Learning Models of Gene Expression from Synthetic DNA Sequences

Thesis (Ph.D.)--University of Washington, 2016-06

Modelling of entrainment in industrial flotation cells: the effect of solids suspension

Solids concentration and particle size distribution gradually change in the vertical dimension of industrial flotation cells, subject primarily to the flotation cell size and design and the cell operating conditions. As entrainment is a two-step process and involves only the suspended solids in the top pulp region near the pulp-froth interface, the solids suspension characteristics have a significant impact on the overall entrainment. In this paper, a classification function is proposed to describe the state of solids suspension in flotation cells, similar to the definition of degree of entrainment for classification in the froth phase found in the literature. A mathematical model for solids suspension is also developed, in which the classification function is expressed as an exponential function of the particle size. Experimental data collected from three different Outokumpu tank flotation cells in three different concentrators are well fitted by the proposed exponential model. Under the prevailing experimental conditions, it was found that the solids content in the top region was relatively independent of cell operating conditions such as froth height and air rate but dependent on the cell size. Moreover, the results obtained from the total solids tend to be similar to those from a particular gangue mineral and hence may be applied to all minerals in entrainment calculation. (C) 2004 Elsevier Ltd. All rights reserved.

Piggery pond sludge as a nitrogen source for crops. 1. Mineral N supply estimated from laboratory incubations and field application of stockpiled and wet sludge

Piggery pond sludge (PPS) was applied, as-collected (Wet PPS) and following stockpiling for 12 months ( Stockpiled PPS), to a sandy Sodosol and clay Vertosol at sites on the Darling Downs of Queensland. Laboratory measures of N availability were carried out on unamended and PPS-amended soils to investigate their value in estimating supplementary N needs of crops in Australia's northern grains region. Cumulative net N mineralised from the long-term ( 30 weeks) leached aerobic incubation was described by a first-order single exponential model. The mineralisation rate constant (0.057/week) was not significantly different between Control and PPS treatments or across soil types, when the amounts of initial mineral N applied in PPS treatments were excluded. Potentially mineralisable N (N-o) was significantly increased by the application of Wet PPS, and increased with increasing rate of application. Application of Wet PPS significantly increased the total amount of inorganic N leached compared with the Control treatments. Mineral N applied in Wet PPS contributed as much to the total mineral N status of the soil as did that which mineralised over time from organic N. Rates of CO2 evolution during 30 weeks of aerobic leached incubation indicated that the Stockpiled PPS was more stabilised (19-28% of applied organic C mineralised) than the Wet PPS (35-58% of applied organic C mineralised), due to higher lignin content in the former. Net nitrate-N produced following 12 weeks of aerobic non-leached incubation was highly correlated with net nitrate-N leached during 12 weeks of aerobic incubation (R-2 = 0.96), although it was

Strong electronic correlations in superconducting organic charge transfer salts

We review the role of strong electronic correlations in quasi-two-dimensional organic charge transfer salts such as (BEDT-TTF)(2)X, (BETS)(2)Y, and beta'-[Pd(dmit)(2)](2)Z. We begin by defining minimal models for these materials. It is necessary to identify two classes of material: the first class is strongly dimerized and is described by a half-filled Hubbard model; the second class is not strongly dimerized and is described by a quarter-filled extended Hubbard model. We argue that these models capture the essential physics of these materials. We explore the phase diagram of the half-filled quasi-two-dimensional organic charge transfer salts, focusing on the metallic and superconducting phases. We review work showing that the metallic phase, which has both Fermi liquid and 'bad metal' regimes, is described both quantitatively and qualitatively by dynamical mean field theory (DMFT). The phenomenology of the superconducting state is still a matter of contention. We critically review the experimental situation, focusing on the key experimental results that may distinguish between rival theories of superconductivity, particularly probes of the pairing symmetry and measurements of the superfluid stiffness. We then discuss some strongly correlated theories of superconductivity, in particular the resonating valence bond (RVB) theory of superconductivity. We conclude by discussing some of the major challenges currently facing the field. These include parameterizing minimal models, the evidence for a pseudogap from nuclear magnetic resonance (NMR) experiments, superconductors with low critical temperatures and extremely small superfluid stiffnesses, the possible spin- liquid states in kappa-(ET)(2)Cu-2(CN)(3) and beta'-[Pd(dmit)(2)](2)Z, and the need for high quality large single crystals.

Macromolecular interactions during gelatinisation and retrogradation in starch-whey systems as studied by rapid visco-analyser

Gelatinisation and retrogradation of starch-whey mixtures were studied in water (pH 7) using the Rapid Visco-Analyser (RVA). The starch:whey ratios ranged from 0:100 - 100:0. Wheat starch, and whey protein concentrate (about 80% solids basis) and isolate (about 96% solids basis) were used. Mixtures with whey isolates were generally more viscous than those with whey concentrates, and this was attributed to fewer non-protein milk components in the former. Whey protein concentrates and isolates reduced the peak, trough and final viscosities of the mixtures, but the breakdown and setback ratios of the mixtures were increased. The gelatinisation temperature increased with whey substitutions indicating that whey protein delayed starch gelatinisation. The temperature of fastest viscosity development decreased as the amount of whey was increased. Whey protein isolate generally exercised a lesser effect than the concentrate. At between 40 - 50% whey substitutions, the dominant phase changed from starch to protein irrespective of the source of the whey protein. An additive law poorly defined selected RVA parameters. Both macromolecules interacted to define the viscosity of the mixture, and an exponential model predicted the viscosity better than the additive law. The results obtained in this study are discussed to assist the understanding of extrusion processing of starch-whey systems as models for whey-fortified snack and ready-to-eat foods. Copyright ©2006 The Berkeley Electronic Press. All rights reserved.

GTM through time

The standard GTM (generative topographic mapping) algorithm assumes that the data on which it is trained consists of independent, identically distributed (iid) vectors. For time series, however, the iid assumption is a poor approximation. In this paper we show how the GTM algorithm can be extended to model time series by incorporating it as the emission density in a hidden Markov model. Since GTM has discrete hidden states we are able to find a tractable EM algorithm, based on the forward-backward algorithm, to train the model. We illustrate the performance of GTM through time using flight recorder data from a helicopter.

Brand extensions in emerging markets:theory development and testing in China

Brand extensions are increasingly used by multinational corporations in emerging markets such as China. However, understanding how consumers in the emerging markets evaluate brand extensions is hampered by a lack of research in the emerging markets contexts. To address the knowledge void, we built on an established brand extension evaluation framework in the West, namely Aaker and Keller (1990)1. Aaker , D. A. and Keller , K. L. 1990 . Consumer evaluations of brand extensions . Journal of Marketing , 54 ( 1 ) : 27 – 41 . [CrossRef], [Web of Science ®] View all references, and extended the model by incorporating two new factors: perceived fit based on brand image consistency and competition intensity in the brand extension category. The additions of two factors are made in recognition of the uniqueness of the considerations of consumers in the emerging markets in their brand extension evaluations. The extended model was tested by an empirical experiment using consumers in China. The results partly validated the Aaker and Keller model, and evidence that both newly added factors were significant in influencing consumers' evaluation of brand extensions was also found. More important, one new factor proposed, namely, consumer-perceived fit based on brand image consistency, was found to be more significant than all the factors in Aaker and Keller's original model, suggesting that the Aaker and Keller model may be limited in explaining how consumers in the emerging markets evaluate brand extensions. Further research implications and limitations are discussed in the paper.

Openness and economic growth

The themes of this thesis are that international trade and foreign direct investment (FDI) are closely related and that they have varying impacts on economic growth in countries at different stages of development. The thesis consists of three empirical studies. The first one examines the causal relationship between FDI and trade in China. The empirical study is based on a panel of bilateral data for China and 19 home countries/regions over the period 1984-98. The specific feature of the study is that econometric techniques designed specially for panel data are applied to test for unit roots and causality. The results indicate a virtuous procedure of development for China. The growth of China’s imports causes growth in inward FDI from a home country/region, which in turn causes the growth of exports from China to the home country/region. The growth of exports causes the growth of imports. This virtuous procedure is the result of China’s policy of opening to the outside world. China has been encouraging export-oriented FDI and reducing trade barriers. Such policy instruments should be further encouraged in order to enhance economic growth. In the second study, an extended gravity model is constructed to identify the main causes of recent trade growth in OECD countries. The specific features include (a) the explicit introduction of R&D and FDI as two important explanatory variables into an augmented gravity equation; (b) the adoption of a panel data approach, and (c) the careful treatment of endogeneity. The main findings are that the levels and similarities of market size, domestic R&D stock and inward FDI stock are positively related to the volume of bilateral trade, while the geographical distance, exchange rate and relative factor endowments, has a negative impact. These findings lend support to new trade, FDI and economic growth theories. The third study evaluates the impact of openness on growth in different country groups. This research distinguishes itself from many existing studies in three aspects: first, both trade and FDI are included in the measurement of openness. Second, countries are divided' into three groups according to their development stages to compare the roles of FDI and trade in different groups. Third, the possible problems of endogeneity and multicollinearity of FDI and trade are carefully dealt with in a panel data setting. The main findings are that FDI and trade are both beneficial to a country's development. However, trade has positive effects on growth in all country groups but FDI has positive effects on growth only in the country groups which have had moderate development. The findings suggest FDI and trade may affect growth under different conditions.

Visualisation of heterogeneous data with the generalised generative topographic mapping

Heterogeneous and incomplete datasets are common in many real-world visualisation applications. The probabilistic nature of the Generative Topographic Mapping (GTM), which was originally developed for complete continuous data, can be extended to model heterogeneous (i.e. containing both continuous and discrete values) and missing data. This paper describes and assesses the resulting model on both synthetic and real-world heterogeneous data with missing values.

Dynamic decision-making based on NFR for managing software variability and configuration selection

Due to dynamic variability, identifying the specific conditions under which non-functional requirements (NFRs) are satisfied may be only possible at runtime. Therefore, it is necessary to consider the dynamic treatment of relevant information during the requirements specifications. The associated data can be gathered by monitoring the execution of the application and its underlying environment to support reasoning about how the current application configuration is fulfilling the established requirements. This paper presents a dynamic decision-making infrastructure to support both NFRs representation and monitoring, and to reason about the degree of satisfaction of NFRs during runtime. The infrastructure is composed of: (i) an extended feature model aligned with a domain-specific language for representing NFRs to be monitored at runtime; (ii) a monitoring infrastructure to continuously assess NFRs at runtime; and (iii) a exible decision-making process to select the best available configuration based on the satisfaction degree of the NRFs. The evaluation of the approach has shown that it is able to choose application configurations that well fit user NFRs based on runtime information. The evaluation also revealed that the proposed infrastructure provided consistent indicators regarding the best application configurations that fit user NFRs. Finally, a benefit of our approach is that it allows us to quantify the level of satisfaction with respect to NFRs specification.

The analysis of bullwhip effect in a HMMS-type supply chain

The aim of the paper is to investigate the well-known bullwhip effect of supply chains. Control theoretic analysis of bullwhip effect is extensively analyzed in the literature with the Laplace transform. This paper tries to examine the effect for an extended Holt–Modigliani–Muth–Simon model. A two-stage supply chain (supplier–manufacturer) is studied with quadratic costs functional. It is assumed that both firms minimize the relevant costs. The order of the manufacturer is delayed with a known constant. Two cases are examined: supplier and manufacturer minimize the relevant costs decentralized, and a centralized decision rule. The question is answered, how to decrease the bullwhip effect.

Changes in mass and nutrient content of wood during decomposition in a south Florida mangrove forest

1. Large pools of dead wood in mangrove forests following disturbances such as hurricanes may influence nutrient fluxes. We hypothesized that decomposition of wood of mangroves from Florida, USA (Avicennia germinans, Laguncularia racemosa and Rhizophora mangle), and the consequent nutrient dynamics, would depend on species, location in the forest relative to freshwater and marine influences and whether the wood was standing, lying on the sediment surface or buried. 2. Wood disks (8–10 cm diameter, 1 cm thick) from each species were set to decompose at sites along the Shark River, either buried in the sediment, on the soil surface or in the air (above both the soil surface and high tide elevation). 3. A simple exponential model described the decay of wood in the air, and neither species nor site had any effect on the decay coefficient during the first 13 months of decomposition. 4. Over 28 months of decomposition, buried and surface disks decomposed following a two-component model, with labile and refractory components. Avicennia germinans had the largest labile component (18 ± 2% of dry weight), while Laguncularia racemosa had the lowest (10 ± 2%). Labile components decayed at rates of 0.37–23.71% month−1, while refractory components decayed at rates of 0.001–0.033% month−1. Disks decomposing on the soil surface had higher decay rates than buried disks, but both were higher than disks in the air. All species had similar decay rates of the labile and refractory components, but A. germinans exhibited faster overall decay because of a higher proportion of labile components. 5. Nitrogen content generally increased in buried and surface disks, but there was little change in N content of disks in the air over the 2-year study. Between 17% and 68% of total phosphorus in wood leached out during the first 2 months of decomposition, with buried disks having the greater losses, P remaining constant or increasing slightly thereafter. 6. Newly deposited wood from living trees was a short-term source of N for the ecosystem but, by the end of 2 years, had become a net sink. Wood, however, remained a source of P for the ecosystem. 7. As in other forested ecosystems, coarse woody debris can have a significant impact on carbon and nutrient dynamics in mangrove forests. The prevalence of disturbances, such as hurricanes, that can deposit large amounts of wood on the forest floor accentuates the importance of downed wood in these forests.

AdaptMCloud: uma estratégia para adaptação dinâmica de aplicações Multi-Cloud

Multi-Cloud Applications are composed of services offered by multiple cloud platforms where the user/developer has full knowledge of the use of such platforms. The use of multiple cloud platforms avoids the following problems: (i) vendor lock-in, which is dependency on the application of a certain cloud platform, which is prejudicial in the case of degradation or failure of platform services, or even price increasing on service usage; (ii) degradation or failure of the application due to fluctuations in quality of service (QoS) provided by some cloud platform, or even due to a failure of any service. In multi-cloud scenario is possible to change a service in failure or with QoS problems for an equivalent of another cloud platform. So that an application can adopt the perspective multi-cloud is necessary to create mechanisms that are able to select which cloud services/platforms should be used in accordance with the requirements determined by the programmer/user. In this context, the major challenges in terms of development of such applications include questions such as: (i) the choice of which underlying services and cloud computing platforms should be used based on the defined user requirements in terms of functionality and quality (ii) the need to continually monitor the dynamic information (such as response time, availability, price, availability), related to cloud services, in addition to the wide variety of services, and (iii) the need to adapt the application if QoS violations affect user defined requirements. This PhD thesis proposes an approach for dynamic adaptation of multi-cloud applications to be applied when a service is unavailable or when the requirements set by the user/developer point out that other available multi-cloud configuration meets more efficiently. Thus, this work proposes a strategy composed of two phases. The first phase consists of the application modeling, exploring the similarities representation capacity and variability proposals in the context of the paradigm of Software Product Lines (SPL). In this phase it is used an extended feature model to specify the cloud service configuration to be used by the application (similarities) and the different possible providers for each service (variability). Furthermore, the non-functional requirements associated with cloud services are specified by properties in this model by describing dynamic information about these services. The second phase consists of an autonomic process based on MAPE-K control loop, which is responsible for selecting, optimally, a multicloud configuration that meets the established requirements, and perform the adaptation. The adaptation strategy proposed is independent of the used programming technique for performing the adaptation. In this work we implement the adaptation strategy using various programming techniques such as aspect-oriented programming, context-oriented programming and components and services oriented programming. Based on the proposed steps, we tried to assess the following: (i) the process of modeling and the specification of non-functional requirements can ensure effective monitoring of user satisfaction; (ii) if the optimal selection process presents significant gains compared to sequential approach; and (iii) which techniques have the best trade-off when compared efforts to development/modularity and performance.

A Search for a New Particle Decaying to Pairs of Weak Gauge Bosons with the ATLAS Detector

A search for new heavy resonances decaying to boson pairs (WZ, WW or ZZ) using 20.3 inverse femtobarns of proton-proton collision data at a center of mass energy of 8 TeV is presented. The data were recorded by the ATLAS detector at the Large Hadron Collider (LHC) in 2012. The analysis combines several search channels with the leptonic, semi-leptonic and fully hadronic final states. The diboson invariant mass spectrum is studied for local excesses above the Standard Model background prediction, and no significant excess is observed for the combined analysis. 95$\%$ confidence limits are set on the cross section times branching ratios for three signal models: an extended gauge model with a heavy W boson, a bulk Randall-Sundrum model with a spin-2 graviton, and a simplified model with a heavy vector triplet. Among the individual search channels, the fully-hadronic channel is predominantly presented where boson tagging technique and jet substructure cuts are used. Local excesses are found in the dijet mass distribution around 2 TeV, leading to a global significance of 2.5 standard deviations. This deviation from the Standard Model prediction results in many theory explanations, and the possibilities could be further explored using the LHC Run 2 data.

Phase coexistence of cluster crystals: beyond the Gibbs phase rule

We report a study of the phase behavior of multiple-occupancy crystals through simulation. We argue that in order to reproduce the equilibrium behavior of such crystals it is essential to treat the number of lattice sites as a constraining thermodynamic variable. The resulting free-energy calculations thus differ considerably from schemes used for single-occupancy lattices. Using our approach, we obtain the phase diagram and the bulk modulus for a generalized exponential model that forms cluster crystals at high densities. We compare the simulation results with existing theoretical predictions. We also identify two types of density fluctuations that can lead to two sound modes and evaluate the corresponding elastic constants.