Simulación eficiente de mecanismos flexibles mediante formulaciones topológicas

El objetivo de esta Tesis es presentar un método eficiente para la evaluación de sistemas multi-cuerpo con elementos flexibles con pequeñas deformaciones, basado en métodos topológicos para la simulación de sistemas tan complejos como los que se utilizan en la práctica y en tiempo real o próximo al real. Se ha puesto un especial énfasis en la resolución eficiente de aquellos aspectos que conllevan mayor coste computacional, tales como la evaluación de las ecuaciones dinámicas y el cálculo de los términos de inercia. Las ecuaciones dinámicas se establecen en función de las variables independientes del sistema, y la integración de las mismas se realiza mediante formulaciones implícitas de index-3. Esta Tesis se articula en seis Capítulos. En el Capítulo 1 se realiza una revisión bibliográfica de la simulación de sistemas flexibles y los métodos más relevantes de integración de las ecuaciones diferenciales del movimiento. Asimismo, se presentan los objetivos de esta Tesis. En el Capítulo 2 se presenta un método semi-recursivo para la evaluación de las ecuaciones de los sistemas multi-cuerpo con elementos flexibles basado en formulaciones topológicas y síntesis modal. Esta Tesis determina la posición de cada punto del cuerpo flexible en función de un sistema de referencia flotante que se mueve con dicho cuerpo y de las amplitudes de ciertos modos de deformación calculados a partir de un mallado obtenido mediante el Método de Elementos Finitos. Se presta especial atención en las condiciones de contorno que se han de tener en cuenta a la hora de establecer las variables que definen la deformación del cuerpo flexible. El Capítulo 3 se centra en la evaluación de los términos de inercia de los sistemas flexibles que generalmente conllevan un alto coste computacional. Se presenta un método que permite el cálculo de dichos términos basado en el uso de 24 matrices constantes que pueden ser calculadas previamente al proceso de integración. Estas matrices permiten evaluar la matriz de masas y el vector de fuerzas de inercia dependientes de la velocidad sin que sea necesario evaluar la posición deformada de todos los puntos del cuerpo flexible. Se realiza un análisis pormenorizado de dichas matrices con el objetivo de optimizar su cálculo estableciendo aproximaciones que permitan reducir el número de dichos términos y optimizar aún más su evaluación. Se analizan dos posibles simplificaciones: la primera utiliza una discretización no-consistente basada en elementos finitos en los que se definen únicamente los desplazamientos axiales de los nodos; en la segunda propuesta se hace uso de una matriz de masas concentradas (Lumped Mass). Basándose en la formulación presentada, el Capítulo 4 aborda la integración eficiente de las ecuaciones dinámicas. Se presenta un método iterativo para la integración con fórmulas de index-3 basado en la proyección de las ecuaciones dinámicas según las variables independientes del sistema multi-cuerpo. El cálculo del residuo del sistema de ecuaciones no lineales que se ha de resolver de modo iterativo se realiza mediante un proceso recursivo muy eficiente que aprovecha la estructura topológica del sistema. Se analizan tres formas de evaluar la matriz tangente del citado sistema no lineal: evaluación aproximada, numérica y recursiva. El método de integración presentado permite el uso de distintas fórmulas. En esta Tesis se analizan la Regla Trapezoidal, la fórmula BDF de segundo orden y un método híbrido TR-BDF2. Para este último caso se presenta un algoritmo de paso variable. En el Capítulo 5 plantea la implementación del método propuesto en un programa general de simulación de mecanismos que permita la resolución de cualquier sistema multi-cuerpo definiéndolo mediante un fichero de datos. La implementación de este programa se ha realizado tanto en C++ como en Java. Se muestran los resultados de las formulaciones presentadas en esta Tesis mediante la simulación de cuatro ejemplos de distinta complejidad. Mediante análisis concretos se comparan la formulación presentada con otras existentes. También se analiza el efecto del lenguaje de programación utilizado en la implementación y los efectos de las posibles simplificaciones planteadas. Por último, el Capítulo 6 resume las principales conclusiones alcanzadas en la Tesis y las futuras líneas de investigación que con ella se abren. ABSTRACT This Thesis presents an efficient method for solving the forward dynamics of a multi-body sys-tem formed by rigid and flexible bodies with small strains for real-time simulation of real-life models. It is based on topological formulations. The presented work focuses on the efficient solution of the most time-consuming tasks of the simulation process, such as the numerical integration of the motion differential equations and in particular the evaluation of the inertia terms corresponding to the flexible bodies. The dynamic equations are formulated in terms of independent variables of the muti-body system, and they are integrated by means of implicit index-3 formulae. The Thesis is arranged in six chapters. Chapter 1 presents a review of the most relevant and recent contributions related to the modelization of flexible multi-body systems and the integration of the corresponding dynamic equations. The main objectives of the Thesis are also presented in detail. Chapter 2 presents a semi-recursive method for solving the equations of a multi-body system with flexible bodies based on topological formulations and modal synthesis. This Thesis uses the floating frame approach and the modal amplitudes to define the position of any point at the flexible body. These modal deformed shapes are obtained by means of the Finite Element Method. Particular attention has been taken to the boundary conditions used to define the deformation of the flexible bodies. Chapter 3 focuses on the evaluation of the inertia terms, which is usually a very time-consuming task. A new method based on the use of 24 constant matrices is presented. These matrices are evaluated during the set-up step, before the integration process. They allow the calculation of the inertia terms in terms of the position and orientation of the local coordinate system and the deformation variables, and there is no need to evaluate the position and velocities of all the nodes of the FEM mesh. A deep analysis of the inertia terms is performed in order to optimize the evaluation process, reducing both the terms used and the number of arithmetic operations. Two possible simplifications are presented: the first one uses a non-consistent approach in order to define the inertia terms respect to the Cartesian coordinates of the FEM mesh, rejecting those corresponding to the angular rotations; the second approach makes use of lumped mass matrices. Based on the previously presented formulation, Chapter 4 is focused on the numerical integration of the motion differential equations. A new predictor-corrector method based on index-3 formulae and on the use of multi-body independent variables is presented. The evaluation of the dynamic equations in a new time step needs the solution of a set on nonlinear equations by a Newton-Raphson iterative process. The computation of the corresponding residual vector is performed efficiently by taking advantage of the system’s topological structure. Three methods to compute the tangent matrix are presented: an approximated evaluation that considers only the most relevant terms, a numerical approach based on finite differences and a recursive method that uses the topological structure. The method presented for integrating the dynamic equations can use a variety of integration formulae. This Thesis analyses the use of the trapezoidal rule, the 2nd order BDF formula and the hybrid TR-BDF2 method. A variable-time step strategy is presented for the last one. Chapter 5 describes the implementation of the proposed method in a general purpose pro-gram for solving any multibody defined by a data file. This program is implemented both in C++ and Java. Four examples are used to check the validity of the formulation and to compare this method with other methods commonly used to solve the dynamic equations of multi-body systems containing flexible bodies. The efficiency of the programming methodology used and the effect of the possible simplifications proposed are also analyzed. Chapter 6 summarizes the main Conclusions obtained in this Thesis and the new lines of research that have been opened.

Health monitoring of a new hysteretic damper subjected to earthquakes on a shaking table

This paper presents the experimental results obtained by applying frequency-domain structural health monitoring techniques to assess the damage suffered on a special type of damper called Web Plastifying Damper (WPD). The WPD is a hysteretic type energy dissipator recently developed for the passive control of structures subjected to earthquakes. It consists of several I-section steel segments connected in parallel. The energy is dissipated through plastic deformations of the web of the I-sections, which constitute the dissipative parts of the damper. WPDs were subjected to successive histories of dynamically-imposed cyclic deformations of increasing magnitude with the shaking table of the University of Granada. To assess the damage to the web of the I-section steel segments after each history of loading, a new damage index called Area Index of Damage (AID) was obtained from simple vibration tests. The vibration signals were acquired by means of piezoelectric sensors attached on the I-sections, and non-parametric statistical methods were applied to calculate AID in terms of changes in frequency response functions. The damage index AID was correlated with another energy-based damage index-ID- which past research has proven to accurately characterize the level of mechanical damage. The ID is rooted in the decomposition of the load-displacement curve experienced by the damper into the so-called skeleton and Bauschinger parts. ID predicts the level of damage and the proximity to failure of the damper accurately, but it requires costly instrumentation. The experiments reported in this paper demonstrate a good correlation between AID and ID in a realistic seismic loading scenario consisting of dynamically applied arbitrary cyclic loads. Based on this correlation, it is possible to estimate ID indirectly from the AID, which calls for much simpler and less expensive instrumentation.

Rates of nucleotide substitution in sexual and anciently asexual rotifers

The class Bdelloidea of the phylum Rotifera is the largest well studied eukaryotic taxon in which males and meiosis are unknown, and the only one for which these indications of ancient asexuality are supported by cytological and molecular genetic evidence. We estimated the rates of synonymous and nonsynonymous substitutions in the hsp82 heat shock gene in bdelloids and in facultatively sexual rotifers of the class Monogononta, employing distance based and maximum likelihood methods. Relative-rate tests, using acanthocephalan rotifers as an outgroup, showed slightly higher rates of nonsynonymous substitution and slightly lower rates of synonymous substitution in bdelloids as compared with monogononts. The opposite trend, however, was seen in intraclass pairwise comparisons. If, as it seems, bdelloids have evolved asexually, an equality of bdelloid and monogonont substitution rates would suggest that the maintenance of sexual reproduction in monogononts is not attributable to an effect of sexual reproduction in limiting the load of deleterious nucleotide substitutions.

Molecular characterization of the mosquito vitellogenin receptor reveals unexpected high homology to the Drosophila yolk protein receptor.

The mosquito (Aedes aegypti) vitellogenin receptor (AaVgR) is a large membrane-bound protein (214 kDa when linearized) that mediates internalization of vitellogenin, the major yolk-protein precursor, by oocytes during egg development. We have cloned and sequenced two cDNA fragments encompassing the entire coding region of AaVgR mRNA, to our knowledge the first insect VgR sequence to be reported. The 7.3-kb AaVgR mRNA is present only in female germ-line cells and is abundant in previtellogenic oocytes, suggesting that the AaVgR gene is expressed early in oocyte differentiation. The deduced amino acid sequence predicts a 202.7-kDa protein before posttranslational processing. The AaVgR is a member of the low density lipoprotein receptor superfamily, sharing significant homology with the chicken (Gallus gallus) VgR and particularly the Drosophila melanogaster yolk protein receptor, in spite of a very different ligand for the latter. Distance-based phylogenetic analyses suggest that the insect VgR/yolk protein receptor lineage and the vertebrate VgR/low density lipoprotein receptor lineage diverged before the bifurcation of nematode and deuterostome lines.

Proteção compartilhada e restauração de tráfego em redes ópticas de segmentação espectral flexível

A busca de sistemas de comunicação eficientes e econômicos é cada vez maior, principalmente com o aumento da demanda por tráfego e banda de transmissão. Conhecidas pela utilização eficiente de largura de banda, as redes ópticas de segmentação espectral flexível têm sido intensamente estudadas e são consideradas boas candidatas para a próxima geração de redes. Tais redes flexíveis utilizam formatos de modulação multinível e multiplexação multiportadora. Sistemas com alta capacidade de transmissão devem ser extremamente confiáveis, pois a falha em um dispositivo ou enlace da rede acarreta enorme perda de dados. Por isso, as técnicas de proteção e restauração do tráfego devem ser eficientes, de modo a garantir a sobrevivência da rede. Neste trabalho, foi desenvolvido um algoritmo capaz de lidar com cada requisição de conexão, encontrar um caminho óptico para transmissão e reservar outro caminho para recuperação do tráfego em caso de falha na rede. A seleção dos caminhos primário e de proteção utiliza a técnica smart-fit, que escolhe a solução com menor custo final, definido pela distância da rota percorrida somada ao custo do índice inicial da faixa espectral alocada, buscando equilibrar a escolha entre a posição no espectro e rota escolhida. Além disso, são definidos custos diferentes para slots de frequência livres e compartilhados, a fim de incentivar o compartilhamento espectral em caminhos de proteção. Dentre as técnicas de alocação espectral, a varredura com janela espectral varre o espectro em todos os enlaces da rota, slot por slot, em busca de uma faixa livre com tamanho suficiente para atender uma demanda. Neste trabalho, foi desenvolvida uma técnica chamada busca lógica, que lida simultaneamente com todos os enlaces da rota ao realizar operações lógicas com seus espectros. Em seguida, é realizada uma convolução entre a janela espectral, com tamanho da demanda, e o espectro resultante. A partir desse resultado, é possível saber as posições no espectro onde a demanda poderá ser alocada. Tal técnica, como será demonstrado, é mais veloz que a varredura com janela espectral. Para garantir a eficácia e confiabilidade do algoritmo, utilizando o software MATLAB, avaliou-se a probabilidade de bloqueio e probabilidade de bloqueio de banda, a fragmentação espectral média na rede, o grau de compartilhamento, a taxa de utilização espectral e a taxa de capacidade reservada. O algoritmo desenvolvido foi capaz de organizar o tráfego na rede de modo ordenado e pouco fragmentado, além de utilizar de maneira eficiente os recursos destinados à proteção.

Advanced optical fibre gratings and applications

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT This thesis describes a detailed study of advanced optical fibre sensors based on fibre Bragg grating (FBG), tilted fibre Bragg grating (TFBG) and long-period grating (LPG) and their applications in optical communications and sensing. The major contributions presented in this thesis are summarised below.The most important contribution from the research work presented in this thesis is the implementation of in-fibre grating based refractive index (RI) sensors, which could be the good candidates for optical biochemical sensing. Several fibre grating based RI sensors have been proposed and demonstrated by exploring novel grating structures and different fibre types, and employing efficient hydrofluoric acid etching technique to enhance the RI sensitivity. All the RI devices discussed in this thesis have been used to measure the concentration of sugar solution to simulate the chemical sensing. Efforts have also been made to overcome the RI-temperature cross-sensitivity for practical application. The demonstrated in-fibre grating based RI sensors could be further implemented as potential optical biosensors by applying bioactive coatings to realise high bio-sensitivity and bio-selectivity.Another major contribution of this thesis is the application of TFBGs. A prototype interrogation system by the use of TFBG with CCD-array was implemented to perform wavelength division multiplexing (WDM) interrogation around 800nm wavelength region with the advantages of compact size, fast detection speed and low-cost. As a high light, a novel in-fibre twist sensors utilising strong polarisation dependant coupling behaviour of an 81°-TFBG was presented to demonstrate the high torsion sensitivity and capability of direction recognition.

Fibre Bragg gratings in polymer optical fibre for applications in sensing

This thesis presents the potential sensing applications of fibre Bragg gratings in polymer optical fibres. Fibre Bragg gratings are fabricated in different kinds of polymer optical fibres, including Poly methyl methacrylate (PMMA) and TOPAS cyclic olefin copolymer based microstructured polymer optical fibres and PMMA based step-index photosensitive polymer optical fibre, using the 325nm continuous wave ultraviolet laser and phase mask technique. The thermal response of fabricated microstructured polymer optical fibre Bragg gratings has been characterized. The PMMA based single mode microstructured polymer optical fibre Bragg gratings exhibit negative non-linear Bragg wavelength shift with temperature, including a quasi-linear region. The thermal sensitivity of such Bragg gratings in the linear region is up to -97pm/°C. A permanent shift in the grating wavelength at room temperature is observed when such gratings are heated above a threshold temperature which can be extended by annealing the fibre before grating inscription. The largest positive Bragg wavelength shift with temperature in transmission is observed in TOPAS based few moded microstructured polymer optical fibre Bragg gratings and the measured temperature sensitivity is 250±0.5pm/°C. Gluing method is developed to maintain stable optical coupling between PMMA based single mode step index polymer optical fibre Bragg gratings and single mode step index silica optical fibre. Being benefit from this success, polymer optical fibre Bragg gratings are able to be characterised for their temperature, humidity and strain sensitivity, which are -48.2±1pm/°C, 38.3±0.5pm per %RH and 1.33±0.04 pm/µ??respectively. These sensitivities have been utilised to achieve several applications. The strain sensitivity of step index polymer optical fibre Bragg grating devices has been exploited in the potential application of the strain condition monitoring of heavy textiles and when being attached to textile specimens with certain type of adhesives. These polymer fibre Bragg grating devices show better strain transfer and lower structure reinforcement than silica optical fibre Bragg grating devices. The humidity sensitivity of step index polymer optical fibre Bragg grating devices is applied to detecting water in jet fuel and is proved to be able to measure water content of less than 20 ppm in Jet fuel. A simultaneous temperature and humidity sensor is also made by attaching a polymer fibre Bragg grating to a silica optical fibre Bragg grating and it shows better humidity measurement accuracy than that of electronic competitors.

Uses of frontier efficiency methodologies and multi-criteria decision making for performance measurement in the energy sector

Guest editorial Ali Emrouznejad is a Senior Lecturer at the Aston Business School in Birmingham, UK. His areas of research interest include performance measurement and management, efficiency and productivity analysis as well as data mining. He has published widely in various international journals. He is an Associate Editor of IMA Journal of Management Mathematics and Guest Editor to several special issues of journals including Journal of Operational Research Society, Annals of Operations Research, Journal of Medical Systems, and International Journal of Energy Management Sector. He is in the editorial board of several international journals and co-founder of Performance Improvement Management Software. William Ho is a Senior Lecturer at the Aston University Business School. Before joining Aston in 2005, he had worked as a Research Associate in the Department of Industrial and Systems Engineering at the Hong Kong Polytechnic University. His research interests include supply chain management, production and operations management, and operations research. He has published extensively in various international journals like Computers & Operations Research, Engineering Applications of Artificial Intelligence, European Journal of Operational Research, Expert Systems with Applications, International Journal of Production Economics, International Journal of Production Research, Supply Chain Management: An International Journal, and so on. His first authored book was published in 2006. He is an Editorial Board member of the International Journal of Advanced Manufacturing Technology and an Associate Editor of the OR Insight Journal. Currently, he is a Scholar of the Advanced Institute of Management Research. Uses of frontier efficiency methodologies and multi-criteria decision making for performance measurement in the energy sector This special issue aims to focus on holistic, applied research on performance measurement in energy sector management and for publication of relevant applied research to bridge the gap between industry and academia. After a rigorous refereeing process, seven papers were included in this special issue. The volume opens with five data envelopment analysis (DEA)-based papers. Wu et al. apply the DEA-based Malmquist index to evaluate the changes in relative efficiency and the total factor productivity of coal-fired electricity generation of 30 Chinese administrative regions from 1999 to 2007. Factors considered in the model include fuel consumption, labor, capital, sulphur dioxide emissions, and electricity generated. The authors reveal that the east provinces were relatively and technically more efficient, whereas the west provinces had the highest growth rate in the period studied. Ioannis E. Tsolas applies the DEA approach to assess the performance of Greek fossil fuel-fired power stations taking undesirable outputs into consideration, such as carbon dioxide and sulphur dioxide emissions. In addition, the bootstrapping approach is deployed to address the uncertainty surrounding DEA point estimates, and provide bias-corrected estimations and confidence intervals for the point estimates. The author revealed from the sample that the non-lignite-fired stations are on an average more efficient than the lignite-fired stations. Maethee Mekaroonreung and Andrew L. Johnson compare the relative performance of three DEA-based measures, which estimate production frontiers and evaluate the relative efficiency of 113 US petroleum refineries while considering undesirable outputs. Three inputs (capital, energy consumption, and crude oil consumption), two desirable outputs (gasoline and distillate generation), and an undesirable output (toxic release) are considered in the DEA models. The authors discover that refineries in the Rocky Mountain region performed the best, and about 60 percent of oil refineries in the sample could improve their efficiencies further. H. Omrani, A. Azadeh, S. F. Ghaderi, and S. Abdollahzadeh presented an integrated approach, combining DEA, corrected ordinary least squares (COLS), and principal component analysis (PCA) methods, to calculate the relative efficiency scores of 26 Iranian electricity distribution units from 2003 to 2006. Specifically, both DEA and COLS are used to check three internal consistency conditions, whereas PCA is used to verify and validate the final ranking results of either DEA (consistency) or DEA-COLS (non-consistency). Three inputs (network length, transformer capacity, and number of employees) and two outputs (number of customers and total electricity sales) are considered in the model. Virendra Ajodhia applied three DEA-based models to evaluate the relative performance of 20 electricity distribution firms from the UK and the Netherlands. The first model is a traditional DEA model for analyzing cost-only efficiency. The second model includes (inverse) quality by modelling total customer minutes lost as an input data. The third model is based on the idea of using total social costs, including the firm’s private costs and the interruption costs incurred by consumers, as an input. Both energy-delivered and number of consumers are treated as the outputs in the models. After five DEA papers, Stelios Grafakos, Alexandros Flamos, Vlasis Oikonomou, and D. Zevgolis presented a multiple criteria analysis weighting approach to evaluate the energy and climate policy. The proposed approach is akin to the analytic hierarchy process, which consists of pairwise comparisons, consistency verification, and criteria prioritization. In the approach, stakeholders and experts in the energy policy field are incorporated in the evaluation process by providing an interactive mean with verbal, numerical, and visual representation of their preferences. A total of 14 evaluation criteria were considered and classified into four objectives, such as climate change mitigation, energy effectiveness, socioeconomic, and competitiveness and technology. Finally, Borge Hess applied the stochastic frontier analysis approach to analyze the impact of various business strategies, including acquisition, holding structures, and joint ventures, on a firm’s efficiency within a sample of 47 natural gas transmission pipelines in the USA from 1996 to 2005. The author finds that there were no significant changes in the firm’s efficiency by an acquisition, and there is a weak evidence for efficiency improvements caused by the new shareholder. Besides, the author discovers that parent companies appear not to influence a subsidiary’s efficiency positively. In addition, the analysis shows a negative impact of a joint venture on technical efficiency of the pipeline company. To conclude, we are grateful to all the authors for their contribution, and all the reviewers for their constructive comments, which made this special issue possible. We hope that this issue would contribute significantly to performance improvement of the energy sector.

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships. Results Analysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042). Conclusion Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.

Metacommunity Structure Along Resource and Disturbance Gradients in Everglades Wetlands

We evaluated metacommunity hypotheses of landscape arrangement (indicative of dispersal limitation) and environmental gradients (hydroperiod and nutrients) in structuring macroinvertebrate and fish communities in the southern Everglades. We used samples collected at sites from the eastern boundary of the southern Everglades and from Shark River Slough, to evaluate the role of these factors in metacommunity structure. We used eigenfunction spatial analysis to model community structure among sites and distance-based redundancy analysis to partition the variability in communities between spatial and environmental filters. For most animal communities, hydrological parameters had a greater influence on structure than nutrient enrichment, however both had large effects. The influence of spatial effects indicative of dispersal limitation was weak and only periphyton infauna appeared to be limited by regional dispersal. At the landscape scale, communities were well-mixed, but strongly influenced by hydrology. Local-scale species dominance was influenced by water-permanence and nutrient enrichment. Nutrient enrichment is limited to water inflow points associated with canals, which may explain its impact in this data set. Hydroperiod and nutrient enrichment are controlled by water managers; our analysis indicates that the decisions they make have strong effects on the communities at the base of the Everglades food web.

Grain size distribution and sea level changes in Gåsfjärden fjord

We analysed long-term variations in grain-size distribution in sediments from Gåsfjärden, a fjord-like inlet on the south-west Baltic Sea, and explored potential drivers of the recorded changes in sediment grain-size data. Over the last 5.4 thousand years (ka), the relative sea level decreased 17 m in the study region, caused by isostatic land uplift. As a consequence, Gåsfjärden has been transformed from an open coastal setting into a semi-closed inlet surrounded on the east by numerous small islands. To quantitatively estimate the morphological changes in Gåsfjärden over the last 5.4 ka and to further link the changes to our grain-size data, a digital elevation model (DEM)-based openness index was calculated. In the period between 5.4 and 4.4 ka BP, the inlet was characterised by the largest openness index. During this interval, the highest sand contents (~0.4 %) and silt/clay ratios (~0. 3) in the sediment sequence were recorded, indicating relatively high bottom water energy. After 4.4 ka BP, the average sand content was halved to ~0.2 % and the silt/clay ratios showed a significant decreasing trend over the last 4 ka. These changes are found to be associated with the gradual embayment of Gåsfjärden as represented in the openness index. The silt/clay ratios exhibited a delayed and slower change compared with the sand contents, which further suggest that finer particles are less sensitive to changes in hydrodynamic energy. Our DEM-based coastal openness index has proved to be a useful tool for interpreting the sedimentary grain-size record.

XDX, Mg/Ca, and delta18O analyses of core top sediments

Mg/Ca and d18O data for four species of planktic foraminifera (G. ruber (white), G. sacculifer (without sac), N. dutertrei, and P. obliquiloculata) from core top sediments from the tropical Pacific, Atlantic, and western Indian Ocean. Deepwater calcite saturation values (Delta[CO3**2-]) at the sites range from 55 to -23 µmol/kg.

Concentrations and abundance ratios of long-chain alkenones and glycerol dialkyl glycerol tetraethers in sinking particles south of Java

In this study, we obtained concentrations and abundance ratios of long-chain alkenones and glycerol dialkyl glycerol tetraethers (GDGTs) in a one-year time-series of sinking particles collected with a sediment trap moored from December 2001 to November 2002 at 2200 m water depth south of Java in the eastern Indian Ocean. We investigate the seasonality of alkenone and GDGT fluxes as well as the potential habitat depth of the Thaumarchaeota producing the GDGTs entrained in sinking particles. The alkenone flux shows a pronounced seasonality and ranges from 1 µg m-**2 d**-1 to 35 µg m**-2 d**-1. The highest alkenone flux is observed in late September during the Southeast monsoon, coincident with high total organic carbon fluxes as well as high net primary productivity. Flux-weighted mean temperature for the high flux period using the alkenone-based sea-surface temperature (SST) index UK'37 is 26.7°C, which is similar to satellite-derived Southeast (SE) monsoon SST (26.4°C). The GDGT flux displays a weaker seasonality than that of the alkenones. It is elevated during the SE monsoon period compared to the Northwest (NW) monsoon and intermonsoon periods (approximately 2.5 times), which is probably related to seasonal variation of the abundance of Thaumarchaeota, or to enhanced export of GDGTs by aggregation with sinking phytoplankton detritus. Flux-weighted mean temperature inferred from the GDGT-based TEXH86 index is 26.2°C, which is 1.8 °C lower than mean annual (ma) SST but similar to SE monsoon SST. As the time series of TEXH86 temperature estimates, however, does not record a strong seasonal amplitude, we infer that TEXH86 reflects ma upper thermocline temperature at approximately 50 m water depth.

Deletions of CDKN2C in Multiple Myeloma: Biological and Clinical Implications

Purpose: Deletions of chromosome 1 have been described in 7% to 40% of cases of myeloma with inconsistent clinical consequences. CDKN2C at 1p32.3 has been identified in myeloma cell lines as the potential target of the deletion. We tested the clinical impact of 1p deletion and used high-resolution techniques to define the role of CDKN2C in primary patient material.Experimental Design: We analyzed 515 cases of monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), and newly diagnosed multiple myeloma using fluorescence in situ hybridization (FISH) for deletions of CDKN2C. In 78 myeloma cases, we carried out Affymetrix single nucleotide polymorphism mapping and U133 Plus 2.0 expression arrays. In addition, we did mutation, methylation, and Western blotting analysis.Results: By FISH we identified deletion of 1p32.3 (CDKN2C) in 3 of 66 MGUS (4.5%), 4 of 39 SMM (10.3%), and 55 of 369 multiple myeloma cases (15%). We examined the impact of copy number change at CDKN2C on overall survival (OS), and found that the cases with either hemizygous or homozygous deletion of CDKN2C had a worse OS compared with cases that were intact at this region (22 months versus 38 months; P = 0.003). Using gene mapping we identified three homozygous deletions at 1p32.3, containing CDKN2C, all of which lacked expression of CDKN2C. Cases with homozygous deletions of CDKN2C were the most proliferative myelomas, defined by an expression-based proliferation index, consistent with its biological function as a cyclin-dependent kinase inhibitor.Conclusions: Our results suggest that deletions of CDKN2C are important in the progression and clinical outcome of myeloma.

Socioeconomic Status and Health Behavior in Nepal

Thesis (Master's)--University of Washington, 2016-07