Development of protein-catalyzed capture (PCC) agents with application to the specific targeting of the E17K Point mutation of Akt1

This thesis describes the expansion and improvement of the iterative in situ click chemistry OBOC peptide library screening technology. Previous work provided a proof-of-concept demonstration that this technique was advantageous for the production of protein-catalyzed capture (PCC) agents that could be used as drop-in replacements for antibodies in a variety of applications. Chapter 2 describes the technology development that was undertaken to optimize this screening process and make it readily available for a wide variety of targets. This optimization is what has allowed for the explosive growth of the PCC agent project over the past few years.

These technology improvements were applied to the discovery of PCC agents specific for single amino acid point mutations in proteins, which have many applications in cancer detection and treatment. Chapter 3 describes the use of a general all-chemical epitope-targeting strategy that can focus PCC agent development directly to a site of interest on a protein surface. This technique utilizes a chemically-synthesized chunk of the protein, called an epitope, substituted with a click handle in combination with the OBOC in situ click chemistry libraries in order to focus ligand development at a site of interest. Specifically, Chapter 3 discusses the use of this technique in developing a PCC agent specific for the E17K mutation of Akt1. Chapter 4 details the expansion of this ligand into a mutation-specific inhibitor, with applications in therapeutics.

Plasma loop and strapping field dynamics: reproducing solar eruptions in the laboratory

Coronal mass ejections (CMEs) are dramatic eruptions of large, plasma structures from the Sun. These eruptions are important because they can harm astronauts, damage electrical infrastructure, and cause auroras. A mysterious feature of these eruptions is that plasma-filled solar flux tubes first evolve slowly, but then suddenly erupt. One model, torus instability, predicts an explosive-like transition from slow expansion to fast acceleration, if the spatial decay of the ambient magnetic field exceeds a threshold.

We create arched, plasma filled, magnetic flux ropes similar to CMEs. Small, independently-powered auxiliary coils placed inside the vacuum chamber produce magnetic fields above the decay threshold that are strong enough to act on the plasma. When the strapping field is not too strong and not too weak, expansion force build up while the flux rope is in the strapping field region. When the flux rope moves to a critical height, the plasma accelerates quickly, corresponding to the observed slow-rise to fast-acceleration of most solar eruptions. This behavior is in agreement with the predictions of torus instability.

Historically, eruptions have been separated into gradual CMEs and impulsive CMEs, depending on the acceleration profile. Recent numerical studies question this separation. One study varies the strapping field profile to produce gradual eruptions and impulsive eruptions, while another study varies the temporal profile of the voltage applied to the flux tube footpoints to produce the two eruption types. Our experiment reproduced these different eruptions by changing the strapping field magnitude, and the temporal profile of the current trace. This suggests that the same physics underlies both types of CME and that the separation between impulsive and gradual classes of eruption is artificial.

Prevalência de sintomas depressivos em uma população de idosos usuários de serviços públicos

Esta dissertação pretende estimar a prevalência de sintomas depressivos em idosos segundo três níveis de complexidade de atenção à saúde e estudar a co-ocorrência de sintomas depressivos e incapacidade funcional. No Brasil, a transição demográfica ocorreu de forma rápida e explosiva. À medida que o número de idosos cresce ocorre o aumento da prevalência de doenças crônicas e suas complicações. A habilidade funcional pode ser vista como uma medida de resumo do impacto geral das condições médicas no contexto do ambiente e do sistema de apoio social do indivíduo, e deve ser uma consideração importante em qualquer planejamento de saúde. Uma enfermidade associada a elevado grau de incapacidade funcional é a depressão. Entre os agravos de saúde mental, a depressão é um dos mais comuns e importantes problemas psiquiátricos entre indivíduos idosos. Trata-se de estudo transversal com tamanho amostral de 643 idosos com idade de 65 ou mais anos selecionados aleatoriamente e usuários de três serviços públicos de saúde com níveis crescentes de complexidade (primário, secundário e terciário). A prevalência de sintomas depressivos foi estimada a partir da EDG-15, já traduzida e validada para uso no Brasil. O nível de estado funcional foi definido conforme os escores dos instrumentos SF-36 e HAQ. A prevalência de sintomas depressivos na amostra total foi de 45,2% (IC=41,1 49,3). Estratificando por unidade, a prevalência foi de 35,3% no nível primário, 47,6% no nível secundário e 51,7% no nível terciário (p=0,004). As prevalências encontradas foram altas nos três níveis de complexidade de atendimento, inclusive na população de idosos da unidade básica de saúde, apesar de serem idosos mais independentes e mais saudáveis. A prevalência geral de sintomas depressivos aumentou à medida que o grau de incapacidade funcional também aumentou. A busca ativa por idosos com sintomas depressivos é importante em todos os níveis de complexidade de atendimento do sistema de saúde.

Caracterização de um sistema digital de aquisição de imagens radiográficas utilizando nêutrons térmicos e raios gama para a inspeção de componentes mecânicos.

Ensaio não destrutivo é uma ferramenta essencial quando um equipamento, dispositivo ou componente não pode ser submetido a procedimentos destrutivos ou invasivos devido a razões de segurança, alto custo ou outras restrições físicas ou logísticas. Dentro deste quadro radiografias por transmissão com raios gama e nêutrons térmicos são técnicas singulares para inspecionar um objeto e desvendar sua estrutura interna devido à capacidade de atravessar uma vasta gama de materiais utilizados na indústria. Grosso modo, raios gama são mais atenuados por materiais pesados enquanto nêutrons térmicos são mais atenuados por materiais mais leves, tornando-as ferramentas complementares. Este trabalho apresenta os resultados obtidos na inspeção de vários componentes mecânicos, através da radiografia por transmissão com nêutrons térmicos e raios gama. O fluxo de nêutrons térmicos de 4,46x105 n.cm-2.s-1 disponível no canal principal do reator de pesquisa Argonauta do Instituto de Engenharia Nuclear foi usado como fonte para as imagens radiográficas com nêutrons. Raios dekeV emitidos pelo 198Au, também produzido no reator, foram usados como fonte de radiação para radiografias . Imaging Plates, especificamente produzidos para operar com nêutrons térmicos ou com raios X, foram empregados como detectores e dispositivos de armazenamento e captação de imagens para cada uma dessas radiações. Esses dispositivos exibem varias vantagens quando comparados ao filme radiográfico convencional. Com efeito, além de maior sensibilidade e serem reutilizáveis não são necessários câmaras escuras e processamento químico para a revelação. Em vez disso, ele é lido por um feixe de laser que libera elétrons armadilhados na rede cristalina durante a exposição à radiação, fornecendo uma imagem final digital. O desempenho de ambos os sistemas de aquisição de imagens, assim constituído, foi avaliado com respeito à sensibilidade, resolução espacial, linearidade e range dinâmico, incluído uma comparação com sistemas radiográficos com nêutrons empregando filmes e folhas de gadolínio como conversor de nêutrons em partículas carregadas. Além desta caracterização, diversos equipamentos e componentes foram radiografados com ambos os sistemas visando-se avaliar suas capacidades de desvendar a estrutura interna desses objetos e detectar estruturas e estados anormais. Dentro desta abordagem, uma neutrongrafia detectou a presença de material cerâmico remanescente empregado como molde no processo de fabricação nos canais de refrigeração de uma aleta do estator de uma turbina tipo turbo-fan, que deveria estar livre desse material. O reostato danificado de um sensor de pressão automotivo, foi identificado por neutrongrafia, embora nesse caso a radiografia também conseguiu realizar essa tarefa com melhor resolução, corroborando assim as curvas de resolução espacial obtidas na caracterização dos dois sistemas. A homogeneidade da distribuição do material encapsulado em uma gaxeta explosiva de chumbo utilizada na indústria aeroespacial foi igualmente verificada por neutrongrafia porque esse metal é relativamente transparente para nêutrons, mas suficientemente opaco para o explosivo rico em hidrogênio. Diversos outros instrumentos e componentes tais como variômetro, altímetro, bússola aeronáutica, injetor automotivo de combustível, foto-camera, disco rígido de computador, motor de passo, conectores eletrônicos e projéteis foram radiografados com ambos os sistemas visando avaliar suas habilidades em desvendar diferentes peculiaridades em função do agente interrogador.

The Feasibility of Enhancing Red Sea Urchin, Strongylocentrotus iranciscanus, Stocks in California: An Analysis of the Options

The California fishery for red sea urchins, Strongylocentrotus franciscanus, has undergone explosive growth in recent years and is approaching full exploitation. Thus, there is considerable interest in enhancing stocks to maintain a high rate of landings. Fishable stocks of red sea urchins in different areas appear to be limited at three stages in their life history: By the availability of larvae, by the survival of newly settled to mid-sized animals, and by the food available to support growth and reproduction of larger animals. Here I review other efforts, notably the extensive Japanese work, to enhance fishable stocks of benthic marine invertebrates, and consider the potential options for red sea urchins at different points of limitation. These include collecting or culturing seed for outplanting, physical habitat improvement measures, improving the food supply, and conservation measures to protect existing stocks until alternate methods are proven and in place. The options are compared in terms of biological feasibility, capital and labor requirements, and potential implications for change in the structure of the fishing industry.

Genetic status of selected fish taxa in relation to conservation of genetic and species diversity in the Victoria and Kyoga Lake basins

Cichlids are known for their explosive radiation especially in the African Great Lakes marked with a high level of lake endemism. These fishes have been characterized mainly along trophic and habitat differences, by variation in morphological structures such as teeth and jaws and by differences in body shape and coloration. Cichlids are important as a microcosm of macroevolution. The explosive radiation, young evolutionary scale, and the isolation of groups characterized with high levels of endemism and presence of living fossils makes the group important for evolutionary and genetic studies. Lake Victoria region cichlids which are isolated and relatively more recent in evolution were the last to be appreciated in their diversity. Recently Ole Seehausen has found scores of rock fishes in Lake Victoria which were up to then thought to be absent from the Lake and only known to occur in Lakes Malawi and Tanganyika. Greenwood put together the species groups of Lake Victoria, and later in the early 1980's revised the classification of haplochromine species to reflect the phyletic origin and interrelationship of the various groups in Lake Victoria region. Melan Stiassny has been interested in early evolution of cichlids while the likes of Paul Fuerst and Lees Kaufman and Axel Meyer have been interested and are working to explain the speciation mechanisms responsible for the explosive radiation and evolution of cichlids. Locally S.B Wandera and his student Getrude Narnulemo are spearheading the biodiversity and taxonomic studies of cichlids in Lake Victoria region

The increased fishing pressure and the future of the fish stocks of Lake Victoria, Uganda

The Uganda sector of Lake Victoria occupies 29,580 km2 (43%). The lake used to boast of a multi-species fishery but presently relies on three major species Lates niloticus, Oreochromis niloticus and Rastrineobola argentea. During the past decade the total fish production on the Ugandan sector increased drastically from 17,000 tonnes in 1981 to about 13,000 tonnes 1991, indicating a healthy state of the fishery. This was contributed by a combination of factors including the explosive establishment of the introduced L. niloticus which contributed 60.8% in 1991 and the increase in the number of fishing canoes from 3470 in 1988 to 8000 in 1990. Isolated fishery resources studies carried out in different areas of the lake since 1971 seem, however, to indicate contrary trends in the available stocks and, therefore, the status of the fishery. In the experimental fishery, continued decline in catch rates have been recorded. Similarly, in the commercial fishery catch per unit of effort has been considerably poor (33 kg per canoe during January - March 1992) and the average size of individual fish laRded continued to decline, obviously pointing at possible over-fishing. This, therefore, calls for further urgent research on the available stocks for proper management strategies to be formulated.

Marine Vertebrates and Low Frequency Sound: Technical Report for LFA EIS

Over the past 50 years, economic and technological developments have dramatically increased the human contribution to ambient noise in the ocean. The dominant frequencies of most human-made noise in the ocean is in the low-frequency range (defined as sound energy below 1000Hz), and low-frequency sound (LFS) may travel great distances in the ocean due to the unique propagation characteristics of the deep ocean (Munk et al. 1989). For example, in the Northern Hemisphere oceans low-frequency ambient noise levels have increased by as much as 10 dB during the period from 1950 to 1975 (Urick 1986; review by NRC 1994). Shipping is the overwhelmingly dominant source of low-frequency manmade noise in the ocean, but other sources of manmade LFS including sounds from oil and gas industrial development and production activities (seismic exploration, construction work, drilling, production platforms), and scientific research (e.g., acoustic tomography and thermography, underwater communication). The SURTASS LFA system is an additional source of human-produced LFS in the ocean, contributing sound energy in the 100-500 Hz band. When considering a document that addresses the potential effects of a low-frequency sound source on the marine environment, it is important to focus upon those species that are the most likely to be affected. Important criteria are: 1) the physics of sound as it relates to biological organisms; 2) the nature of the exposure (i.e. duration, frequency, and intensity); and 3) the geographic region in which the sound source will be operated (which, when considered with the distribution of the organisms will determine which species will be exposed). The goal in this section of the LFA/EIS is to examine the status, distribution, abundance, reproduction, foraging behavior, vocal behavior, and known impacts of human activity of those species may be impacted by LFA operations. To focus our efforts, we have examined species that may be physically affected and are found in the region where the LFA source will be operated. The large-scale geographic location of species in relation to the sound source can be determined from the distribution of each species. However, the physical ability for the organism to be impacted depends upon the nature of the sound source (i.e. explosive, impulsive, or non-impulsive); and the acoustic properties of the medium (i.e. seawater) and the organism. Non-impulsive sound is comprised of the movement of particles in a medium. Motion is imparted by a vibrating object (diaphragm of a speaker, vocal chords, etc.). Due to the proximity of the particles in the medium, this motion is transmitted from particle to particle in waves away from the sound source. Because the particle motion is along the same axis as the propagating wave, the waves are longitudinal. Particles move away from then back towards the vibrating source, creating areas of compression (high pressure) and areas of rarefaction (low pressure). As the motion is transferred from one particle to the next, the sound propagates away from the sound source. Wavelength is the distance from one pressure peak to the next. Frequency is the number of waves passing per unit time (Hz). Sound velocity (not to be confused with particle velocity) is the impedance is loosely equivalent to the resistance of a medium to the passage of sound waves (technically it is the ratio of acoustic pressure to particle velocity). A high impedance means that acoustic particle velocity is small for a given pressure (low impedance the opposite). When a sound strikes a boundary between media of different impedances, both reflection and refraction, and a transfer of energy can occur. The intensity of the reflection is a function of the intensity of the sound wave and the impedances of the two media. Two key factors in determining the potential for damage due to a sound source are the intensity of the sound wave and the impedance difference between the two media (impedance mis-match). The bodies of the vast majority of organisms in the ocean (particularly phytoplankton and zooplankton) have similar sound impedence values to that of seawater. As a result, the potential for sound damage is low; organisms are effectively transparent to the sound – it passes through them without transferring damage-causing energy. Due to the considerations above, we have undertaken a detailed analysis of species which met the following criteria: 1) Is the species capable of being physically affected by LFS? Are acoustic impedence mis-matches large enough to enable LFS to have a physical affect or allow the species to sense LFS? 2) Does the proposed SURTASS LFA geographical sphere of acoustic influence overlap the distribution of the species? Species that did not meet the above criteria were excluded from consideration. For example, phytoplankton and zooplankton species lack acoustic impedance mis-matches at low frequencies to expect them to be physically affected SURTASS LFA. Vertebrates are the organisms that fit these criteria and we have accordingly focused our analysis of the affected environment on these vertebrate groups in the world’s oceans: fishes, reptiles, seabirds, pinnipeds, cetaceans, pinnipeds, mustelids, sirenians (Table 1).

Deformation and fracture of impulsively loaded sandwich panels

Light metal sandwich panel structures with cellular cores have attracted interest for multifunctional applications which exploit their high bend strength and impact energy absorption. This concept has been explored here using a model 6061-T6 aluminum alloy system fabricated by friction stir weld joining extruded sandwich panels with a triangular corrugated core. Micro-hardness and miniature tensile coupon testing revealed that friction stir welding reduced the strength and ductility in the welds and a narrow heat affected zone on either side of the weld by approximately 30%. Square, edge clamped sandwich panels and solid plates of equal mass per unit area were subjected to localized impulsive loading by the impact of explosively accelerated, water saturated, sand shells. The hydrodynamic load and impulse applied by the sand were gradually increased by reducing the stand-off distance between the test charge and panel surfaces. The sandwich panels suffered global bending and stretching, and localized core crushing. As the pressure applied by the sand increased, face sheet fracture by a combination of tensile stretching and shear-off occurred first at the two clamped edges of the panels that were parallel with the corrugation and weld direction. The plane of these fractures always lay within the heat affected zone of the longitudinal welds. For the most intensively loaded panels additional cracks occurred at the other clamped boundaries and in the center of the panel. To investigate the dynamic deformation and fracture processes, a particle-based method has been used to simulate the impulsive loading of the panels. This has been combined with a finite element analysis utilizing a modified Johnson-Cook constitutive relation and a Cockcroft-Latham fracture criterion that accounted for local variation in material properties. The fully coupled simulation approach enabled the relationships between the soil-explosive test charge design, panel geometry, spatially varying material properties and the panel's deformation and dynamic failure responses to be explored. This comprehensive study reveals the existence of a strong instability in the loading that results from changes in sand particle reflection during dynamic evolution of the panel's surface topology. Significant fluid-structure interaction effects are also discovered at the sample sides and corners due to changes of the sand reflection angle by the edge clamping system. © 2012 Elsevier Ltd. All rights reserved.

The dynamic response of edge clamped plates loaded by spherically expanding sand shells

The dynamic deformation of both edge clamped stainless steel sandwich panels with a pyramidal truss core and equal mass monolithic plates loaded by spherically expanding shells of dry and water saturated sand has been investigated, both experimentally and via a particle based simulation methodology. The spherically expanding sand shell is generated by detonating a sphere of explosive surrounded by a shell of either dry or water saturated synthetic sand. The measurements show that the sandwich panel and plate deflections decrease with increasing stand-off between the center of the charge and the front of the test structures. Moreover, for the same charge and sand mass, the deflections of the plates are significantly higher in the water saturated sand case compared to that of dry sand. For a given stand-off, the mid-span deflection of the sandwich panel rear faces was substantially less than that of the corresponding monolithic plate for both the dry and water saturated sand cases. The experiments were simulated via a coupled discrete-particle/ finite element scheme wherein the high velocity impacting sand is modeled by interacting particles while the plate is modeled within a Lagrangian finite element setting. The simulations are in good agreement with the measurements for the dry sand impact of both the monolithic and sandwich structures. However, the simulations underestimate the effect of stand-off in the case of the water saturated sand explosion, i.e. the deflections decrease more sharply with increasing stand-off in the experiments compared to the simulations. The simulations reveal that the momentum transmitted into the sandwich and monolithic plate structures by the sand shell is approximately the same, consistent with a small fluid-structure interaction effect. The smaller deflection of the sandwich panels is therefore primarily due to the higher bending strength of sandwich structures. © 2013 The Authors. Published by Elsevier Ltd. All rights reserved.

Sand column impact onto a Kolsky pressure bar

A laboratory-based methodology to launch cylindrical sand slugs at high velocities is developed. The methodology generates well-characterised soil ejecta without the need for detonation of an explosive; this laboratory-based tool thereby allows for the experimental investigation of the soil-structure events. The experimental set-up comprises a launcher with a cylindrical cavity and a piston to push out the sand slug. The apparatus is used to launch both dry and water-saturated sand slugs. High speed photography is used to characterise the evolution of the sand slugs after launch. We find that the diameter of the slugs remains unchanged, and the sand particles possess only an axial component of velocity. However, the sand particles have a uniform spatial gradient of axial velocity and this results in lengthening of the slugs as they travel towards their target. Thus, the density of the sand slugs remains spatially homogenous but decreases with increasing time. The velocity gradient is typically higher in the dry sand slugs than that of the water-saturated slugs. The pressure exerted by the slugs on a rigid-stationary target is measured by impacting the slugs against a direct impact Kolsky bar. After an initial high transient pressure, the pressure reduces to a value of approximately ρv 2 where ρ is the density of the impacting sand slug and v is the particle velocity. This indicates that loading due to the sand is primarily inertial in nature. The momentum transmitted to the Kolsky bar was approximately equal to the incident momentum of the sand slugs, regardless of whether they are dry or water-saturated. © 2013 Elsevier Ltd. All rights reserved.

A laboratory-scale buried charge simulator

An experimental technique has been developed in order to mimic the effect of landmine loading on materials and structures to be studied in a laboratory setting, without the need for explosives. Compressed gas is discharged beneath a sand layer, simulating the dynamic flow generated by a buried explosive. High speed photography reveals that the stages of soil motion observed during a landmine blast are replicated. The effect of soil saturation and the depth of the sand layer on sand motion are evaluated. Two series of experiments have been performed with the buried charge simulator to characterise subsequent impact of the sand. First, the time variation in pressure and impulse during sand impact on a stationary target is evaluated using a Kolsky bar apparatus. It is found that the pressure pulse imparted to the Kolsky bar consists of two phases: an initial transient phase of high pressure (attributed to wave propagation effects in the impacting sand), followed by a lower pressure phase of longer duration (due to lateral flow of the sand against the Kolsky bar). Both phases make a significant contribution to the total imparted impulse. It is found that wet sand exerts higher peak pressures and imparts a larger total impulse than dry sand. The level of imparted impulse is determined as a function of sand depth, and of stand-off distance between the sand and the impacted end of the Kolsky bar. The second study uses a vertical impulse pendulum to measure the momentum imparted by sand impact to a target which is free to move vertically. The effect of target mass upon imparted momentum is investigated. It is concluded that the laboratory-scale sand impact apparatus is a flexible tool for investigating the interactions between structures and dynamic sand flows. © 2013 Elsevier Ltd. All rights reserved.

Diet overlap between the endemic fish Anablariflus grahami(Cyprinidae) and the exotic noodlefish Neosalanx taihuensis (Salangidae) in lake Fuxian, China

We studied diet composition and overlap of the exotic noodlefish (Neosalanx taihuensis) and the endemic fish Anaborilius grahami in a deep, oligotrophic lake in the Yunnan Plateau. A. grahami dominated the fish community in Lake Fuxian before the invasion of N. taihuensis in 1982, but it is now in the process of extinction, corresponding with an explosive increase in N. taihuensis population. Schoener's index (alpha=0.773) indicate that N. taihuensis and A. grahami have significant diet overlap, with both fish feeding mainly on zooplankton. An increased proportion of littoral prey, such as Procladius spp., Coleoptera, and epiphytes, in the diet of A. grahami indicated that this endemic fish shifted its main habitat from the off-shore zone in the late 1980s to the littoral zone at the present. A difference in reproduction between the two fishes, along with the overfishing, may have exacerbated the occupation of A. grahami's pelagic niche by N. taihuensis. The endemic species has shown large competitive disadvantage for food and space in the presence of N. taihuensis.

Linear multimodal actuation through discrete coupling

Due to technological limitations, robot actuators are often designed for specific tasks with narrow performance goals, whereas a wide range of behaviors is necessary for autonomous robots in uncertain complex environments. In an effort to increase the versatility of actuators, we introduce a new concept of multimodal actuation (MMA) that employs dynamic coupling in the form of clutches and brakes to change its mode of operation. The dynamic coupling allows motors and passive elements such as springs to be engaged and disengaged within a single actuator. We apply the concept to a linear series elastic actuator which uses friction brakes controlled online for the dynamic coupling. With this prototype, we are able to demonstrate several modes of operation including stiff position control, series elastic actuation as well as the possibility to store and release energy in a controlled manner for explosive tasks such as jumping. In this paper, we model the proposed concept of actuation and show a systematic performance analysis of the physical prototype that we developed in our laboratory. © 1996-2012 IEEE.

Effect of pulse heating parameters on the microscale bubble dynamics at a microheater surface

We study the effects of pulse heating parameters on the micro bubble behavior of a platinum microheater (100 mu m x 20 mu m) immersed in a methanol pool. The experiment covers the heat fluxes of 10-37 MW/m(2) and pulse frequencies of 25-500 Hz. The boiling incipience is initiated at the superheat limit of methanol, corresponding to the homogeneous nucleation. Three types of micro boiling patterns are identified. The first type is named as the bubble explosion and regrowth, consisting of a violent explosive boiling and shrinking, followed by a slower bubble regrowth and subsequent shrinking, occurring at lower heat fluxes. The second type, named as the bubble breakup and attraction, consists of the violent explosive boiling, bubble breakup and emission, bubble attraction and coalescence process, occurring at higher heat fluxes than those of the first type. The third type, named as the bubble size oscillation and large bubble formation, involves the initial explosive boiling, followed by a short periodic bubble growth and shrinking. Then the bubble continues to increase its size, until a constant bubble size is reached which is larger than the microheater length.