Submodular Optimization and Data Processing

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

Effect of early marine diagenesis on coral reconstructions of surface-ocean 13C/12C and carbonate saturation state

Recent research suggests that future decreases in the carbonate saturation state of surface seawater associated with the projected build-up of atmospheric CO2 could cause a global decline in coral reef-building capacity. Whether significant reductions in coral calcification are underway is a matter of considerable debate. Multicentury records of skeletal calcification extracted from massive corals have the potential to reconstruct the progressive effect of anthropogenic changes in carbonate saturation on coral reefs. However, early marine aragonite cements are commonly precipitated from pore waters in the basal portions of massive coral skeletons and, if undetected, could result in apparent nonlinear reductions in coral calcification toward the present. To address this issue, we present records of coral skeletal density, extension rate, calcification rate, δ13C, and δ18O for well preserved and diagenetically altered coral cores spanning ∼1830-1994 A.D. at Ningaloo Reef Marine Park, Western Australia. The record for the pristine coral shows no significant decrease in skeletal density or δ13C indicative of anthropogenic changes in carbonate saturation state or δ13C of surface seawater (oceanic Suess effect). In contrast, progressive addition of early marine inorganic aragonite toward the base of the altered coral produces an apparent ∼25% decrease in skeletal density toward the present, which misleadingly matches the nonlinear twentieth century decrease in coral calcification predicted by recent modeling and experimental studies. In addition, the diagenetic aragonite is enriched in 13C, relative to coral aragonite, resulting in a nonlinear decrease in δ13C toward the present that mimics the decrease in δ13C expected from the oceanic Suess effect. Taken together, these diagenetic changes in skeletal density and δ13C could be misinterpreted to reflect changes in surface-ocean carbonate saturation state driven by the twentieth century build-up of atmospheric CO2. Copyright 2004 by the American Geophysical Union.

Rare earth element geochemistry of Late Devonian reefal carbonates, canning basin, Western Australia: Confirmation of a seawater REE proxy in ancient limestones

Rare earth element and yttrium (REE+Y) concentrations were determined in 49 Late Devonian reefal carbonates from the Lennard Shelf, Canning Basin, Western Australia. Shale-normalized (SN) REE+Y patterns of the Late Devonian samples display features consistent with the geochemistry of well-oxygenated, shallow seawater. A variety of different ancient limestone components, including microbialites, some skeletal carbonates (stromatoporoids), and cements, record seawater-like REE+Y signatures. Contamination associated with phosphate, Fe-oxides and shale was tested quantitatively, and can be discounted as the source of the REE+Y patterns. Co-occurring carbonate components that presumably precipitated from the same seawater have different relative REE concentrations, but consistent REE+Y patterns. Clean Devonian early marine cements (n = 3) display REE+Y signatures most like that of modern open ocean seawater and the highest Y/Ho ratios (e.g., 59) and greatest light REE (LREE) depletion (average Nd-SN/Yb-SN = 0.413, SD = 0.076). However, synsedimentary cements have the lowest REE concentrations (e.g., 405 ppb). Non-contaminated Devonian microbialite samples containing a mixture of the calcimicrobe Renalcis and micritic thrombolite aggregates in early marine cement (n = 11) have the highest relative REE concentrations of tested carbonates (average total REE = 11.3 ppm). Stromatoporoid skeletons, unlike modern corals, algae and molluscs, also contain well-developed, seawater-like REE patterns. Samples from an estuarine fringing reef have very different REE+Y patterns with LREE enrichment (Nd-SN/Yb-SN > 1), possibly reflecting inclusion of estuarine colloidal material that contained preferentially scavenged LREE from a nearby riverine input source. Hence, Devonian limestones provide a proxy for marine REE geochemistry and allow the differentiation of co-occurring water masses on the ancient Lennard Shelf. Although appropriate partition coefficients for quantification of Devonian seawater REE concentrations from out data are unknown, hypothetical Devonian Canning Basin seawater REE patterns were obtained with coefficients derived from modern natural proxies and experimental values. Resulting Devonian seawater patterns are slightly enriched in LREE compared to most modem seawaters and suggest higher overall REE concentrations, but are very similar to seawaters from regions with high terrigenous inputs. Our results suggest that most limestones should record important aspects of the REE geochemistry of the waters in which they precipitated, provided they are relatively free of terrigenous contamination and major diagenetic alteration from fluids with high, non-seawater-like REE contents. Hence, we expect that many other ancient limestones will serve as seawater REE proxies, and thereby provide information on paleoceanography, paleogeography and geochemical evolution of the oceans. Copyright (C) 2004 Elsevier Ltd.

Endolithic algae photoacclimate to increased irradiance during coral bleaching

The photoacclimation of endolithic algae ( of the genus Ostreobium) inhabiting the skeleton of the Mediterranean coral Oculina patagonica during a bleaching event was examined. Pulse amplitude modulated (PAM) chlorophyll fluorescence techniques in situ were used to assess the photosynthetic efficiency of endolithic algae in the coral skeleton and the symbiotic dinoflagellates (zooxanthellae) in the coral tissue. Relative photosynthetic electron transport rates (ETRs) of the endolithic algae under bleached areas of the colony were significantly higher than those of endolithic algae from a healthy section of the colony and those of zooxanthellae isolated from the same section. Endolithic algae under healthy parts of the colony demonstrated an ETRmax of 16.5% that of zooxanthellae from tissue in the same section whereas endolithic algae under bleached sections showed ETRmax values that were 39% of those found for healthy zooxanthellae. The study demonstrates that endolithic algae undergo photoacclimation with increased irradiance reaching the skeleton. As PAM fluorometry has become a major tool for assessing levels of stress and bleaching in corals, the importance of considering the contribution of the endolithic algae to the overall chlorophyll fluorescence measured is highlighted.

An expert system on design of liquid-retaining structures with blackboard architecture

The design of liquid-retaining structures involves many decisions to be made by the designer based on rules of thumb, heuristics, judgement, codes of practice and previous experience. Structural design problems are often ill structured and there is a need to develop programming environments that can incorporate engineering judgement along with algorithmic tools. Recent developments in artificial intelligence have made it possible to develop an expert system that can provide expert advice to the user in the selection of design criteria and design parameters. This paper introduces the development of an expert system in the design of liquid-retaining structures using blackboard architecture. An expert system shell, Visual Rule Studio, is employed to facilitate the development of this prototype system. It is a coupled system combining symbolic processing with traditional numerical processing. The expert system developed is based on British Standards Code of Practice BS8007. Explanations are made to assist inexperienced designers or civil engineering students to learn how to design liquid-retaining structures effectively and sustainably in their design practices. The use of this expert system in disseminating heuristic knowledge and experience to practitioners and engineering students is discussed.

Coral mortality increases wave energy reaching shores protected by reef flats: Examples from the Seychelles

In the granitic Seychelles, many shores and beaches are fringed by coral reef flats which provide protection to shores from erosion by waves. The surfaces of these reef flats support a complex ecology. About 10 years ago their seaward zones were extensively covered by a rich coral growth, which reached approximately to mean low water level, but in 1998 this was largely killed by seawater warming. The resulting large expanses of dead coral skeletons in these locations are now disintegrating, and much of the subsequent modest recovery by new coral recruitment was set back by further mortalities. A mathematical model of wave energy reaching shorelines protected by coral reef flats has been applied to 14 Seychelles reefs. It is derived from equations which predict: (1) the raised water level, or wave set-up, on reef flats resulting from wave breaking, which depends upon offshore wave height and period, depth of still water over the reef flat and the reef crest profile, and (2) the decay of energy from reef edge to shoreline that is affected by width of reef flat, surface roughness, sea level rise and 'pseudo-sea level rise' created by increased depth resulting from disintegration of coral colonies. The model treats each reef as one entity, but because biota and zonation on reef flats are not homogenous, all reefs are divided into four zones. In each, cover by both living and dead biota was estimated for calculation of parameters, and then averaged to obtain input data for the model. All possible biological factors were taken into account, such as the ability of seagrass beds to grow upwards to match expected sea level rise, reduction in height of the reef flat in relation to sea level as zones of dead corals decay, and the observed 'rounding' of reef crests as erosion removes corals from those areas. Estimates were also made of all these factors for a time approximately a decade ago, representing a time before the mass coral mortality, and for approximately a decade in the future when the observed rapid state of dead coral colony disintegration is assumed to have reached an end point. Results of increased energy over the past decade explain observations of erosion in some sites in the Seychelles. Most importantly, it is estimated that the rise in energy reaching shores protected by fringing reefs will now accelerate more rapidly, such that the increase expected over the next decade will be approximately double than that seen over the past decade. (c) 2005 Elsevier Ltd. All rights reserved.

Effects of the herbicide diuron on the early life history stages of coral

The effects of the herbicide diuron on the early life history stages of broadcast spawning and brooding corals were examined in laboratory experiments. Fertilisation of Acropora millepora and Montipora aequituberculata oocytes were not inhibited at diuron concentrations of up to 1000 mu gl(-1). Metamorphosis of symbiont-free A. millepora larvae was only significantly inhibited at 300 mu gl(-1) diuron. Pocillopora damicornis larvae, which contain symbiotic dinoflagellates, were able to undergo metamorphosis after 24h exposure to diuron at 1000 mu gl(-1). Two-week old P. damicornis recruits on the other hand were as susceptible to diuron as adult colonies, with expulsion of symbiotic dinoflagellates (bleaching) evident at 10 mu gl(-1) diuron after 96 h exposure. Reversible metamorphosis was observed at high diuron concentrations, with fully bleached polyps escaping from their skeletons. Pulse amplitude modulation (PAM) chlorophyll fluorescence techniques demonstrated a reduction in photosynthetic efficiency (Delta F/F'(m)) in illuminated P. dami- cornis recruits after a 2h exposure to 1 mu gl(-1) diuron. The dark-adapted quantum yields (F-v/F-m also declined, indicating chronic photoinhibition and damage to photosystem H. Crown Copyright (c) 2004 Published by Elsevier Ltd. All rights reserved.

Heavy tails, importance sampling and cross-entropy

We consider the problem of estimating P(Yi + (...) + Y-n > x) by importance sampling when the Yi are i.i.d. and heavy-tailed. The idea is to exploit the cross-entropy method as a toot for choosing good parameters in the importance sampling distribution; in doing so, we use the asymptotic description that given P(Y-1 + (...) + Y-n > x), n - 1 of the Yi have distribution F and one the conditional distribution of Y given Y > x. We show in some specific parametric examples (Pareto and Weibull) how this leads to precise answers which, as demonstrated numerically, are close to being variance minimal within the parametric class under consideration. Related problems for M/G/l and GI/G/l queues are also discussed.

Tolerance of endolithic algae to elevated temperature and light in the coral Montipora monasteriata from the southern Great Barrier Reef

Photosynthetic endolithic algae and cyanobacteria live within the skeletons of many scleractinians. Under normal conditions, less than 5% of the photosynthetically active radiation (PAR) reaches the green endolithic algae because of the absorbance of light by the endosymbiotic dinoflagellates and the carbonate skeleton. When corals bleach (loose dinoflagellate symbionts), however, the tissue of the corals become highly transparent and photosynthetic microendoliths may be exposed to high levels of both thermal and solar stress. This study explores the consequence of these combined stresses on the phototrophic endoliths inhabiting the skeleton of Montipora monasteriata, growing at Heron Island, on the southern Great Barrier Reef. Endoliths that were exposed to sun after tissue removal were by far more susceptible to thermal photoinhibition and photo-damage than endoliths under coral tissue that contained high concentrations of brown dinoflagellate symbionts. While temperature or light alone did not result in decreased photosynthetic efficiency of the endoliths, combined thermal and solar stress caused a major decrease and delayed recovery. Endoliths protected under intact tissue recovered rapidly and photoacclimated soon after exposure to elevated sea temperatures. Endoliths under naturally occurring bleached tissue of M. monasteriata colonies (bleaching event in March 2004 at Heron Island) acclimated to increased irradiance as the brown symbionts disappeared. We suggest that two major factors determine the outcome of thermal bleaching to the endolith community. The first is the microhabitat and light levels under which a coral grows, and the second is the susceptibility of the coral-dinoflagellates symbiosis to thermal stress. More resistant corals may take longer to bleach allowing endoliths time to acclimate to a new light environment. This in turn may have implications for coral survival.

Efficient accommodation of local minima in watershed model calibration

The Gauss-Marquardt-Levenberg (GML) method of computer-based parameter estimation, in common with other gradient-based approaches, suffers from the drawback that it may become trapped in local objective function minima, and thus report optimized parameter values that are not, in fact, optimized at all. This can seriously degrade its utility in the calibration of watershed models where local optima abound. Nevertheless, the method also has advantages, chief among these being its model-run efficiency, and its ability to report useful information on parameter sensitivities and covariances as a by-product of its use. It is also easily adapted to maintain this efficiency in the face of potential numerical problems (that adversely affect all parameter estimation methodologies) caused by parameter insensitivity and/or parameter correlation. The present paper presents two algorithmic enhancements to the GML method that retain its strengths, but which overcome its weaknesses in the face of local optima. Using the first of these methods an intelligent search for better parameter sets is conducted in parameter subspaces of decreasing dimensionality when progress of the parameter estimation process is slowed either by numerical instability incurred through problem ill-posedness, or when a local objective function minimum is encountered. The second methodology minimizes the chance of successive GML parameter estimation runs finding the same objective function minimum by starting successive runs at points that are maximally removed from previous parameter trajectories. As well as enhancing the ability of a GML-based method to find the global objective function minimum, the latter technique can also be used to find the locations of many non-global optima (should they exist) in parameter space. This can provide a useful means of inquiring into the well-posedness of a parameter estimation problem, and for detecting the presence of bimodal parameter and predictive probability distributions. The new methodologies are demonstrated by calibrating a Hydrological Simulation Program-FORTRAN (HSPF) model against a time series of daily flows. Comparison with the SCE-UA method in this calibration context demonstrates a high level of comparative model run efficiency for the new method. (c) 2006 Elsevier B.V. All rights reserved.

Phototrophic microendoliths bloom during coral "white syndrome"

Following rapid lesion progression of white syndrome in tabular Acropora spp., the white bare skeleton gradually changes to green, a result of endolithic algae blooms (primarily Ostreobium spp.). Endolithic algal biomass and chlorophyll concentration were found to be an order of magnitude higher in the green zone compared with healthy appearing parts of each colony. Chl b to Chl a ratio increased from 1:1.6 in the healthy area to 1:2 and 1:3.5 in the white exposed skeleton and green zones, respectively. These observations together with pulse amplitude modulated (PAM) fluorometry suggest photoacclimation of the endoliths in the green zone. Histopathological microscopy revealed that the endolithic algal filaments penetrate the coral tissue. This study highlights the interaction of endolithic algae with both the skeleton and host tissue. This may have a critical role in the processes that accompany the post-disease state in reef-building corals.

A rapidly evolving secretome builds and patterns a sea shell

Background: Instructions to fabricate mineralized structures with distinct nanoscale architectures, such as seashells and coral and vertebrate skeletons, are encoded in the genomes of a wide variety of animals. In mollusks, the mantle is responsible for the extracellular production of the shell, directing the ordered biomineralization of CaCO3 and the deposition of architectural and color patterns. The evolutionary origins of the ability to synthesize calcified structures across various metazoan taxa remain obscure, with only a small number of protein families identified from molluskan shells. The recent sequencing of a wide range of metazoan genomes coupled with the analysis of gene expression in non-model animals has allowed us to investigate the evolution and process of biomineralization in gastropod mollusks. Results: Here we show that over 25% of the genes expressed in the mantle of the vetigastropod Haliotis asinina encode secreted proteins, indicating that hundreds of proteins are likely to be contributing to shell fabrication and patterning. Almost 85% of the secretome encodes novel proteins; remarkably, only 19% of these have identifiable homologues in the full genome of the patellogastropod Lottia scutum. The spatial expression profiles of mantle genes that belong to the secretome is restricted to discrete mantle zones, with each zone responsible for the fabrication of one of the structural layers of the shell. Patterned expression of a subset of genes along the length of the mantle is indicative of roles in shell ornamentation. For example, Has-sometsuke maps precisely to pigmentation patterns in the shell, providing the first case of a gene product to be involved in molluskan shell pigmentation. We also describe the expression of two novel genes involved in nacre (mother of pearl) deposition. Conclusion: The unexpected complexity and evolvability of this secretome and the modular design of the molluskan mantle enables diversification of shell strength and design, and as such must contribute to the variety of adaptive architectures and colors found in mollusk shells. The composition of this novel mantle-specific secretome suggests that there are significant molecular differences in the ways in which gastropods synthesize their shells.

Evolving noisy oscillatory dynamics in genetic regulatory networks

We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.

Inference and optimization of real edges on sparse graphs:A statistical physics perspective

Inference and optimization of real-value edge variables in sparse graphs are studied using the Bethe approximation and replica method of statistical physics. Equilibrium states of general energy functions involving a large set of real edge variables that interact at the network nodes are obtained in various cases. When applied to the representative problem of network resource allocation, efficient distributed algorithms are also devised. Scaling properties with respect to the network connectivity and the resource availability are found, and links to probabilistic Bayesian approximation methods are established. Different cost measures are considered and algorithmic solutions in the various cases are devised and examined numerically. Simulation results are in full agreement with the theory. © 2007 The American Physical Society.

Differences between theoretical predictions and operational performance in a stock control application

Over the past decade, several experienced Operational Researchers have advanced the view that the theoretical aspects of model building have raced ahead of the ability of people to use them. Consequently, the impact of Operational Research on commercial organisations and the public sector is limited, and many systems fail to achieve their anticipated benefits in full. The primary objective of this study is to examine a complex interactive Stock Control system, and identify the reasons for the differences between the theoretical expectations and the operational performance. The methodology used is to hypothesise all the possible factors which could cause a divergence between theory and practice, and to evaluate numerically the effect each of these factors has on two main control indices - Service Level and Average Stock Value. Both analytical and empirical methods are used, and simulation is employed extensively. The factors are divided into two main categories for analysis - theoretical imperfections in the model, and the usage of the system by Buyers. No evidence could be found in the literature of any previous attempts to place the differences between theory and practice in a system in quantitative perspective nor, more specifically, to study the effects of Buyer/computer interaction in a Stock Control system. The study reveals that, in general, the human factors influencing performance are of a much higher order of magnitude than the theoretical factors, thus providing objective evidence to support the original premise. The most important finding is that, by judicious intervention into an automatic stock control algorithm, it is possible for Buyers to produce results which not only attain but surpass the algorithmic predictions. However, the complexity and behavioural recalcitrance of these systems are such that an innately numerate, enquiring type of Buyer needs to be inducted to realise the performance potential of the overall man/computer system.