose a binary searching algorithm to identify optimal coding rate for some specific target packet loss rates given a pre-defined coding block-length. We will focus on capacity-achieving codes and coding schemes with scheduling for representative scenarios and show the achievable rate-delay trade-off between random codes and structured codes with scheduling. In the last part of this thesis, we validate the proposed NCF design for a complete use case to enhance connectivity of Mobile Ad-hoc Network (MANET) devices over converged satellite-cloud networks in emergency applications. The key insight is that in an emergency scenario there may not be direct access to fog or cloud computing, which will then be provided via satellite and the only local computational resources available are the MANET devices. To solve this situation, we define a packet-level NCF with inputs from data service quality targets, local computation constraints and per-path statistics. Outputs are centrally-optimized coding rates balancing per-node computational resources and resulting coverage.

Rates of survival of victims of sudden cardiac arrest (SCA) using cardio pulmonary resuscitation (CPR) have shown little improvement over the past three decades. Since registered nurses (RNs) comprise the largest group of healthcare providers in U.S. hospitals, it is essential that they are competent in performing the four primary measures (compression, ventilation, medication administration, and defibrillation) of CPR in order to improve survival rates of SCA patients. The purpose of this experimental study was to test a color-coded SMOCK system on:1) time to implement emergency patient care measures 2) technical skills performance 3) number of medical errors, and 4) team performance during simulated CPR exercises. The study sample was 260 RNs (M 40 years, SD=11.6) with work experience as an RN (M 7.25 years, SD=9.42).Nurses were allocated to a control or intervention arm consisting of 20 groups of 5-8 RNs per arm for a total of 130 RNs in each arm. Nurses in each study arm were given clinical scenarios requiring emergency CPR. Nurses in the intervention group wore different color labeled aprons (smocks) indicating their role assignment (medications, ventilation, compression, defibrillation, etc) on the code team during CPR. Findings indicated that the intervention using color-labeled smocks for pre-assigned roles had a significant effect on the time nurses started compressions (t=3.03, p=0.005), ventilations (t=2.86, p=0.004) and defibrillations (t=2.00, p=.05) when compared to the controls using the standard of care. In performing technical skills, nurses in the intervention groups performed compressions and ventilations significantly better than those in the control groups. The control groups made significantly (t=-2.61, p=0.013) more total errors (7.55 SD 1.54) than the intervention group (5.60, SD 1.90). There were no significant differences in team performance measures between the groups. Study findings indicate use of colored labeled smocks during CPR emergencies resulted in: shorter times to start emergency CPR; reduced errors; more technical skills completed successfully; and no differences in team performance.

Esta tese de doutorado apresenta o projeto de uma arquitetura de memória híbrida energeticamente eficiente baseada em memórias do tipo scratchpad (Hy-SVM) para a codificação paralela de vídeos segundo o padrão HEVC. A codificação de vídeo se destaca como uma parte extremamente complexa nas aplicações de processamento de vídeo. O padrão HEVC traz inovações que complicam fortemente os requerimentos de memória de tais aplicações, principalmente devido a: (a) novas estruturas de codificação, as quais agravam a complexidade computacional por proporcionarem muitas modos possíveis de codificação que devem ser analisados; além do (b) suporte de alto nível à paralelização da codificação por meio do particionamento das unidades de codificação em múltiplos Tiles, o qual provê a aceleração da performance dos codificadores, porém, ao mesmo tempo, adiciona grandes desafios à infraestrutura de memória. O principal gargalo em termos de comunicação com a memória externa e de armazenamento interno (dentro do chip do codificador) é dados pelas informações dos quadros de referência: que consiste em uma série de quadros completos já codificados (e reconstruídos) que devem ser mantidos em memória e acessados de forma intensa durante o processamento dos quadros futuros. Devido ao grande volume de dados que são necessários para representar os quadros de referência, estes são tipicamente armazenados na memória externa dos codificadores (principalmente quando vídeos de alta e ultra alta resolução são processados) A arquitetura proposta Hy-SVM está inserida em um sistema de codificação baseado no particionamento dos quadros do vídeo de entrada em múltiplos Tiles, de forma a habilitar a codificação paralela das informações segundo o padrão HEVC: neste cenário, cada Tile é assinalado para uma específica unidade de processamento do codificador HEVC, o qual executa o processamento dos diferentes Tiles em paralelo. A ideias chave da arquitetura Hy- SVM incluem: projeto e gerenciamento de memórias para a aplicação específica de codificação de vídeo; uso de múltiplos níveis de memórias privadas e compartilhadas, com o objetivo de explorar o reuso de dados intra-Tile e inter-Tiles de forma combinada; uso de memórias do tipo scratchpad (SPMs) para o armazenamento interno da informações de forma eficiente em termos de consumo de energia; projeto de memórias híbridas utilizando as tecnologias SRAM e STTRAM como base. Uma metodologia de projeto é proposta para a arquitetura Hy-SVM, a qual aproveita propriedades específicas da aplicação para, de forma adequada, definir os parâmetros de projeto das memórias híbridas. De forma a prover adaptação em tempo de execução (para ambas as memórias on-chip e off-chip), a arquitetura Hy-SVM integra uma camada de gerenciamento composta pelas seguintes estratégias (1) predição do overlap (sobreposição de acessos), o qual busca identificar o comportamento dos acessos redundantes entre diferentes unidades de processamento do codificador HEVC a partir da análise dos acessos à memória das codificações dos quadros passados do vídeo, com o objetivo de aumentar o potencial de exploração do reuso de dados inter-Tiles; (2) gerenciamento dos acessos à memória externa, responsável por balancear a vazão de dados com a memória acumulada entre as múltiplas unidades de processamento do codificador HEVC paralelo, com o objetivo de melhorar o uso do barramento de comunicação com a memória externa; e (3) gerenciamento de dados das SPMs implementadas a partir de células de memória STT-RAM, o qual alivia estas células de acessos de escrita com alta atividade de chaveamento dos bits armazenados, com o objetivo de aumentar o tempo de vide destas células, bem como reduzir as penalidades relativas à ineficiência dos acessos de escrita nas memórias STT-RAM. O conhecimento específico da aplicação foi utilizado nas estratégias de gerenciamento em tempo de execução das seguintes formas: explorando parâmetros da codificação HEVC e realizando monitorando em tempo real dos acessos à memória realizados pelo codificador Estas informações são utilizadas tanto pelas técnicas de gerenciamento, quanto pelas metodologias de projeto das memórias. Baseadas nas decisões tomadas pela camada de gerenciamento, a arquitetura Hy-SVM integra unidades de gerenciamento de acessos à memória (memory access management units – MAMUs) para controlar as dinâmicas de acesso das memórias SPM privadas e compartilhadas. Além disso, unidades adaptativas de gerenciamento de potência (adaptive power management units – APMUs) são capazes de reduzir o consumo de energia interno do chip do codificador a partir das estimativas precisas de formação dos overlaps. Os resultados obtidos por meio dos experimentos realizados demonstram economias de consumo energético da arquitetura Hy-SVM, quando comparada a trabalhos relacionados, sob diversos cenários de teste. Quando comparada a estratégias de reuso de dados tradicionais para codificadores de vídeo, como o esquema Level-C, a exploração do reuso de dados combinado nos níveis intra-Tile e inter-Tiles provê 69%-79% de redução de energia. Considerando as arquiteturas de memória de vídeo com foco no padrão HEVC, os ganhos variaram desde 2,8% (pior caso) até 67% (melhor caso) Da perspectiva do consumo de energia relacionado à comunicação com a memória externa, a arquitetura Hy-SVM é capaz de melhorar o reuso de dados (por explorar também o reuso de dados inter-Tiles), resultando em um consumo de energia on-chip 11%-17% menor. Além disso, as APMUs contribuem para reduzir o consumo de energia on-chip da arquitetura Hy-SVM em 56%-95%, para os cenários de teste analisados. Desta forma, comparada aos trabalhos relacionados, a arquitetura Hy-SVM apresenta o menor consumo energético on-chip. O gerenciamento da vazão da comunicação com a memória externa é capaz de reduzir as variações de largura de banda em 37%-83%, quando comparado à ordem tradicional de processamento, para cenários de teste com 4 e 16 Tiles sendo processados em paralelo pelo codificador HEVC. O gerenciamento de dados pôde, de forma significativa, estender o tempo de vida das células de memória STT-RAM, alcançando 0,83 de tempo de vida normalizado (métrica adotada para comparação, ficando muito próximo do caso ideal). Além disso, as sobrecargas causadas pela implementação das unidades de gerenciamento não afetam de foram significativa a performance e a eficiência energética da arquitetura Hy- SVM propostas por este trabalho.
This Thesis presents the design of an energy-efficient hybrid scratchpad video memory architecture (called Hy-SVM) for parallel High-Efficiency Video Coding. Video coding stands out as a high complex part in the video processing applications. HEVC standard brought innovations that increase the memory requirements, mainly due to: (a) the novel coding structures, which aggravates the computational complexity by providing a wider range of possibilities to be analyzed; and (b) the high-level parallelism features provided by the Tiles partitioning, which provides performance acceleration, but, at the same time, strongly adds hard challenges to the memory infrastructure. The main bottleneck in terms of external memory transmission and on-chip storage is the reference frames data: which consists of already coded (and reconstructed) entire frames that must be stored and intensively accessed during the encoding process of future frames. Due to the large volume of data required to represent the reference frames, they are typically stored in the external memory (especially when highdefinition videos are targeted). The proposed Hy-SVM architecture is inserted in a video coding system, which is based on multiple Tiles partitioning to enable parallel HEVC encoding: each Tile is assigned to a specific processing unit. The key ideas of Hy-SVM include: applicationspecific design and management; combined multiple levels of private and shared memories that jointly exploit intra-Tile and inter-Tiles data reuse; scratchpad memories (SPMs) as energyefficient on-chip data storage; combined SRAM and STT-RAM hybrid memory (HyM) design We propose a design methodology for Hy-SVM that leverages application-specific properties to properly define the HyMs parameters. In order to provide run-time adaptation (for both offand on-chip parts), Hy-SVM integrates a memory management layer composed of: (1) overlap prediction, which has the goal of identifying the redundant memory access behavior by analyzing monitored past frames encoding to increase inter-Tiles data reuse exploitation; (2) memory pressure management, which aims on balancing the Tiles-accumulated memory pressure targeting on improving external memory communication channel usage; and (3) lifetime-aware data management scheme that alleviates STT-RAM SPMs of high bit-toggling write accesses to increase the their cells lifetime, as well as to reduce overhead issues related to poor write characteristics of STT-RAM. Application-specific knowledge was exploited by inheriting HEVC properties and performing run-time monitoring of memory accesses. Such information is used to properly design the on-chip video memories, as well as being utilized as input parameters of the run-time memory management layer. Based on the run-time decisions from the proposed Hy-SVM management strategies, Hy-SVM integrates distributed memory access management units (MAMUs) to control the access dynamics of private and shared SPMs. Additionally, adaptive power management units (APMUs) are able to strongly reduce on-chip energy consumption due to an accurate overlap prediction The experimental results demonstrate Hy-SVM overall energy savings over related works under various HEVC encoding scenarios. Compared to traditional data reuse schemes, like Level-C, the combined intra-Tile and inter-Tiles data reuse provides 69%-79% of energy reduction. Regarding related HEVC video memory architectures, the savings varied from 2.8% (worst case) to 67% (best case). From the external memory perspective, Hy-SVM can improve data reuse (by also exploiting inter-Tiles data redundancy), resulting on 11%-71%% of reduced off-chip energy consumption. Additionally, our APMUs contribute by reducing on-chip energy consumption of Hy-SVM by 56%-95%, for the evaluated HEVC scenarios. Thus, compared to related works, Hy-SVM presents the lowest on-chip energy consumption. The memory pressure management scheme can reduce the variations in the memory bandwidth by 37%-83% when compared to the traditional raster scan processing for 4- and 16-core parallelized HEVC encoder. The lifetime-aware data management significantly extends the STT-RAM lifetime, achieving 0.83 of normalized lifetime (near to the optimal case). Moreover, the overhead of implementing our management units insignificantly affects the performance and energyefficiency of Hy-SVM.

Orientador: Renato Vicentini dos Santos
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
Made available in DSpace on 2018-08-25T20:26:13Z (GMT). No. of bitstreams: 1 Canesin_LucasEduardoCosta_M.pdf: 8460459 bytes, checksum: 3fde4864bd253faed92b7dfd9071be3c (MD5) Previous issue date: 2014
Resumo: Recentemente, a análise de dados de genômica comparativa, buscando elucidar melhor a hipótese nula de modelos evolutivos, i.e. evolução neutra, originou uma nova teoria que eleva o tamanho populacional como principal fator evolutivo. Populações pequenas estão sujeitas a forte influência de deriva genética, o que causa o aumento da entropia do genoma. A complexidade genômica, leia-se conteúdo de sequencias informativas, como genes, é então um subproduto do aumento da entropia e a seleção teria então um papel secundário, sobretudo como moduladora do processo evolutivo. Assumindo este modelo, a emergência e degeneração de transcritos linhagem-específicos estão submetidas primariamente a evolução neutra. A transcrição pervasiva, sobretudo em linhagens germinais, é o agente causal do nascimento de genes e a fixação destes, frente ao reduzido tamanho populacional de eucariotos multicelulares, como as plantas Saccarum officinarum e Sorghum bicolor, ocorre por deriva genética. A inserção de novos genes, que são inicialmente neutros ou levemente deletérios, em redes funcionais ainda é pouco compreendida. A integração se torna gradativamente mais robusta com a evolução individual destes loci. Neste contexto, este estudo buscou identificar genes codificadores e não-codificadores de proteínas de recente emergência em cana-de-açúcar e sorgo a fim de se elucidar a hipótese de que sua arquitetura gênica e integração em redes biológicas apresentam padrões evolutivos comuns. Para isso, realizamos a identificação de lncRNAs de cana a partir de bancos de cDNA, o que permitiu a caracterização da expressão desses transcritos contrastando seis variedades distintas. Em decorrência da disponibilidade do genoma de sorgo, a identificação de genes linhagem-específicos codificadores e não codificadores pode ser resolvida com maior precisão. Pudemos determinar uma correlação entre a sua arquitetura gênica e integração nas redes biológicas e sua idade relativa. Apesar da correlação encontrada, o efeito mais forte observado em transcritos não codificadores revelam outros fatores que devem estar influenciando sua evolução. Levantamos a hipótese de que o evento de tradução possa elevar a eficiência da seleção negativa sobre o transcrito emergente, o que resultaria no turnover mais acentuado de lincRNAs e maior conservação de genes linhagem-específicos
Abstract: Recently, comparative genomics studies, aiming to better elucidate the null hypothesis of models of evolution, i. e. the neutral evolution, originate a new theory that elects the population size as the main factor acting in evolution. Small populations are subject to stronger influence of genetic drift, which raises genomic entropy. Genomic complexity, which means the information content in genome, such as genes, is a byproduct of the high entropy levels and selection would then display a secondary role, mainly as a modulator of the evolutionary process. Assuming this model, the emergence and degeneration of lineage-specific transcripts are primarily subject to neutral evolution. The pervasive transcription, especially in germinal cell lines, is the causal agent of birth of genes and their fixation, in face to the reduced population size of multicellular eukaryotes, as Saccarum officinarum and Sorghum bicolor plant species, is ruled by genetic drift. The integration of new genes, initially neutral or weakly deleterious, in functional networks is still poorly understood. The integration becomes more robust with the individual historical evolutionary path of these loci. In this context, this study aimed identify protein coding and noncoding genes of recent emergence in in sugarcane and sorghum to elucidate the hypothesis that the gene architecture and integration in biological networks display common patterns of evolution. We then identified sugarcane lncRNAs from public cDNA databases that allowed us to characterize the expression of these transcripts in six different contrasting varieties of sugarcane. As sorghum bicolor genome is available, the identification of lineage-specific coding and noncoding could be done to a higher resolution. We could then determine a correlation between gene architecture and network integration with its relative age. Despite the correlation observed, a stronger effect seen in noncoding transcripts reveals other factors that may be influencing their evolution. We propose the hypothesis that the translation event may increase negative selection efficiency over the emerging transcript, what would result in the stronger turnover of lincRNAs and higher conservation levels of coding lineage-specific genes
Mestrado
Bioinformatica
Mestre em Genética e Biologia Molecular

Les systèmes de communication optique ont connu plusieurs phases de développement au cours des dernières décennies. Ils approchent aujourd'hui les limites de capacité du cana non-linéaire. L'espace est aujourd'hui le dernier degré de liberté à mettre en œuvre afin de continuer à répondre aux demandes de capacité à venir pour les prochaines années. Par conséquent, des recherches intensives sont menées pour explorer tous les aspects concernant le déploiement du système de multiplexage par division spatiale (SDM). Plusieurs dégradations ont un impact sur les systèmes SDM en raison de l'interaction des canaux spatiaux qui dégrade les performances du système. Dans cette thèse, nous nous concentrons sur les fibres multicœurs (MCF) comme l'approche la plus prometteuse pour être le premier représentant du système SDM. Nous présentons différentes solutions numériques et optiques pour atténuer l'effet non unitaire connu sous le nom de perte dépendante du cœur (CDL). La première partie est consacrée à l'étude des performances de la transmission MCF en tenant compte des dégradations de propagation qui impactent les systèmes MCF. Nous proposons un modèle de canal qui aide à identifier le système MCF. La deuxième partie est consacrée à la technique optique pour améliorer les performances de transmission avec une solution optimale pour la réduction des CDL. Ensuite, nous avons introduit des techniques numériques pour des améliorations supplémentaires, la pré-compensation Zero Forcing et le codage spatio-temporel pour une atténuation CDL supplémentaire. Tous les résultats de simulation sont validés analytiquement en dérivant les bornes supérieures de probabilité d'erreur
Optical communication systems have seen several phases in the last decades. It is predictable that the optical systems as we know will reach the non-linear capacity limits. At the moment, the space is the last degree of freedom to be implemented in order to keep delivering the upcoming capacity demands for the next years. Therefore, intensive researches are conducted to explore all the aspects concerning the deployment of the space-division multiplexing (SDM) system. Several impairments impact the SDM systems as a result from the interaction of the spatial channels which degrades the system performance. In this thesis, we focus on the multi-core fibers (MCFs) as the most promising approach to be the first representative of the SDM system. We present different digital and optical solutions to mitigate the non-unitary effect known as the core dependent loss (CDL). The first part is dedicated to study the performance of the MCF transmission taking into account the propagating impairments that impact the MCF systems. We propose a channel model that helps to identify the MCFs system. The second part is devoted to optical technique to enhance the transmission performance with an optimal solution. After, we introduced digital techniques for further enhancement, the Zero Forcing pre-compensation and the space-time coding for further CDL mitigation. All the simulation results are validated analytically by deriving the error probability upper bounds

La tesi ha come tema di studio la progettazione antincendio degli edifici, con particolare approfondimento del progetto dell’esodo degli occupanti. In Italia, le procedure previste in Italia nella sicurezza antincendio in un’attività a rischio sono stabilite dal D.P.R. 151/2011, con l’elenco delle attività soggette ai controlli di prevenzione incendi, e il D.M. 07/08/2012 inerente le modalità di presentazione della documentazione da allegare ai VVFF. La normativa individua 4 fasi d'incendio: ignizione, crescita, sviluppo (flashover), decadimento. Durante il processo di combustione si crea una colonna di fumo chiamata “fire plume”, con dispersione dei prodotti di combustione. La maggior parte dei decessi durante l'incendio avviene per inalazione di gas di combustione che recano effetti asfissianti, compromettendo la capacità di esodo, portando collasso e perdita di coscienza; se irritanti, provocano irritazione agli occhi e alle vie respiratorie, fino ad incapacità fisica e di movimento. Il “way-finding” è l’orientamento nello spazio fisico nei meccanismi di percezione sensoriale dell’ambiente; per “comportamento umano in emergenza” si intendono le azioni svolte dagli occupanti in situazioni di emergenza. La letteratura individua 7 processi psicologici di emergenza incendio: riconoscimento, validazione, definizione, valutazione, impegno, rivalutazione, e secondo la ISO/TR 13387-8 è necessario valutare lo scenario d'incendio secondo posizione e condizione degli occupanti. L’approccio prestazionale di esodo degli occupanti è basato sul confronto tra il “tempo disponibile per raggiungere un luogo sicuro” (ASET) e il “tempo necessario per la fuga” (RSET), e il criterio fondamentale è: t (ASET) > t (RSET). La tesi analizza criticamente la normativa nazionale ed internazionale, anche in relazione al confronto tra il nuovo ed il vecchio codice di prevenzione incendi, ed affronta il tema della progettazione dell’emergenza per un caso di studio di edilizia industriale.

Codeine-containing medication is commonly used for pain after c-section. In most people, 10% of codeine is biotransformed into morphine by the Cytochrome P450 enzyme 2D6 (CYP2D6). Individuals who convert up to 50 fold more codeine into morphine, ultrarapid metaboizers, are at a greater risk for adverse effects. Conversely poor metabolizers, individuals who convert almost no codeine into morphine, are at risk for untreated pain. The pharmacodynamic relationship between codeine-analgesia and CYP2D6 genotype is studied for possible development of a titration model. To minimize these treatment risks, alternatives to opioids are sought. Reiki, an ancient Japanese form of healing used to treat pain and depression, has not been systematically reviewed for its efficacy in treating pain. My systematic review of Reiki literature (n=12) showed that while most trials yielded a positive result on primary outcomes, all existing Reiki studies lacked in one of the three key areas of proper patient allocation concealment, randomization or blinding which can lead to the introduction of bias. We designed a randomized controlled trial using distant Reiki for postpartum pain, taking careful steps to control for each of those three key areas. Eighty pregnant women scheduled for an elective c-section where recruited and randomly allocated to one of the two arms (n=40 Reiki and n=40 control). Women were monitored in hospital for up to three days. Visual Analogue Scores (VAS) for pain were recorded 4 times per day; and all pain medication, adverse effects and milestone recovery rates after c-section were recorded. Blood samples were taken to determine CYP2D6 genotype. We determined that distant Reiki did not reduce women’s pain; neither the measured pain nor the cumulative dose of pain medication differed between groups. Moreover, rates of recovery after c-section were also not different between the two groups. This led to the conclusion that distant Reiki was not suitable as a primary method of controlling pain after c-section. Our second study (n=45) looked for correlation between CYP2D6 genotype and effectiveness of codeine analgesia. Only a small sample of the women were genetic extremes (n=2 poor metabolizers and n=3 ultrarapid metabolizers), while most were, as expected, extensive or intermediate metabolizers. An individual examination of each of these cases provided valuable insight into patients where CYP2D6 polymorphism is clinically relevant. Two of the three ultrarapid metabolizers stopped opioid analgesia due to adverse effects, while both poor metabolizers complained that the codeine-containing medication was not providing analgesia (i.e. ineffective pain treatment). Healthcare providers need to be aware of patient response to pharmacotherapy and use this information to individualize postpartum opioid analgesia.