Generation, Estimation and Tracking of Faces

This thesis describes techniques for the construction of face models for both computer graphics and computer vision applications. It also details model-based computer vision methods for extracting and combining data with the model. Our face models respect the measurements of populations described by face anthropometry studies. In computer graphics, the anthropometric measurements permit the automatic generation of varied geometric models of human faces. This is accomplished by producing a random set of face measurements generated according to anthropometric statistics. A face fitting these measurements is realized using variational modeling. In computer vision, anthropometric data biases face shape estimation towards more plausible individuals. Having such a detailed model encourages the use of model-based techniques—we use a physics-based deformable model framework. We derive and solve a dynamic system which accounts for edges in the image and incorporates optical flow as a motion constraint on the model. Our solution ensures this constraint remains satisfied when edge information is used, which helps prevent tracking drift. This method is extended using the residuals from the optical flow solution. The extracted structure of the model can be improved by determining small changes in the model that reduce this error residual. We present experiments in extracting the shape and motion of a face from image sequences which exhibit the generality of our technique, as well as provide validation

An enigmatic decoupling between heat stress and coral bleaching on the Great Barrier Reef

Ocean warming threatens the functioning of coral reef ecosystems by inducing mass coral bleaching and mortality events. The link between temperature and coral bleaching is now well-established based on observations that mass bleaching events usually occur when seawater temperatures are anomalously high. However, times of high heat stress but without coral bleaching are equally important because they can inform an understanding of factors that regulate temperature-induced bleaching. Here, we investigate the absence of mass coral bleaching on the Great Barrier Reef (GBR) during austral summer 2004. Using four gridded sea surface temperature data products, validated with in situ temperature loggers, we demonstrate that the summer of 2004 was among the warmest summers of the satellite era (1982–2017) on the GBR. At least half of the GBR experienced temperatures that were high enough to initiate bleaching in other years, yet mass bleaching was not reported during 2004. The absence of bleaching is not fully explained by wind speed or cloud cover. Rather, 2004 is clearly differentiated from bleaching years by the slow speed of the East Australian Current (EAC) offshore of the GBR. An anomalously slow EAC during summer 2004 may have dampened the upwelling of nutrient-rich waters onto the GBR shelf, potentially mitigating bleaching due to the lower susceptibility of corals to heat stress in low-nutrient conditions. Although other factors such as irradiance or acclimatization may have played a role in the absence of mass bleaching, 2004 remains a key case study for demonstrating the dynamic nature of coral responses to marine heatwaves

Factors affecting B/Ca ratios in synthetic aragonite

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Chemical Geology 437 (2016): 67-76, doi:10.1016/j.chemgeo.2016.05.007.Measurements of B/Ca ratios in marine carbonates have been suggested to record seawater carbonate chemistry, however experimental calibration of such proxies based on inorganic partitioning remains limited. Here we conducted a series of synthetic aragonite precipitation experiments to evaluate the factors influencing the partitioning of B/Ca between aragonite and seawater. Our results indicate that the B/Ca ratio of synthetic aragonites depends primarily on the relative concentrations of borate and carbonate ions in the solution from which the aragonite precipitates; not on bicarbonate concentration as has been previously suggested. The influence of temperature was not significant over the range investigated (20 – 40°C), however, partitioning may be influenced by saturation state (and/or growth rate). Based on our experimental results, we suggest that aragonite B/Ca ratios can be utilized as a proxy of [CO32-]. Boron isotopic composition (δ11B) is an established pH proxy, thus B/Ca and δ11B together allow the full carbonate chemistry of the solution from which the aragonite precipitated to be calculated. To the extent that aragonite precipitation by marine organisms is affected by seawater chemistry, B/Ca may also prove useful in reconstructing seawater chemistry. A simplified boron purification protocol based on amberlite resin and the organic buffer TRIS is also described.This work was supported by the Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies. Research conducted at WHOI was supported by NSF grant OCE-1338320. M.H. was supported by an ARC Super Science Fellowship and an NSF International Postdoctoral Fellowship. T.D. was supported by a NSF Graduate Research Fellowship. M.M. was supported by a Western Australian Premiers Fellowship and an ARC Laureate Fellowship

Coral biomineralization, climate proxies and the sensitivity of coral reefs to CO2-driven climate change

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2017Scleractinian corals extract calcium (Ca2+) and carbonate (CO2−3) ions from seawater to construct their calcium carbonate (CaCO3) skeletons. Key to the coral biomineralization process is the active elevation of the CO2−3 concentration of the calcifying fluid to achieve rapid nucleation and growth of CaCO3 crystals. Coral skeletons contain valuable records of past climate variability and contribute to the formation of coral reefs. However, limitations in our understanding of coral biomineralization hinder the accuracy of (1) coral-based reconstructions of past climate, and (2) predictions of coral reef futures as anthropogenic CO2 emissions drive declines in seawater CO2−3 concentration. In this thesis, I investigate the mechanism of coral biomineralization and evaluate the sensitivity of coral reef CaCO3 production to seawater carbonate chemistry. First, I conducted abiogenic CaCO3 precipitation experiments that identified the U/Ca ratio as a proxy for fluid CO2−3 concentration. Based on these experimental results, I developed a quantitative coral biomineralization model that predicts temperature can be reconstructed from coral skeletons by combining Sr/Ca - which is sensitive to both temperature and CO2−3 - with U/Ca into a new proxy called “Sr-U”. I tested this prediction with 14 corals from the Pacific Ocean and the Red Sea spanning mean annual temperatures of 25.7-30.1°C and found that Sr-U has uncertainty of only 0.5°C, twice as accurate as conventional coral-based thermometers. Second, I investigated the processes that differentiate reef-water and open-ocean carbonate chemistry, and the sensitivity of ecosystem-scale calcification to these changes. On Dongsha Atoll in the northern South China Sea, metabolic activity of resident organisms elevates reef-water CO2−3 twice as high as the surrounding open ocean, driving rates of ecosystem calcification higher than any other coral reef studied to date. When high temperatures stressed the resident coral community, metabolic activity slowed, with dramatic effects on reef-water chemistry and ecosystem calcification. Overall, my thesis highlights how the modulation of CO2−3, by benthic communities on the reef and individual coral polyps in the colony, controls the sensitivity of coral reefs to future ocean acidification and influences the climate records contained in the skeleton.This research was funded by a National Science Foundation (NSF) Graduate Research Fellowship, NSF grants OCE 1041106, OCE 1338320, and OCE 1220529, by a thematic project at Academia Sinica, Taiwan, the WHOI Ocean Ventures Fund, and by the WHOI Coastal Ocean Institute

Coral reef drag coefficients – water depth dependence

Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 1061-1075, doi:10.1175/JPO-D-16-0248.1.A major challenge in modeling the circulation over coral reefs is uncertainty in the drag coefficient because existing estimates span two orders of magnitude. Current and pressure measurements from five coral reefs are used to estimate drag coefficients based on depth-average flow, assuming a balance between the cross-reef pressure gradient and the bottom stress. At two sites wind stress is a significant term in the cross-reef momentum balance and is included in estimating the drag coefficient. For the five coral reef sites and a previous laboratory study, estimated drag coefficients increase as the water depth decreases consistent with open channel flow theory. For example, for a typical coral reef hydrodynamic roughness of 5 cm, observational estimates, and the theory indicate that the drag coefficient decreases from 0.4 in 20 cm of water to 0.005 in 10 m of water. Synthesis of results from the new field observations with estimates from previous field and laboratory studies indicate that coral reef drag coefficients range from 0.2 to 0.005 and hydrodynamic roughnesses generally range from 2 to 8 cm. While coral reef drag coefficients depend on factors such as physical roughness and surface waves, a substantial fraction of the scatter in estimates of coral reef drag coefficients is due to variations in water depth.The Red Sea field program was supported by Awards USA 00002 and KSA 00011 made by KAUST to S. Lentz and J. Churchill. The Palau field program was funded by NSF Award OCE-1220529

Relationship between water and aragonite barium concentrations in aquaria reared juvenile corals

This paper is not subject to U.S. copyright. The definitive version was published in Geochimica et Cosmochimica Acta 209 (2017): 123-134, doi:10.1016/j.gca.2017.04.006.Coral barium to calcium (Ba/Ca) ratios have been used to reconstruct records of upwelling, river and groundwater discharge, and sediment and dust input to the coastal ocean. However, this proxy has not yet been explicitly tested to determine if Ba inclusion in the coral skeleton is directly proportional to seawater Ba concentration and to further determine how additional factors such as temperature and calcification rate control coral Ba/Ca ratios. We measured the inclusion of Ba within aquaria reared juvenile corals (Favia fragum) at three temperatures (∼27.7, 24.6 and 22.5 °C) and three seawater Ba concentrations (73, 230 and 450 nmol kg−1). Coral polyps were settled on tiles conditioned with encrusting coralline algae, which complicated chemical analysis of the coral skeletal material grown during the aquaria experiments. We utilized Sr/Ca ratios of encrusting coralline algae (as low as 3.4 mmol mol−1) to correct coral Ba/Ca for this contamination, which was determined to be 26 ± 11% using a two end member mixing model. Notably, there was a large range in Ba/Ca across all treatments, however, we found that Ba inclusion was linear across the full concentration range. The temperature sensitivity of the distribution coefficient is within the range of previously reported values. Finally, calcification rate, which displayed large variability, was not correlated to the distribution coefficient. The observed temperature dependence predicts a change in coral Ba/Ca ratios of 1.1 μmol mol−1 from 20 to 28 °C for typical coastal ocean Ba concentrations of 50 nmol kg−1. Given the linear uptake of Ba by corals observed in this study, coral proxy records that demonstrate peaks of 10–25 μmol mol−1 would require coastal seawater Ba of between 60 and 145 nmol kg−1. Further validation of the coral Ba/Ca proxy requires evaluation of changes in seawater chemistry associated with the environmental perturbation recorded by the coral as well as verification of these results for Porites species, which are widely used in paleo reconstructions.M.E.G. was supported by a NDSEG graduate fellowship. Funding for this research came from the NSF Chemical Oceanography program (OCE-0751525) and the Coastal Ocean Institute, the Ocean and Climate Change Institute and the Ocean Ventures Fund at Woods Hole Oceanographic Institution

Climate modulates internal wave activity in the Northern South China Sea

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 42 (2015): 831–838, doi:10.1002/2014GL062522.Internal waves (IWs) generated in the Luzon Strait propagate into the Northern South China Sea (NSCS), enhancing biological productivity and affecting coral reefs by modulating nutrient concentrations and temperature. Here we use a state-of-the-art ocean data assimilation system to reconstruct water column stratification in the Luzon Strait as a proxy for IW activity in the NSCS and diagnose mechanisms for its variability. Interannual variability of stratification is driven by intrusions of the Kuroshio Current into the Luzon Strait and freshwater fluxes associated with the El Niño–Southern Oscillation. Warming in the upper 100 m of the ocean caused a trend of increasing IW activity since 1900, consistent with global climate model experiments that show stratification in the Luzon Strait increases in response to radiative forcing. IW activity is expected to increase in the NSCS through the 21st century, with implications for mitigating climate change impacts on coastal ecosystems.This work was supported by NSF award 1220529 to Anne Cohen, by the Academia Sinica (Taiwan) through a thematic project grant to G.T.F.W. and Anne Cohen, by the Alfred P. Sloan Foundation and the WHOI Oceans and Climate Change Institute/Moltz Fellowship through awards to K.B.K., and by an NSF Graduate Research Fellowship to T.M.D.2015-08-1

Folsom Mammoth Hunters? The Terminal Pleistocene Assemblage from Owl Cave (10BV30), Wasden Site, Idaho

The 1960s and 1970s excavations at Owl Cave (10BV30) recovered mammoth bone and Folsom-like points from the same strata, suggesting evidence for a post-Clovis mammoth kill. However, a synthesis of the excavation data was never published, and the locality has since been purged from the roster of sites with human / extinct megafauna associations. Here, we present data on bone from the oldest stratum, review provenience data, conduct a bone-surface modification study, and present the results of a protein-residue analysis. Our study fails to make the case for mammoth hunting by Folsom peoples. Although two of the fragments tested positive for horse or elephant protein, recent AMS dates indicate that all mammoth remains predate Folsom, and horse remains absent from the Owl Cave collection. Further, In unambiguously cultural surface modifications were identified on any of the mammoth remains. Given the available data, the Owl Cave deposits are most parsimoniously read as containing a Folsom-age occupation in the buried context, the first of its kind in the West West, but one nonetheless part of the Palimpsest of Pleistocene materials terminal

A framework for digital sunken relief generation based on 3D geometric models

Sunken relief is a special art form of sculpture whereby the depicted shapes are sunk into a given surface. This is traditionally created by laboriously carving materials such as stone. Sunken reliefs often utilize the engraved lines or strokes to strengthen the impressions of a 3D presence and to highlight the features which otherwise are unrevealed. In other types of reliefs, smooth surfaces and their shadows convey such information in a coherent manner. Existing methods for relief generation are focused on forming a smooth surface with a shallow depth which provides the presence of 3D figures. Such methods unfortunately do not help the art form of sunken reliefs as they omit the presence of feature lines. We propose a framework to produce sunken reliefs from a known 3D geometry, which transforms the 3D objects into three layers of input to incorporate the contour lines seamlessly with the smooth surfaces. The three input layers take the advantages of the geometric information and the visual cues to assist the relief generation. This framework alters existing techniques in line drawings and relief generation, and then combines them organically for this particular purpose

Comparison of equatorial Pacific sea surface temperature variability and trends with Sr/Ca records from multiple corals

Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 31 (2016): 252–265, doi:10.1002/2015PA002897.Coral Sr/Ca is widely used to reconstruct past ocean temperatures. However, some studies report different Sr/Ca-temperature relationships for conspecifics on the same reef, with profound implications for interpretation of reconstructed temperatures. We assess whether these differences are attributable to small-scale oceanographic variability or “vital effects” associated with coral calcification and quantify the effect of intercolony differences on temperature estimates and uncertainties. Sr/Ca records from four massive Porites colonies growing on the east and west sides of Jarvis Island, central equatorial Pacific, were compared with in situ logger temperatures spanning 2002–2012. In general, Sr/Ca captured the occurrence of interannual sea surface temperature events but their amplitude was not consistently recorded by any of the corals. No long-term trend was identified in the instrumental data, yet Sr/Ca of one coral implied a statistically significant cooling trend while that of its neighbor implied a warming trend. Slopes of Sr/Ca-temperature regressions from the four different colonies were within error, but offsets in mean Sr/Ca rendered the regressions statistically distinct. Assuming that these relationships represent the full range of Sr/Ca-temperature calibrations in Jarvis Porites, we assessed how well Sr/Ca of a nonliving coral with an unknown Sr/Ca-temperature relationship can constrain past temperatures. Our results indicate that standard error of prediction methods underestimate the actual error as we could not reliably reconstruct the amplitude or frequency of El Niño–Southern Oscillation events as large as ± 2°C. Our results underscore the importance of characterizing the full range of temperature-Sr/Ca relationships at each study site to estimate true error.This study was supported by an NSF Graduate Research Fellowship to A.A. and by NSF-OCE-0926986 and NSF-OCE-1031971.2016-08-0