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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
11

Hippocampal Representations of Targeted Memory Reactivation and Reactivated Temporal Sequences

Alm, Kylie H January 2017 (has links)
Why are some memories easy to retrieve, while others are more difficult to access? Here, we tested whether we could bias memory replay, a process whereby newly learned information is reinforced by reinstating the neuronal patterns of activation that were present during learning, towards particular memory traces. The goal of this biasing is to strengthen some memory traces, making them more easily retrieved. To test this, participants were scanned during interleaved periods of encoding and rest. Throughout the encoding runs, participants learned triplets of images that were paired with semantically related sound cues. During two of the three rest periods, novel, irrelevant sounds were played. During one critical rest period, however, the sound cues learned in the preceding encoding period were played in an effort to preferentially increase reactivation of the associated visual images, a manipulation known as targeted memory reactivation. Representational similarity analyses were used to compare multi-voxel patterns of hippocampal activation across encoding and rest periods. Our index of reactivation was selectively enhanced for memory traces that were targeted for preferential reactivation during offline rest, both compared to information that was not targeted for preferential reactivation and compared to a baseline rest period. Importantly, this neural effect of targeted reactivation was related to the difference in delayed order memory for information that was cued versus uncued, suggesting that preferential replay may be a mechanism by which specific memory traces can be selectively strengthened for enhanced subsequent memory retrieval. We also found partial evidence of discrimination of unique temporal sequences within the hippocampus. Over time, multi-voxel patterns associated with a given triplet sequence became more dissimilar to the patterns associated with the other sequences. Furthermore, this neural marker of sequence preservation was correlated with the difference in delayed order memory for cued versus uncued triplets, signifying that the ability to reactivate particular temporal sequences within the hippocampus may be related to enhanced temporal order memory for the cued information. Taken together, these findings support the claim that awake replay can be biased towards preferential reactivation of particular memory traces and also suggest that this preferential reactivation, as well as representations of reactivated temporal sequences, can be detected within patterns of hippocampal activation. / Psychology
12

How does context variability affect representational pattern similarity to support subsequent item memory?

Lim, Ye-Lim 13 September 2022 (has links)
Episodic memories are neurally coded records of personally experienced events across a lifetime. These records are encoded via medial temporal lobe structures in the brain, including the hippocampus, and are commonly called "representations" or "memory traces". Existing studies indicate that information about the neural signal corresponding to a memory representation can be found in functional magnetic resonance imaging (fMRI) data when the pattern across its smallest units (voxels, often 3mm3 sections of the brain) is measured. Many prior studies have measured these voxel patterns in response to stimuli as if they are a spontaneous brain function, regardless of cognitive factors. These studies sometimes find that similarity in the voxel patterns across repetition of a to-be-remembered event predicts later memory retrieval, but the results are inconsistent. The current fMRI study investigated the possibility that cognitive goals during encoding affect the type of neural representation (voxel pattern) that will later support memory retrieval. This seems likely because prior behavioral studies indicate that cognitive variability across repetitions of an event benefits later memory retrieval, which is difficult to reconcile with the common finding that voxel pattern variability across repetitions of an event harms later memory. We tested this hypothesis by comparing voxel patterns that support later memory retrieval to those associated with forgotten items in the medial temporal lobe, including the hippocampus, and lateral occipital cortex. Overall, as previously demonstrated, the behavioral results showed that exposure to variable cognitive goals across repetition of events during encoding benefited subsequent memory retrieval. Voxel patterns in the hippocampus indicated a significant interaction between cognitive goals (variable vs. consistent) and memory (remembered vs. forgotten) such that less voxel pattern similarity for the repeated events with variable cognitive goals, but not consistent cognitive goals, supported later memory success. In other words, variable hippocampal neural activations for the same events under different cognitive goals predicted better later memory performance. However, there was no significant interaction in neural pattern similarity between cognitive goals and memory success in medial temporal cortices or lateral occipital lobe. Instead, higher similarity in voxel patterns in right medial temporal cortices was associated with later memory retrieval, regardless of cognitive goals. In the lateral occipital lobe, the main effects of cognitive goals, hemisphere, and memory success were found but no interactions. In conclusion, we found that the relationship between pattern similarity and memory success in the hippocampus (but not the medial temporal lobe cortex) changes when the cognitive goal during encoding does or does not vary across repetitions of the event. / Master of Science / Episodic memory is a long-term memory of personal experiences which are encoded via the medial temporal lobe in the brain, primarily in the hippocampus. The records of personal experiences in these areas are commonly called "patterns", "representations", or "memory traces". Prior investigations indicate that the way of measuring the neural signals corresponding to personal events is functional magnetic resonance imaging (fMRI). The brain images taken by an fMRI scanner represent the patterns of the smallest unit (voxels, often 3mm3 sections of the brain). Many prior investigations of episodic memory used the voxel patterns but showed mixed results in whether similarity in the voxel patterns across repetition of a repeated event leads to subsequent memory retrieval. One of the possible explanations for mixed results is that the cognitive factors during encoding were neglected. Therefore, the current fMRI study examined how cognitive goals during encoding influence the voxel patterns that later support memory retrieval. During encoding, participants were shown an image repeated with the same or different questions and answered the question on the screen in an fMRI scanner. After 10 days, they were invited to the item memory test on the images that they were given during the encoding phase. The voxel patterns in the medial temporal lobe, including the hippocampus, and the lateral occipital lobe were compared across the repetitions of each image. The behavioral results showed that variable cognitive goals across repeated events during encoding benefited later memory retrieval. Furthermore, less similar voxel patterns in the hippocampus for the images repeated with different questions, but not the same questions, during encoding predicted better later memory success. In the right medial temporal cortices, higher similarity in voxel patterns was significantly associated with later memory retrieval, regardless of cognitive goals. In the lateral occipital lobe, higher voxel pattern similarity was found in the right hemisphere, for images repeated with the same question, and for images successfully retrieved later. In conclusion, we found that the relationship between voxel pattern similarity and memory success in the hippocampus (but not the medial temporal lobe cortex) changes when the cognitive goal during encoding does or does not vary across repetitions of the event.
13

Unsupervised anomaly detection for structured data - Finding similarities between retail products

Fockstedt, Jonas, Krcic, Ema January 2021 (has links)
Data is one of the most contributing factors for modern business operations. Having bad data could therefore lead to tremendous losses, both financially and for customer experience. This thesis seeks to find anomalies in real-world, complex, structured data, causing an international enterprise to miss out on income and the potential loss of customers. By using graph theory and similarity analysis, the findings suggest that certain countries contribute to the discrepancies more than other countries. This is believed to be an effect of countries customizing their products to match the market’s needs. This thesis is just scratching the surface of the analysis of the data, and the number of opportunities for future work are therefore many.
14

Segmentação geomorfométrica associada com tipos de solos via geotecnologias / Geomorphometric segmentation associated with soils types via geotechnologies

Marques, Karina Patricia Prazeres 03 February 2017 (has links)
Os solos são vitais para todos os ecossistemas terrestres e deles depende a maior parte dos recursos para a manutenção dos seres vivos. Seu uso é importante para a agricultura e, para assim serem usados, é necessário conhecê-los, tanto como são como onde estão na paisagem. Esse conhecimento pode ser adquirido através de levantamentos de solos para os quais existem muitas limitações, como alta demanda financeira, elevado tempo para sua execução e subjetividade associada ao conhecimento tácito dos pedólogos. Por isso, são necessárias novas estratégias que auxiliem a execução de mapas de solos. Uma abordagem promissora é a identificação de unidades naturais do relevo em nível de detalhe, uma vez que é possível predizer a ocorrência de atributos e tipos de solos na paisagem quando associando as feições dos seus perfis com as de sua superfície. Diante disto, este trabalho objetiva testar procedimentos digitais para segmentação detalhada de elementos das encostas e relacioná-los com os atributos e classes taxonômicas de solos. Em uma área de estudo de 2.500 ha, situada na região de Piracicaba (SP), parâmetros geomorfométricos organizados hierarquicamente em regras em uma árvore de decisão foram utilizados para classificar, em escala detalhada (1:10.000), os cinco elementos da encosta (topo, ombro, meia-encosta, sopé coluvial e sopé colúvio-aluvial). Avaliou-se uma estratégia de análise de similaridade visando à identificação de agrupamentos de amostras de solos da mesma classe, a partir de diferentes conjuntos de variáveis. Essa segmentação digital mostrou que é possível explicitar a localização de cada um dos elementos da encosta e que neles dominam perfis de solos que se assemelham. Na maioria dos casos, essa semelhança pode ser comprovada com o uso tanto de análises convencionais como espectrais das amostras de solo coletadas até 1 m de profundidade. Essa classificação digital dos elementos da encosta pode auxiliar no mapeamento de solos detalhados e ultradetalhados (escalas 20.000 ou maiores). / Soils are vital for all terrestrial ecosystems and the majority of resources for maintenance of human beings depend on them. Their use is important for agriculture and, in order to be used in this manner, it is essential to know them, as well as how they are and where they are located in the landscape. This knowledge can be acquired through soil surveys, that have several limitations, such as high financial demand, time-consuming execution and subjectivity associated with the pedologists tacit knowledge. Considering this, new strategies are needed to support the elaboration of soil maps. One promising approach is the identification of detailed natural units of relief, since it is possible to predict the occurrence of attributes and types of soils in the landscape when associating the features of their profiles with those of their surface. Therefore, this research aims to test digital procedures for detailed segmentation of hillslope elements and to relate them to soil attributes and taxonomic classes. In a study area of 2,500 ha located in the Piracicaba (SP) region, geomorphometric parameters hierarchically organized into rules in a decision tree were used in order to classify, in a detailed scale (1:10,000), five hillslope elements (summit, shoulder, backslope, footslope and toeslope). A similarity analysis strategy was used to identify groupings of soil samples from the same class, from different sets of variables. This digital segmentation showed that it is possible to make explicit the location of each one of the hillslope elements, where similar soil profiles are dominant. In most cases, this similarity can be verified with the use of both conventional and spectral analyses of soil samples collected up to a depth of 1 m. This digital classification of hillslope elements can support 1st and 2nd order soil survey (scales 1:36,680 or greater).
15

Diversidade de anuros (Amphibia) do Parque Estadual Morro do Diabo, SP /

Santos, Tiago Gomes dos. January 2009 (has links)
Orientador: Célio Fernando Baptista Haddad / Banca: Cynthia Peralta de Almeida Prado / Banca: Cinthia Aguirre Brasileiro / Banca: Luis Felipe de Toledo Ramos Pereira / Banca: Marianna Botelho de Oliveira Dixo / Resumo: Estudamos a riqueza, composição taxonômica e os padrões de distribuição espaciais e temporais de taxocenoses de anuros do Parque Estadual Morro do Diabo (PEMD), o maior remanescente de Floresta Estacional Semidecídua no estado de São Paulo, Brasil. Registramos 28 espécies de anuros (Apêndice I) de setembro de 2005 a março de 2007, que compreenderam um misto de espécies de Mata Atlântica, do Cerrado e de formas amplamente distribuídas na América do Sul, geralmente consideradas tolerantes a modificações antropogênicas. A baixa riqueza de espécies e de modos reprodutivos, a predominância de espécies habitatgeneralistas e a alta similaridade de espécies de anuros com áreas de Cerrado podem ser explicadas pela sazonalidade climática da área estudada (estação seca pronunciada), além da grande distância em relação a centros de diversificação de anuros, como as montanhas costeiras da Floresta Atlântica úmida. Chuva e fotoperíodo explicaram aproximadamente 77% da atividade de vocalização de toda a taxocenose, enquanto somente a chuva e o fotoperíodo explicaram a temporada de vocalização em ambientes temporários e permanentes, respectivamente. Registramos alta sobreposição na temporada de vocalização dos machos, mas segregação na fase larval. A distribuição das espécies de anuros entre sítios de reprodução (Apêndice II) diferiu da esperada pelo acaso e compreendeu três taxocenoses distintas de anuros que foram explicadas pelo conjunto de variáveis ambientais de riachos permanentes, represas permanentes e poças temporárias. Registramos que 19 espécies de anuros (aproximadamente 83% da riqueza total de espécies registradas nos corpos d'água monitorados) foram indicadoras da heterogeneidade ambiental: três espécies indicaram riachos permanentes, quatro indicaram represas permanentes e 12 espécies indicaram poças temporárias... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: We studied richness, composition, and patterns of temporal and spatial distributions of anuran assemblages of Morro do Diabo State Park (MDSP), the major remnant of Mesophytic Semideciduous Forest (MSF) in the state of São Paulo, Brazil. From September 2005 to March 2007 we recorded 28 anuran species (Appendix I), comprising a mix of Atlantic, Cerrado, and South American widespread species, usually considered tolerant to anthropic modifications. The low richness of species and reproductive modes, the predominance of habitat generalist species, and the high similarity with Cerrado areas can be explained by climatic seasonality of the studied area (pronounced dry season), besides its large distance in relation to centers of anuran diversification, such as coastal mountains of the wet Atlantic Forest. Rainfall and photoperiod explained about 77% of calling activity of the whole assemblage, while rainfall alone in temporary habitats and photoperiod in permanent ones explained the calling season. We recorded high temporal overlap for calling males, but segregation for tadpoles. Spatial distribution of anuran species among breeding sites of the MDSP (Appendix II) differed of expected by chance and comprised three distinct anuran assemblages that were explained by the suite environmental variables of permanent streams, permanent dams, and temporary ponds. We recorded that 19 species (about 83% of total anuran species recorded in monitored sites) were indicators of environmental heterogeneity: three anuran species indicated permanent streams, four indicated permanents dams, and 12 anuran species indicated temporary ponds. Regarding to micro-spatial distribution of anuran species at two temporary ponds of MDSP, we recorded that males of most pairs of species (96%) used distinct sites for calling activities. The best combination of variables discriminating anuran species regarding male... (Complete abstract click electronic access below) / Doutor
16

Segmentação geomorfométrica associada com tipos de solos via geotecnologias / Geomorphometric segmentation associated with soils types via geotechnologies

Karina Patricia Prazeres Marques 03 February 2017 (has links)
Os solos são vitais para todos os ecossistemas terrestres e deles depende a maior parte dos recursos para a manutenção dos seres vivos. Seu uso é importante para a agricultura e, para assim serem usados, é necessário conhecê-los, tanto como são como onde estão na paisagem. Esse conhecimento pode ser adquirido através de levantamentos de solos para os quais existem muitas limitações, como alta demanda financeira, elevado tempo para sua execução e subjetividade associada ao conhecimento tácito dos pedólogos. Por isso, são necessárias novas estratégias que auxiliem a execução de mapas de solos. Uma abordagem promissora é a identificação de unidades naturais do relevo em nível de detalhe, uma vez que é possível predizer a ocorrência de atributos e tipos de solos na paisagem quando associando as feições dos seus perfis com as de sua superfície. Diante disto, este trabalho objetiva testar procedimentos digitais para segmentação detalhada de elementos das encostas e relacioná-los com os atributos e classes taxonômicas de solos. Em uma área de estudo de 2.500 ha, situada na região de Piracicaba (SP), parâmetros geomorfométricos organizados hierarquicamente em regras em uma árvore de decisão foram utilizados para classificar, em escala detalhada (1:10.000), os cinco elementos da encosta (topo, ombro, meia-encosta, sopé coluvial e sopé colúvio-aluvial). Avaliou-se uma estratégia de análise de similaridade visando à identificação de agrupamentos de amostras de solos da mesma classe, a partir de diferentes conjuntos de variáveis. Essa segmentação digital mostrou que é possível explicitar a localização de cada um dos elementos da encosta e que neles dominam perfis de solos que se assemelham. Na maioria dos casos, essa semelhança pode ser comprovada com o uso tanto de análises convencionais como espectrais das amostras de solo coletadas até 1 m de profundidade. Essa classificação digital dos elementos da encosta pode auxiliar no mapeamento de solos detalhados e ultradetalhados (escalas 20.000 ou maiores). / Soils are vital for all terrestrial ecosystems and the majority of resources for maintenance of human beings depend on them. Their use is important for agriculture and, in order to be used in this manner, it is essential to know them, as well as how they are and where they are located in the landscape. This knowledge can be acquired through soil surveys, that have several limitations, such as high financial demand, time-consuming execution and subjectivity associated with the pedologists tacit knowledge. Considering this, new strategies are needed to support the elaboration of soil maps. One promising approach is the identification of detailed natural units of relief, since it is possible to predict the occurrence of attributes and types of soils in the landscape when associating the features of their profiles with those of their surface. Therefore, this research aims to test digital procedures for detailed segmentation of hillslope elements and to relate them to soil attributes and taxonomic classes. In a study area of 2,500 ha located in the Piracicaba (SP) region, geomorphometric parameters hierarchically organized into rules in a decision tree were used in order to classify, in a detailed scale (1:10,000), five hillslope elements (summit, shoulder, backslope, footslope and toeslope). A similarity analysis strategy was used to identify groupings of soil samples from the same class, from different sets of variables. This digital segmentation showed that it is possible to make explicit the location of each one of the hillslope elements, where similar soil profiles are dominant. In most cases, this similarity can be verified with the use of both conventional and spectral analyses of soil samples collected up to a depth of 1 m. This digital classification of hillslope elements can support 1st and 2nd order soil survey (scales 1:36,680 or greater).
17

Contribució a l'estudi de l'efecte del canvi d'escala en l'experimentació en incendis forestals

Pérez Ramírez, Yolanda 20 May 2010 (has links)
Any rere any milions d'hectàrees són destruïdes pels incendis forestals, no només a Europa sinó arreu del món, tan sols cal recordar els dramàtics episodis viscuts a Califòrnia i Austràlia recentment. A banda de l'evident impacte mediambiental que això provoca -emissió de gasos d'efecte hivernacle, pèrdua de biodiversitat, acceleració de l'erosió del sòl, etc.- els incendis són també un problema social de primer ordre, que posa en perill a les persones i els seus béns. Davant d'aquesta situació, en les darreres dècades s'ha impulsat fortament la recerca en l'àmbit dels incendis forestals. Tanmateix, l'estudi dels incendis forestals és certament complex per les condicions i l'entorn on aquests es desenvolupen, a banda també del gran nombre de fenòmens -físics, químics i socials- que interaccionen al llarg de diferents escales espacials i temporals, per a donar lloc a l'inici i propagació del foc. És per això que bona part de la recerca sobre el comportament dels incendis forestals ha tingut lloc bàsicament al laboratori, tot i que qüestions com ara com traslladar aquests resultats experimentals als incendis reals, o bé fins a quin punt aquest tipus d'experimentació és útil o què és el que realment es pot extrapolar i què no, no han tingut encara cap resposta clara.L'objectiu d'aquesta tesi ha estat doncs el de contribuir a l'estudi del canvi d'escala en l'experimentació en incendis forestals pel què fa al comportament del foc, mitjançant les tècniques de l'anàlisi dimensional i de semblança. En primer lloc s'ha realitzat una extensa revisió bibliogràfica centrada bàsicament en aquells treballs que havien aplicat d'alguna manera o altra l'anàlisi dimensional i de semblança a l'estudi dels incendis i en particular dels incendis forestals. S'ha vist que no es possible realitzar un escalatge complet d'aquest fenomen i que el més utilitzat ha estat l'escalatge de Froude. A més s'ha detectat que mai abans s'ha aplicat aquest tipus d'anàlisi als models que s'utilitzen normalment avui dia en l'experimentació de laboratori. A continuació s'ha fet doncs una anàlisi exhaustiva de totes les variables que determinen el comportament d'un incendi forestal en els diferents escenaris experimentals (de laboratori i de camp). A partir d'aquestes variables s'ha realitzat una anàlisi dimensional per a estudiar la propagació d'un front de flames -tan bàsic com en condicions de vent i pendent- així com una anàlisi de semblança que ha permès obtenir les lleis d'escala per a les diferents variables que caracteritzen la propagació d'un incendi forestal. S'ha dissenyat i executat un programa experimental al laboratori amb l'objectiu de validar si es complien les lleis d'escala trobades i de determinar-ne el rang de validesa i les possibles causes en cas que no es complissin.Els resultats obtinguts han mostrat que per a fronts de flama bàsics propagant-se sense vent ni pendent, totes les variables analitzades segueixen les lleis d'escala derivades de l'estudi teòric, en el rang de longituds de front de flama abraçat que va dels 25 cm als 3 m. Nogensmenys cal remarcar que paràmetres com la humitat i el tipus de combustible o les característiques de la instal·lació experimental utilitzada poden alterar enormement els resultats si no es controlen adequadament. En el cas dels fronts de flama propagant pendent amunt, els resultats han mostrat que les lleis d'escala de la geometria de flama es compleixen per a tot el rang de pendents estudiat que va de 0 fins a 30°, mentre que en el cas de la llei d'escala de la velocitat de propagació deixa de complir-se per a pendents de 30°. Finalment, en el cas dels fronts de flama propagant en condicions de vent, els resultats han mostrat que per a velocitats del vent superiors a aproximadament 2,5 m/s les lleis d'escala tant de la velocitat de propagació com de la geometria de flama deixen de complir-se.Al final d'aquest treball s'apunten les causes que poden conduir a l'incompliment de les lleis d'escala així com als factors que poden restar validesa als experiments efectuats a escala de laboratori, quan es vol extrapolar els resultats a escales més grans o fins i tot a incendis reals. / Year after year millions of hectares are destroyed by wildland fires, not only in Europe but all over the world; just remember the dramatic episodes recently occurred in California or Australia. Besides the evident environmental impact caused by these fires -emission of greenhouse gases, biodiversity loss, soil erosion, etc- wildland fires represent also a social problem of primary order that threatens human life and their assets.Because of this situation, during the last decades research on wildland fires has been greatly boosted. Nevertheless, the study of forest fires is really complex due to the conditions and the environment in which they develop and to the number of phenomena -physical, chemical and social- that interact all along the different spatial and temporal scales that give rise to the start and development of a fire. That is partly the reason because the study of wildland fire behaviour has mainly been developed in laboratories, but questions like how these experimental results can be translated to real fires?, or is really this kind of experimentation useful?, or what can be extrapolated? These questions have not yet received a clear answer.The goal of this work was to improve the knowledge on the effect of changing the scale in the experimental study of forest fire behaviour, by means of dimensional and similarity analysis. First an extended bibliographic review has been done, centred on those works that had applied in one or another way the dimensional and similarity analysis to the study of fires and more specifically to forest fires. It was observed that it is not possible to undergo a complete scaling of a forest fire and that the most used partial scaling technique was the Froude scaling. Moreover it was detected that this kind of analysis was never before applied to the laboratory models used currently to obtain experimental data on wildland fires. Thus, an exhaustive analysis of all the variables affecting forest fire behaviour has been carried out for the diverse experimental scenario (in the lab and field). From these variables, a complete dimensional analysis has been developed in order to study the spread of a flames front -both in basic conditions and with slop or wind- and a subsequent similarity analysis has provided the scaling laws governing all the variables under study. A complete experimental program has been designed and developed in the laboratory with the aim of validating the scaling laws previously found and to establish the possible causes of any failure of the laws. The results obtained show that in the case of a basic flame front, spreading under no wind and no slope conditions, all the variables analysed followed the scaling laws obtained during the theoretical study for flames front lengths ranging from 25 cm to 3 m. For the tests under slop conditions, the results indicate that the scaling laws corresponding to the flame geometry are verified for all the slopes tested which range from 0 to 30°, while in the case of the rate of spread scaling law is no longer verified for the 30° slope. Finally, in the case of flame fronts spreading under wind conditions, the results show that for wind speed values greater than 2,5 m/s neither of the scaling laws corresponding to the flame geometry and the rate of spread, are verified. It has also been observed that parameters such as moisture content, the type of fuel or the specific design of the experimental device used can have a big influence on the results obtained if they are not adequately controlled.At the end of this work, the main causes leading to the failure of the scaling laws are pointed out together with the factors that can make the laboratory experiments less reliable when trying to extrapolate the results to larger scales or even to real fires.
18

Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins

January 2017 (has links)
abstract: In a typical living cell, millions to billions of proteins—nanomachines that fluctuate and cycle among many conformational states—convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible. Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code. / Dissertation/Thesis / Doctoral Dissertation Physics 2017
19

The Development and Application of Multivariate Analyses for Guiding Clinical Interventions and Mapping Representations of Human Memory

Nielson, Dylan Miles 22 May 2015 (has links)
No description available.
20

AURA : a hybrid approach to identify framework evolution

Wu, Wei 02 1900 (has links)
Les cadriciels et les bibliothèques sont indispensables aux systèmes logiciels d'aujourd'hui. Quand ils évoluent, il est souvent fastidieux et coûteux pour les développeurs de faire la mise à jour de leur code. Par conséquent, des approches ont été proposées pour aider les développeurs à migrer leur code. Généralement, ces approches ne peuvent identifier automatiquement les règles de modification une-remplacée-par-plusieurs méthodes et plusieurs-remplacées-par-une méthode. De plus, elles font souvent un compromis entre rappel et précision dans leur résultats en utilisant un ou plusieurs seuils expérimentaux. Nous présentons AURA (AUtomatic change Rule Assistant), une nouvelle approche hybride qui combine call dependency analysis et text similarity analysis pour surmonter ces limitations. Nous avons implanté AURA en Java et comparé ses résultats sur cinq cadriciels avec trois approches précédentes par Dagenais et Robillard, M. Kim et al., et Schäfer et al. Les résultats de cette comparaison montrent que, en moyenne, le rappel de AURA est 53,07% plus que celui des autre approches avec une précision similaire (0,10% en moins). / Software frameworks and libraries are indispensable to today's software systems. As they evolve, it is often time-consuming for developers to keep their code up-to-date. Approaches have been proposed to facilitate this. Usually, these approaches cannot automatically identify change rules for one-replaced-by-many and many-replaced-by-one methods, and they trade off recall for higher precision using one or more experimentally-evaluated thresholds. We introduce AURA (AUtomatic change Rule Assistant), a novel hybrid approach that combines call dependency and text similarity analyses to overcome these limitations. We implement it in a Java system and compare it on five frameworks with three previous approaches by Dagenais and Robillard, M. Kim et al., and Schäfer et al. The comparison shows that, on average, the recall of AURA is 53.07% higher while its precision is similar (0.10% lower).

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