五轴框架式机器人激光加工系统轨迹算法研究

在集成化智能激光加工系统工作原理的基础上提出了五轴机器人的激光加工轨迹算法。将三维离散数据点集拟合为空间参数曲面，在此参数曲面上规划五轴激光加工的等距轨迹。给出了冲压模具激光强化加工实例，取得了理想的加工效果。

The influence of disparate levels of submersed aquatic vegetation on largemouth bass population characteristics in a Georgia reservoir

Population characteristics of largemouth bass (Micropterous salmoides L.) including growth, body condition (relative weight), size structure, survival, and fecundity were examined in relation to abundance of submersed aquatic vegetation (SAV) coverage (primarily hydrilla Hydrilla verticillata L.f. Royle) in three major embayments of Lake Seminole, Georgia. Relative weight, fecundity, and growth of large-mouth bass in the Spring Creek embayment (76% areal SAV coverage) was considerably less than measured in the Chattahoochee and Flint river arms that contained lower SAV coverages (26% and 32%). It took fish 1.8 years longer to reach 406 mm in Spring Creek compared to the Chattahoochee-Flint arms. Consequently, fish were smaller in Spring Creek than in the Chattahoochee-Flint arms. In addition, due to slower growth rates and lower fecundity-to-body weight relation, we predicted a 47% reduction in total potential ova production in Spring Creek compared to the other two reservoir embayments. The annual survival rate of 3 to 10 year old largemouth bass was higher in Spring Creek (84%) than in the Chattahoochee-Flint arms (72%) and suggested either lower harvest and/or lower accessibility of particularly larger fish to angling in dense vegetation. Contrary to our expectaions, the fit between number-at-age and age in a catch-curve regression was weaker for fish collected in Spring Creek and suggested greater recruitment variability has occurred over time in this highly vegetated embayment. In Lake Seminole, spatial differences in largemouth bass population characterstics were associated with disparate levels of SAV. Our data suggest that a reduction in hydrilla, but maintenance of an intermediate level of SAV in Spring Creek, should improve largermouth bass population in this arm of the reservoir.

Designing High Performance Factory Automation Applications on Top of DDS

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Developing peptide based capture agents for diagnostics and therapeutics

Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions.

Complex behavior and perception in Drosophila emerges from iterative feedback-regulated reflexes

For a hungry fruit fly, locating and landing on a fermenting fruit where it can feed, find mates, and lay eggs, is an essential and difficult task requiring the integration of both olfactory and visual cues. Understanding how flies accomplish this will help provide a comprehensive ethological context for the expanding knowledge of their neural circuits involved in processing olfaction and vision, as well as inspire novel engineering solutions for control and estimation in computationally limited robotic applications. In this thesis, I use novel high throughput methods to develop a detailed overview of how flies track odor plumes, land, and regulate flight speed. Finally, I provide an example of how these insights can be applied to robotic applications to simplify complicated estimation problems. To localize an odor source, flies exhibit three iterative, reflex-driven behaviors. Upon encountering an attractive plume, flies increase their flight speed and turn upwind using visual cues. After losing the plume, flies begin zigzagging crosswind, again using visual cues to control their heading. After sensing an attractive odor, flies become more attracted to small visual features, which increases their chances of finding the plume source. Their changes in heading are largely controlled by open-loop maneuvers called saccades, which they direct towards and away from visual features. If a fly decides to land on an object, it begins to decelerate so as to maintain a stereotypical ratio of expansion to retinal size. Once they reach a stereotypical distance from the target, flies extend their legs in preparation for touchdown. Although it is unclear what cues they use to trigger this behavior, previous studies have indicated that it is likely under visual control. In Chapter 3, I use a nonlinear control theoretic analysis and robotic testbed to propose a novel and putative mechanism for how a fly might visually estimate distance by actively decelerating according to a visual control law. Throughout these behaviors, a common theme is the visual control of flight speed. Using genetic tools I show that the neuromodulator octopamine plays an important role in regulating flight speed, and propose a neural circuit for how this controller might be implemented in the flies brain. Two general biological and engineering principles are evident across my experiments: (1) complex behaviors, such as foraging, can emerge from the interactions of simple independent sensory-motor modules; (2) flies control their behavior in such a way that simplifies complex estimation problems.

Topics in LIGO-related physics: interferometric speed meters and tidal work

In the quest to develop viable designs for third-generation optical interferometric gravitational-wave detectors, one strategy is to monitor the relative momentum or speed of the test-mass mirrors, rather than monitoring their relative position. The most straightforward design for a speed-meter interferometer that accomplishes this is described and analyzed in Chapter 2. This design (due to Braginsky, Gorodetsky, Khalili, and Thorne) is analogous to a microwave-cavity speed meter conceived by Braginsky and Khalili. A mathematical mapping between the microwave speed meter and the optical interferometric speed meter is developed and used to show (in accord with the speed being a quantum nondemolition observable) that in principle the interferometric speed meter can beat the gravitational-wave standard quantum limit (SQL) by an arbitrarily large amount, over an arbitrarily wide range of frequencies . However, in practice, to reach or beat the SQL, this specific speed meter requires exorbitantly high input light power. The physical reason for this is explored, along with other issues such as constraints on performance due to optical dissipation.

Chapter 3 proposes a more sophisticated version of a speed meter. This new design requires only a modest input power and appears to be a fully practical candidate for third-generation LIGO. It can beat the SQL (the approximate sensitivity of second-generation LIGO interferometers) over a broad range of frequencies (~ 10 to 100 Hz in practice) by a factor h/h_SQL ~ √W^(SQL)_(circ)/W_circ. Here W_circ is the light power circulating in the interferometer arms and W_SQL ≃ 800 kW is the circulating power required to beat the SQL at 100 Hz (the LIGO-II power). If squeezed vacuum (with a power-squeeze factor e^-2R) is injected into the interferometer's output port, the SQL can be beat with a much reduced laser power: h/h_SQL ~ √W^(SQL)_(circ)/W_circe^-2R. For realistic parameters (e^-2R ≃ 10 and W_circ ≃ 800 to 2000 kW), the SQL can be beat by a factor ~ 3 to 4 from 10 to 100 Hz. [However, as the power increases in these expressions, the speed meter becomes more narrow band; additional power and re-optimization of some parameters are required to maintain the wide band.] By performing frequency-dependent homodyne detection on the output (with the aid of two kilometer-scale filter cavities), one can markedly improve the interferometer's sensitivity at frequencies above 100 Hz.

Chapters 2 and 3 are part of an ongoing effort to develop a practical variant of an interferometric speed meter and to combine the speed meter concept with other ideas to yield a promising third- generation interferometric gravitational-wave detector that entails low laser power.

Chapter 4 is a contribution to the foundations for analyzing sources of gravitational waves for LIGO. Specifically, it presents an analysis of the tidal work done on a self-gravitating body (e.g., a neutron star or black hole) in an external tidal field (e.g., that of a binary companion). The change in the mass-energy of the body as a result of the tidal work, or "tidal heating," is analyzed using the Landau-Lifshitz pseudotensor and the local asymptotic rest frame of the body. It is shown that the work done on the body is gauge invariant, while the body-tidal-field interaction energy contained within the body's local asymptotic rest frame is gauge dependent. This is analogous to Newtonian theory, where the interaction energy is shown to depend on how one localizes gravitational energy, but the work done on the body is independent of that localization. These conclusions play a role in analyses, by others, of the dynamics and stability of the inspiraling neutron-star binaries whose gravitational waves are likely to be seen and studied by LIGO.

Functional genomic studies of the structure and regulation of eukaryotic transcriptomes

The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project.

The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations.

The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes.

The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented.

The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13).

The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.

Modelling soil erosion and transport in the Burrishoole catchment, Newport, Co. Mayo, Ireland

The Burrishoole catchment is situated in County Mayo, on the northwest coast of the Republic of Ireland. Much of the catchment is covered by blanket peat that, in many areas, has become heavily eroded in recent years. This is thought to be due, primarily, to the adverse effects of forestry and agricultural activities in the area. Such activities include ploughing, drainage, the planting and harvesting of trees, and sheep farming, all of which are potentially damaging to such a sensitive landscape if not managed carefully. This article examines the sediment yield and hydrology of the Burrishoole catchment. Flow and sediment concentrations were measured at 8-hourly intervals from 5 February 2001 to 8 November 2001 with an automatic sampler and separate flow gauge, and hourly averages were recorded between 4 July 2002 and 6 September 2002 using an automatic river monitoring system [ARMS]. The authors describe the GIS-based model of soil erosion and transport that was applied to the Burrishoole catchment during this study. The results of these analyses were compared, in a qualitative manner, with the aerial photography available for the Burrishoole catchment to see whether areas that were predicted to contribute large proportions of eroded material to the drainage network corresponded with areas where peat erosion could be identified through photo-interpretation.

A phase-shifting vectorial-shearing interferometer with wedge plate phase-shifter

We present a novel phase-shifting vectorial-shearing interferometer with a wedge plate phase-shifter. The interferometer is based on a modified Mach-Zehnder configuration; the common-path nature makes it capable of testing the wavefront of a short coherence-length light source, such as a laser diode. Vectorial shear (shearing in the x and y directions simultaneously) in an arbitrary direction is introduced by inserting two wedge plates orthogonally in two arms, respectively. One of the wedge plates is split into two parts (parallel part and wedge part); phase shift is produced by moving the wedge part in contact along the parallel part. The moving distance for a 2 pi phase shift is a few millimetres in specific conditions. The wedge plate phase-shifter increases the moving distance for phase shift and makes the control of phase shift relatively easy. We also discuss the lateral shear error and phase shift errors induced by wedge plates. The lateral shear error is small enough to be ignored; the phase shift error is determined mainly by the wedge angle error. Lastly, we give the experimental results of phase-shifting interference fringes in vectorial shear mode.

Two and Three Finger Caging of Polygons and Polyhedra

Multi-finger caging offers a rigorous and robust approach to robot grasping. This thesis provides several novel algorithms for caging polygons and polyhedra in two and three dimensions. Caging refers to a robotic grasp that does not necessarily immobilize an object, but prevents it from escaping to infinity. The first algorithm considers caging a polygon in two dimensions using two point fingers. The second algorithm extends the first to three dimensions. The third algorithm considers caging a convex polygon in two dimensions using three point fingers, and considers robustness of this cage to variations in the relative positions of the fingers.

This thesis describes an algorithm for finding all two-finger cage formations of planar polygonal objects based on a contact-space formulation. It shows that two-finger cages have several useful properties in contact space. First, the critical points of the cage representation in the hand’s configuration space appear as critical points of the inter-finger distance function in contact space. Second, these critical points can be graphically characterized directly on the object’s boundary. Third, contact space admits a natural rectangular decomposition such that all critical points lie on the rectangle boundaries, and the sublevel sets of contact space and free space are topologically equivalent. These properties lead to a caging graph that can be readily constructed in contact space. Starting from a desired immobilizing grasp of a polygonal object, the caging graph is searched for the minimal, intermediate, and maximal caging regions surrounding the immobilizing grasp. An example constructed from real-world data illustrates and validates the method.

A second algorithm is developed for finding caging formations of a 3D polyhedron for two point fingers using a lower dimensional contact-space formulation. Results from the two-dimensional algorithm are extended to three dimension. Critical points of the inter-finger distance function are shown to be identical to the critical points of the cage. A decomposition of contact space into 4D regions having useful properties is demonstrated. A geometric analysis of the critical points of the inter-finger distance function results in a catalog of grasps in which the cages change topology, leading to a simple test to classify critical points. With these properties established, the search algorithm from the two-dimensional case may be applied to the three-dimensional problem. An implemented example demonstrates the method.

This thesis also presents a study of cages of convex polygonal objects using three point fingers. It considers a three-parameter model of the relative position of the fingers, which gives complete generality for three point fingers in the plane. It analyzes robustness of caging grasps to variations in the relative position of the fingers without breaking the cage. Using a simple decomposition of free space around the polygon, we present an algorithm which gives all caging placements of the fingers and a characterization of the robustness of these cages.

Nos braços da lei: o uso daviolência negociada no interior das prisões

O presente estudo objetiva, a partir da narrativa do trabalhador prisional da SEAP-RJ, abordar em que situações e com base em quais justificativas esse profissional recorre ao uso da força física em seu cotidiano prisional. A rotina de trabalho dos agentes penitenciários é apresentada a partir de um estudo de caso realizado no Instituto Presídio Hélio Gomes. Nele, os relatos dos integrantes das turmas de guardas se constituíram em nossa principal fonte de informações. Em outra fase da pesquisa, o processo de formação profissional dos servidores prisionais admitidos em 2004, pela SEAP-RJ, foi acompanhado através das aulas ministradas na Escola de Gestão Penitenciária. Em ambos os casos, a observação participante foi o instrumento metodológico que me permitiu a coleta de dados e a interação com o grupo estudado. A narrativa está centrada no processo de socialização por que passam os servidores prisionais para se integrarem a (s) moralidade (s) vigente nas prisões. Sugere-se que a integração plena do operador da lei ao universo prisional, implique em sua socialização no mundo do crime. A possibilidade de uso da violência física como mecanismo de controle, em sua modalidade violência negociada, mostrou-se uma hipótese viável. Porém, ainda necessita de maiores comprovações empíricas, em especial junto aos internos penitenciários, para que possa ser formalmente validada.

Efeitos da privação de sono paradoxal na nocicepção e ansiedade em ratos

A privação de sono paradoxal (PSP) provoca diversas alterações neuroquímicas e comportamentais relacionadas a mudanças nas funções de sistemas de neurotransmissores. São descritas na literatura respostas aumentadas a estímulos álgicos em animais privados desta fase de sono. Os métodos de PSP frequentemente utilizados têm sido associados à geração de ansiedade nos animais, e a hiperalgesia observada poderia, portanto, ser conseqüência aos estímulos ansiogênicos gerados pelo método. Neste trabalho tivemos como objetivos avaliar se o método utilizado para a PSP é ansiogênico e investigar o efeito dos fármacos ansiolítico, diazepam e analgésico, ácido acetilsalicílico sobre a ansiedade e resposta a estímulos térmicos álgicos em animais PSP. Ratos machos Wistar com 90 dias de vida foram privados de sono paradoxal por 96 horas, sendo a resposta álgica avaliada pelo tempo de retirada da pata traseira em ratos expostos à placa quente (46C). A avaliação do nível de ansiedade dos animais foi feita através do teste do campo aberto, através da relação entre a permanência nos quadrantes centrais e nos quadrantes periféricos, e também pelo teste do labirinto em cruz elevado, sendo quantificado o número de vezes que o animal entrava nos braços abertos do labirinto e o tempo gasto pelo animal nos mesmos braços. Os animais PSP apresentaram aumento no índice de locomoção em relação aos animais controles (+314,8%, p<0,05), aumento no número de entradas (+257,1%) e no tempo gasto nos braços abertos do labirinto em cruz elevado (+319,2%, p<0,05), e redução na latência de retirada da pata traseira da placa quente (-64,2%, p<0,05). O fármaco diazepam, não influenciou nas respostas apresentadas pelos animais PSP no teste de campo aberto e no teste da placa quente, mas influenciou nas repostas apresentadas por estes animais no teste do labirinto em cruz elevado tanto no tempo (+308, p<0,05), quanto no número de entradas (+316,6%, p<0,05). O fármaco ácido acetilsalicílico promoveu uma diminuição do índice de locomoção nos animais PSP submetidos ao teste de campo aberto que também foram administrados com o diazepam (-99,5%, p<0,05). No teste da placa quente o ácido acetilsalicílico não apresentou nenhuma influência na percepção de dor nos animais. Os resultados obtidos neste trabalho indicam que o método de privação de sono paradoxal por período de 96 horas não induz ansiedade, e a redução farmacológica dos níveis de ansiedade não influencia na resposta álgica induzida pela privação de sono paradoxal.

Composição corporal de indivíduos com lesão medular cervical: influência do exercício físico e comparação de métodos

Objetivo: Comparar a composição corporal total e regional e a distribuição de gordura de homens com lesão medular LM cervical fisicamente ativos e não ativos, e sua relação com a concentração de proteína C reativa ultra-sensível (PCR-us). Além disso, identificar um protocolo de impedância bioelétrica (BIA) que forneça resultados de percentual de massa gorda (MG) total concordantes com os obtidos pelo método de referência, absorciometria de dupla emissão de raios-X (DXA). Métodos: Os participantes possuíam lesão medular entre C5-C7 e foram classificados em ativos (n=15) e não ativos (n=10). Consideraram-se ativos os indivíduos que praticavam exercícios físicos há pelo menos três meses, três vezes por semana ou mais, totalizando tempo mínimo de 150 minutos de atividades físicas por semana. A determinação da composição corporal total e regional (braços, pernas e tronco) foi realizada por DXA. A PCR-us foi mensurada por imunoturbidimetria. Os protocolos de BIA testados foram: a) para indivíduos com LM (KOCINA & HEYWARD, 1997); b) para grupos que incluem idosos (GRAY et al 1989); c) validado para idosos brasileiros (DEY et al, 2003). A análise estatística dos dados incluiu ANCOVA para comparar a massa corporal total, composição corporal e PCR-us entre os grupos; e correlação parcial com correção pelo tempo de lesão (TL) para identificar a associação de exercício físico com MG e da PCR-us com exercício físico e MG tronco. A comparação dos resultados de percentual de gordura obtidos por DXA e cada um dos protocolos de BIA foi realizada por ANOVA one way e Dunnet pós teste. A análise de Bland-Altman foi realizada para verificação da concordância entre os métodos testados. Conclusão: O exercício físico praticado de forma contínua e controlada é importante para manter menores valores de MG e evitar acúmulo de gordura na região do tronco. A melhor composição corporal e distribuição de gordura corporal observadas no grupo ativo possivelmente levaram à menor concentração de PCR-us sérica. Juntas, estas adaptações provavelmente contribuíram para a redução dos riscos de desenvolvimento de doenças cardiometabólicas. A semelhança na modificação da composição corporal entre idosos e indivíduos com LM sugere que protocolos de BIA propostos para idosos podem ser adequados para avaliação da composição corporal de indivíduos com lesão medular cervical.