<p>Protein conformational transitions are fundamental to the functions of many proteins, and computational methods are valuable for elucidating the transitions that are not readily accessible by experimental techniques. Here we developed accelerated sampling methods to calculate optimized all-atom protein conformational transition paths. Adaptively biased path optimization (ABPO) is a computational simulation method to optimize the conformational transition path between two states. We first examined the transition paths of three systems with relatively simple transitions. The ways to define reduced variables were explored and transition paths were built at convergence of the optimizations. We constructed the all-atom conformational transition path between the active and the inactive states of the Src kinase domain. The C helix rotation was identified as the main free energy barrier in the all‑atom system, and the intermediate conformations and key interactions along the transition path were analyzed. This is the first demonstration of the robustness of a computational method for calculating protein conformational transitions without restraints to a specified path. We also evaluated protein‑peptide interactions using both molecular dynamics simulations and peptide docking. Long unbiased simulations were used to evaluate Src‑SSP interactions and complex stability in both implicit and explicit solvent. Molecular docking was used to build possible protein‑peptide interaction models, using both Src regulatory domain SH2 and the kinase domain. Possible Src‑SSP complexes were built as the first Src‑substrate complex structure models.</p>

Made available in DSpace on 2014-06-11T19:22:17Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-02-19Bitstream added on 2014-06-13T19:27:24Z : No. of bitstreams: 1 gajego_eb_me_botfca.pdf: 318258 bytes, checksum: 12cb83bcb0e1495ce86ee6ad0f1ddef9 (MD5) / Nas grandes culturas agrícolas é cada vez maior a interferência de plantas daninhas e dentre os problemas existentes este é um dos que mais oneram a produção. O objetivo deste estudo foi avaliar em condições de casa de vegetação a eficácia de diferentes herbicidas, sobre diferentes espécies de braquiárias, pulverizados em pré-emergência em solo seco, bem como o efeito de épocas de chuva após a aplicação destes, em dois tipos de solo. Foi instalado um estudo para cada herbicida em cada tipo de solo testado, sendo um solo de textura argilosa (Neossolo Litólico) e outro de textura média (Latossolo Vermelho-escuro Distrófico). Utilizou-se as espécies, Brachiaria decumbens, B. plantaginea e B. ruziziensis. A semeadura foi realizada em vasos de plástico com capacidade de 4,0 L. Os herbicidas e doses testados foram: imazapic 130 g. ha-1, metribuzin 1.920 g. ha-1, e trifluralin 3.000 g. ha-1. Foi aplicada uma lâmina d‟água de 20 mm em 0, 1, 2, 4, 6, 8, 10 e 16 dias após a pulverização dos herbicidas. O delineamento experimental utilizado foi o inteiramente casualizado; com quatro repetições e os tratamentos foram dispostos em um esquema fatorial 8x2, no qual se testou oito períodos de chuva após a aplicação do herbicida em dois tipos de solo para cada espécie. Avaliações visuais de fitotoxicidade foram realizadas em intervalos de dois dias após a emergência das plantas (DAE), por um período de 15 dias. O herbicida metribuzin e trifluralin podem permanecer após a sua pulverização em solo seco por até 16 dias sem chuva, sem que sua eficiência de controle das espécies B. decumbens, B. plantaginea, e B. ruziziensis seja afetada. A eficiência de controle do herbicida metribuzin sobre as espécies de braquiárias estudadas foi dependente da textura do solo avaliado. A eficiência do herbicida trifluralin sobre... / In major crops is growing weed interference and problems among this is one of the main factors that increase the production. The aim of this study was to evaluate in terms of greenhouse effectiveness of different species of brachiaria, sprayed pre-emergence in dry soil, and the effect of extreme rainfall after application of these in two soil types. It was installed a study for each herbicide in each soil type tested, being a clay soil (Neossolo Litólico) and a medium texture (Latossolo Vermelho-escuro Distrófico). We used species, Brachiaria decumbens, B. plantaginea and B. ruziziensis. The seeds were sown in plastic pots with a capacity of 4.0 L. Herbicides and doses were tested: 130 g imazapic. ha-1 metribuzin 1.920 g. ha-1 and 3.000 g trifluralin. ha-1. Was applied to a water depth of 20 mm at 0, 1, 2, 4, 6, 8, 10 and 16 days after spraying of the herbicides. The experimental design was completely randomized, with four replications and treatments were arranged in a 8x2 factorial design, in which we tested eight periods of rain after herbicide application in two soil types for each species. Review of visual phytotoxicity were made every two days after plant emergence (DAE), for a period of 15 days. The herbicide trifluralin and metribuzin may remain after spraying in dry soil for up to 16 days without rain, without his control efficiency of species Brachiaria decumbens, B. plantaginea and B. ruziziensis be affected. The control efficiency of the herbicide metribuzin on brachiaria species studied was dependent on soil texture evaluated. The efficiency of trifluralin on the species B. decumbens and B. ruziziensis was dependent on the texture of the soil studied, as for B. plantaginea the type of soil texture evaluated did not affect the control efficiency of the herbicide trifluralin. The imazapic independent of the control was not satisfactory... (Complete abstract click electronic access below)

A detecção é um fator que afeta a magnitude estimada de fauna atropelada, informação relevante nos estudos e trabalhos de biologia da conservação. Em rodovias, a estimativa da detecção é afetada por diferentes elementos, como os tipos de pavimento; os atributos das carcaças; as particularidades dos diferentes observadores e o método utilizado para aferição. Nosso trabalho avalia essas questões, especifica o esforço amostral e corrige a estimativa de fauna atropelada em relação à detecção. Encontramos diferença na estimativa de detecção entre os diferentes pavimentos; entre as carcaças similares e contrastantes ao substrato; entre os diferentes observadores e verificamos que através do monitoramento a pé não se detecta a totalidade das carcaças. Esses resultados e a estimativa de fauna atropelada corrigida comprovam a importância da aferição da detecção antes e depois da pavimentação das rodovias, através de método experimental. Sendo que o experimento deve contemplar a implantação de diferentes carcaças e ser realizado pelas equipes que participaram dos monitoramentos de fauna. / Detection is a factor that affects the estimated magnitude of the roadkill and is relevant information in biological conservation studies. In roads, the detection estimation is affected by many factors, such as type of paving, the carcasses traits, the particularities of different observers and the method used for measurement. Our study evaluates these questions, specify the sample effort and correct the roadkill magnitude in relation to detection. We found differences in the estimation of detection between the different kinds of paving, between carcasses similar to the paving and between those contrasting to the substrate. We also found differences between different observers and thus monitoring by walking does not detect all carcasses. These results and the roadkill magnitude corrected demonstrate the importance of the standardization of the detection before and after the paving of roads, via experimental methods. However, the experiment should include the implementation of different substrates and should be carried out by the teams that have already participated in the monitoring of fauna.

O controle de qualidade na indústria mineira visa à extração de recursos naturais com confiabilidade e efetividade a um custo mínimo. A compreensão e a aplicação da teoria da amostragem (Theory of Sampling ou TOS), desenvolvida por Pierre Gy, de forma integrada ao gerenciamento do processo, são essenciais para alcançar esse objetivo. Por este motivo, ressalta-se a importância de expor os benefícios de uma amostragem correta a todos os níveis hierárquicos de um empreendimento mineiro, a fim de se obter o engajamento da equipe técnica e operacional, assim como o orçamento necessário para financiar treinamentos e compra de equipamentos adequados para uma amostragem precisa e acurada. Uma amostra jamais apresentará características idênticas àquelas do material de origem, devido à existência do erro fundamental de amostragem, que está associado à heterogeneidade constitucional do material. Ainda existem os demais erros que surgem no decorrer das operações de amostragem, como, por exemplo, o erro de segregação e agrupamento, associado à heterogeneidade distribucional e onde a força da gravidade assume papel preponderante. Cada etapa do processo de amostragem gera um erro que deve ser conhecido para a determinação da confiabilidade das estimativas. Neste contexto, os testes de heterogeneidade são uma ferramenta imprescindível para adquirir o conhecimento sobre a variabilidade natural da jazida e para conduzir a amostragem de uma forma correta, gerando amostras representativas. O presente trabalho estuda a heterogeneidade do minério de alumínio da região oeste do Pará, a partir dos resultados obtidos em diferentes experimentos descritos na literatura com base na teoria da amostragem. Os resultados dos experimentos permitem, então, otimizar os protocolos de amostragem, assim como determinar as massas mínimas representativas para amostras de bauxita. / Quality control in the mineral industry context is directed to extraction of natural resources with reliability, effectiveness and minimum cost. The understanding and application of the Theory of Sampling (TOS), developed by Pierre Gy, integrated with, process management are essential for reaching this objective. For this reason, it is important that all levels of personnel in a mining enterprise are made aware of the benefits of correct sampling so as to gain the engagement of the technical and operational team and equally, the necessary budget for training and purchase of appropriate equipment for sampling that is precise and accurate. Samples will never present exactly the same characteristics as the lot from which they originate because of the constitutional heterogeneity which generates the fundamental sampling error. Other errors arise in sampling operations; for example, the grouping and segregation errors related to distributional heterogeneity, where gravity assumes the most important role. Each stage of the sampling process produces an error which must be known for determining the reliability of the estimates. In this context, the heterogeneity tests are an essential tool for knowing the natural variability of the deposit, and to conduct sampling in a correct manner to generate representative samples. The present work studies the heterogeneity of the aluminum ore in western Pará, based on the results of different heterogeneity experiments described by the TOS. Results allow the optimization of sampling protocols as well as the determination of the minimum masses representative samples of bauxite.

Zhang, Wei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 95-109). / Abstract also in Chinese. / Abstract --- p.i / Acknowledgement --- p.iv / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Area of Machine Learning --- p.1 / Chapter 1.1.1 --- Types of Algorithms --- p.2 / Chapter 1.1.2 --- Modeling Assumptions --- p.4 / Chapter 1.2 --- Dimensionality Reduction --- p.4 / Chapter 1.3 --- Structure of the Thesis --- p.8 / Chapter 2 --- Dimensionality Reduction --- p.10 / Chapter 2.1 --- Feature Extraction --- p.11 / Chapter 2.1.1 --- Linear Feature Extraction --- p.11 / Chapter 2.1.2 --- Nonlinear Feature Extraction --- p.16 / Chapter 2.1.3 --- Sparse Feature Extraction --- p.19 / Chapter 2.1.4 --- Nonnegative Feature Extraction --- p.19 / Chapter 2.1.5 --- Incremental Feature Extraction --- p.20 / Chapter 2.2 --- Feature Selection --- p.20 / Chapter 2.2.1 --- Viewpoint of Feature Extraction --- p.21 / Chapter 2.2.2 --- Feature-Level Score --- p.22 / Chapter 2.2.3 --- Subset-Level Score --- p.22 / Chapter 3 --- Various Views of Feature Extraction --- p.24 / Chapter 3.1 --- Probabilistic Models --- p.25 / Chapter 3.2 --- Matrix Factorization --- p.26 / Chapter 3.3 --- Graph Embedding --- p.28 / Chapter 3.4 --- Manifold Learning --- p.28 / Chapter 3.5 --- Distance Metric Learning --- p.32 / Chapter 4 --- Tensor linear Laplacian discrimination --- p.34 / Chapter 4.1 --- Motivation --- p.35 / Chapter 4.2 --- Tensor Linear Laplacian Discrimination --- p.37 / Chapter 4.2.1 --- Preliminaries of Tensor Operations --- p.38 / Chapter 4.2.2 --- Discriminant Scatters --- p.38 / Chapter 4.2.3 --- Solving for Projection Matrices --- p.40 / Chapter 4.3 --- Definition of Weights --- p.44 / Chapter 4.3.1 --- Contextual Distance --- p.44 / Chapter 4.3.2 --- Tensor Coding Length --- p.45 / Chapter 4.4 --- Experimental Results --- p.47 / Chapter 4.4.1 --- Face Recognition --- p.48 / Chapter 4.4.2 --- Texture Classification --- p.50 / Chapter 4.4.3 --- Handwritten Digit Recognition --- p.52 / Chapter 4.5 --- Conclusions --- p.54 / Chapter 5 --- Semi-Supervised Semi-Riemannian Metric Map --- p.56 / Chapter 5.1 --- Introduction --- p.57 / Chapter 5.2 --- Semi-Riemannian Spaces --- p.60 / Chapter 5.3 --- Semi-Supervised Semi-Riemannian Metric Map --- p.61 / Chapter 5.3.1 --- The Discrepancy Criterion --- p.61 / Chapter 5.3.2 --- Semi-Riemannian Geometry Based Feature Extraction Framework --- p.63 / Chapter 5.3.3 --- Semi-Supervised Learning of Semi-Riemannian Metrics --- p.65 / Chapter 5.4 --- Discussion --- p.72 / Chapter 5.4.1 --- A General Framework for Semi-Supervised Dimensionality Reduction --- p.72 / Chapter 5.4.2 --- Comparison to SRDA --- p.74 / Chapter 5.4.3 --- Advantages over Semi-supervised Discriminant Analysis --- p.74 / Chapter 5.5 --- Experiments --- p.75 / Chapter 5.5.1 --- Experimental Setup --- p.76 / Chapter 5.5.2 --- Face Recognition --- p.76 / Chapter 5.5.3 --- Handwritten Digit Classification --- p.82 / Chapter 5.6 --- Conclusion --- p.84 / Chapter 6 --- Summary --- p.86 / Chapter A --- The Relationship between LDA and LLD --- p.89 / Chapter B --- Coding Length --- p.91 / Chapter C --- Connection between SRDA and ANMM --- p.92 / Chapter D --- From S3RMM to Graph-Based Approaches --- p.93 / Bibliography --- p.95

Networks have been widely used to represent and analyze a system of connected elements. Online social media networks, as a result of the expansion of the Internet and increased need of communication, have become an increasingly important part of people's lives. This thesis focuses on the statistical analysis of network data motivated by problems in online social media. It discusses problems arising from both explicit network data and implicit network data. Explicit network data are data where network structures are observable, implicit network data are those that do not have a network structure but occur under the influence of an underlying network. For the explicit network data analysis, we develop a novel method of recovering a fundamental characteristic -- network degree distributions -- under sampling. We formulate the problem of estimating degree distribution as an inverse problem. We show that this problem is ill-conditioned for many sampling methods in practice, and accordingly propose a constrained, penalized weighted least-squares approach to solve this problem. We demonstrate the ability of our method to accurately reconstruct the degree distributions from simulated network data and real world social network data. We also propose practical usage of the estimates relevant to marketing and advertising. For the implicit network data analysis, we look at review data from the popular review websites. Motivated by articles from the popular press and the research community which publicized that the average rating for top review sites is above 4 out of 5 stars, we study the phenomena of review rating trends and convergence using restaurant review data from TripAdvisor. We analyze the trend on different levels -- a rough analysis of the characteristics of the ratings, and a subtler statistical modeling with ordinal logistic regressions. Taking into account the implicit network underlying the review data, we suggest the upward trend observed in restaurant review ratings may be explained by social influence on an individual's perception of qualities. We use the intensity of review postings as an indicator of how popular a restaurant is and to test to what extent the increase in review intensity explains increases in average rating. After that, we consider a more nuanced approach to the joint modeling of ratings and review intensity which would allow for interaction between the two, rather than intensity serving only as an explanatory variable to ratings. Specifically, a state-space model is used to test the interaction between review intensity and review ratings.

Thesis. 1978. M.S.--Massachusetts Institute of Technology. Dept. of Civil Engineering. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING. / Bibliography: leaves 117-120. / M.S.

Whilst drum replacement, the act of replacing the sound of a particular drum with a pre-recorded sample, has been in practice since the 1970s it is only towards the end of the first decade of the 21st century that software drum machines such as Toontrack’s Superior Drummer 2.0 and Steven Slate Drums have become an popular alternative to actual drum recordings within music production. With the increasing popularity there have been voices from the music community in protest claiming that a machine could never replace an actual drummer. What I aimed to do in this project was to do a comparative study, where I analyse and compare various aspects of both alternatives – a recorded performance with an actual drummer and a MIDI programmed performance sampled drum machine – and see whether or not a human drummer could possibly be replaceable. The results indicated that, given the circumstances and project restrictions, the differences were mostly too miniscule to have any practical value and therefore a drummer was in this scenario replaceable by a MIDI programmable drum machine. / Trots att “drum replacement”, att ersätta ljudet av en specifik trumma med ett förinspelat ljudklipp, har använts sedan 70-talet så är det först mot slutet av 2000-talets första decennium som mjukvarubaserade trumbibliotek, så som Toontracks Superior Drummer 2.0 och Steven Slate Drums, har blivit ett populärt alternativ för faktiska truminspelningar inom musikproduktion. I och med den ökade populäriteten har många från musikvärlden protesterat och hävdat att en maskin aldrig kan ersätta en riktig trumslagare. Tanken med det här projektet var att göra en jämförande studie där jag analyserar och jämför olika aspekter av de båda alternativen - ett inspelat framförande med en riktig trumslagare och ett framförande programmerat i MIDI med en samplingsbaserad trummaskin - för att se huruvida en mänsklig trummis skulle kunna vara ersättningsbar. Resultaten visade, med hänsyn tagen till projektets begränsningar, att skillnaderna var för små för att ha något praktiskt värde och att en trummisen i det här scenariot därför kunde ersättas med en midiprogrammerbar trummaskin.

Den här uppsatsen undersöker alternativ till dyra inspelningar av trummor genom att visa hur man kan göra egna truminspelningar med bara en mikrofon, ett DAW och vanligaföremål som finns i hemmet. Undersökningen går in på ett djupare tänk kring hur man med olika lager kan forma sina egna trumljud med ett fåtal hjälpmedel för inspelning ochbearbetning. För att omsätta mitt tänkande kring olika lager i trumljud har jag tagit fram tretrumsound inom tre genre: Popsoul, house och indiepop. Resultatet säger att dessa trumsetvisar sig vara användbara i popmusik från ett kreativt perspektiv, då popmusik tillåter mer bredd i trumljuden. Uppsatsen kommer också fram till att det ekonomiska värdet i att göra egna trumljud sjunker något, då färdiga samplingar går snabbt och är billiga att använda.

Two-dimensional infrared spectroscopy (2D IR) is a powerful tool to investigate molecular structures and dynamics on femtosecond to picosecond time scales and is applied to diverse systems. Current technologies allow for the acquisition of a single 2D IR spectrum in a few hundreds of milliseconds using a pulse shaper and an array detector, but demanding applications require spectra for many waiting times and involve considerable signal averaging, resulting in data acquisition times that can be many days of laboratory measurement time. Compressive sampling is an emerging signal processing technique to reduce data acquisition time in diverse fields by requiring only a fraction of the traditional number of measurements while yielding much of the same information as the fully-sampled data. Here we combine cutting-edge 2D IR methodology with a novel compressive sampling reconstruction algorithm to reduce the data acquisition time of 2D IR spectroscopy without distorting lineshapes. We introduce the Generic Iteratively Reweighted Annihilating Filter (GIRAF) algorithm re-engineered to the specific problem of 2D IR reconstruction and show its effectiveness applied to various systems, including those with low signal, with multiple peaks, and with differing amounts of frequency shifting. Additionally, we lay the groundwork for 2D IR microscopic imaging using compressive sampling in the spatial image domain. The first instance of a single-pixel camera in the infrared is introduced.