High resolution ultrastructural mapping of total calcium: electron spectroscopic imaging/electron energy loss spectroscopy analysis of a physically/chemically processed nerve-muscle preparation.

We report on a procedure for tissue preparation that combines thoroughly controlled physical and chemical treatments: quick-freezing and freeze-drying followed by fixation with OsO4 vapors and embedding by direct resin infiltration. Specimens of frog cutaneous pectoris muscle thus prepared were analyzed for total calcium using electron spectroscopic imaging/electron energy loss spectroscopy (ESI/EELS) approach. The preservation of the ultrastructure was excellent, with positive K/Na ratios revealed in the fibers by x-ray microanalysis. Clear, high-resolution EELS/ESI calcium signals were recorded from the lumen of terminal cisternae of the sarcoplasmic reticulum but not from longitudinal cisternae, as expected from previous studies carried out with different techniques. In many mitochondria, calcium was below detection whereas in others it was appreciable although at variable level. Within the motor nerve terminals, synaptic vesicles as well as some cisternae of the smooth endoplasmic reticulum yielded positive signals at variance with mitochondria, that were most often below detection. Taken as a whole, the present study reveals the potential of our experimental approach to map with high spatial resolution the total calcium within individual intracellular organelles identified by their established ultrastructure, but only where the element is present at high levels.

Spatial heterogeneity of inhibitory surrounds in the middle temporal visual area.

A recurrent theme in the organization of vertebrate visual cortex is that of receptive fields with an associated "silent" opponency component. In the middle temporal area (area MT), a cortical visual area involved in the analysis of retinal motion in primates, this opponency appears in the form of a region outside the classical receptive field (CRF) that in itself gives no response but suppresses responses to motion evoked within the CRF. This antagonistic motion surround has been described as very large and symmetrically arrayed around the CRF. On the basis of this view, the primary function of the surround has long been thought to consist of simple figure-ground segregation based on movement. We have made use of small stimulus patches to map the form and extent of the surround and find evidence that the surround inhibition of many MT cells is in fact confined to restricted regions on one side or on opposite sides of the CRF. Such regions endow MT cells with the ability to make local-to-local motion comparisons, capable of extracting more complex features from the visual environment, and as such, may be better viewed as intrinsic parts of the receptive field, rather than as separate entities responsible for local-to-global comparisons.

Stability and sensitivity analysis of Be-CoDiS, an epidemiological model to predict the spread of human diseases between countries. Validation with data from the 2014-16 West African Ebola Virus Disease epidemic.

Ebola virus disease is a lethal human and primate disease that requires a particular attention from the international health authorities due to important recent outbreaks in some Western African countries and isolated cases in European and North-America continents. Regarding the emergency of this situation, various decision tools, such as mathematical models, were developed to assist the authorities to focus their efforts in important factors to eradicate Ebola. In a previous work, we have proposed an original deterministic spatial-temporal model, called Be-CoDiS (Between-Countries Disease Spread), to study the evolution of human diseases within and between countries by taking into consideration the movement of people between geographical areas. This model was validated by considering numerical experiments regarding the 2014-16 West African Ebola Virus Disease epidemic. In this article, we propose to perform a stability analysis of Be-CoDiS. Our first objective is to study the equilibrium states of simplified versions of this model, limited to the cases of one an two countries, and to determine their basic reproduction ratios. Then, in order to give some recommendations for the allocation of resources used to control the disease, we perform a sensitivity analysis of those basic reproduction ratios regarding the model parameters. Finally, we validate the obtained results by considering numerical experiments based on data from the 2014-16 West African Ebola Virus Disease epidemic.

Forensic analysis of buildings affected by mining subsidence based on Differential Interferometry (Part III)

This work presents a forensic analysis of buildings affected by mining subsidence, which is based on deformation data obtained by Differential Interferometry (DInSAR). The proposed test site is La Union village (Murcia, SE Spain) where subsidence was triggered in an industrial area due to the collapse of abandoned underground mining labours occurred in 1998. In the first part of this work the study area was introduced, describing the spatial and temporal evolution of ground subsidence, through the elaboration of a cracks map on the buildings located within the affected area. In the second part, the evolution of the most significant cracks found in the most damaged buildings was monitored using biaxial extensometric units and inclinometers. This article describes the work performed in the third part, where DInSAR processing of satellite radar data, available between 1998 and 2008, has permitted to determine the spatial and temporal evolution of the deformation of all the buildings of the study area in a period when no continuous in situ instrumental data is available. Additionally, the comparison of these results with the forensic data gathered in the 2005–2008 period, reveal that there is a coincidence between damaged buildings, buildings where extensometers register significant movements of cracks, and buildings deformation estimated from radar data. As a result, it has been demonstrated that the integration of DInSAR data into forensic analysis methodologies contributes to improve significantly the assessment of the damages of buildings affected by mining subsidence.

Spatial Distribution of Marine Epibenthic Communities in the Hola Trough (Vesterålen, Northern Norway)

The Lofoten-Vesterålen marine shelf is one of the most geologically diverse coast and offshore margin areas in Norway. This leads to huge heterogeneity in marine environments, and often high biodiversity. However, little is known yet about the benthic communities in this region. Within the ARCTOS LoVe MarineEco project the epibenthic communities of the Hola trough (Vesterålen) are analysed to give a first description of their spatial distribution. In this trough both a complex hydrodynamic system and varied topographic submarine elements occur. Trawling samples were collected for two different approaches: one in a meso-scale and another in a small-scale. For the broad scale a transect consisting in three stations was developed, while for the fine scale a small area on a sand wave field, consisting in five stations called HolaBox, was sampled. All organisms were intended to be identified to species level and colonial fauna was discarded for the analysis. Different diversity indexes were assessed (Shannon index (H’) and Pielou’s eveness (J’)). Clustering and nMDS analyses identified four statistically significant groups in terms of abundance (ind./100m2). A total amount of 211 different taxa were found within all stations. The more outer part of the transect (close to the shelf edge) presented a huge abundance of organisms and was dominated by the hemi sessile tube-builder polychaetes Nothria conchylega and Eunice dubitata and the sea urchin Gacilechinus acutus, while the more inner parts presented less abundance of individuals. Probably some upwelling produced by the Norwegian Atlantic Current (NWAC) is influencing the shelf edge increasing the primary production and, therefore, enriching the seafloor in this region. The sand wave field presented two different groups with few amount of individuals. Small-scale variability could be produced by the high heterogeneity within the different types of sand waves, while the scarce abundance of animals can be produced by the permanent changing environment that movable sand waves produce. Here more active and mobile fauna was found such as brittle stars and hermit crabs (among others). Finally, a fourth group was found in the most inner station of the transect, laying on a ridge in the central part of the trough. This station, with coarse substrate, was mainly dominated again by brittle stars and sea urchins. We can conclude that this is a really heterogeneous trough in environments and therefore in communities (even in a local scale). More detailed studies that focus in the local environmental drivers have to be carried out to get an integrated understanding of the structure of benthic communities in this system.

Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces

In this article we present a computational framework for isolating spatial patterns arising in the steady states of reaction-diffusion systems. Such systems have been used to model many different phenomena in areas such as developmental and cancer biology, cell motility and material science. Often one is interested in identifying parameters which will lead to a particular pattern. To attempt to answer this, we compute eigenpairs of the Laplacian on a variety of domains and use linear stability analysis to determine parameter values for the system that will lead to spatially inhomogeneous steady states whose patterns correspond to particular eigenfunctions. This method has previously been used on domains and surfaces where the eigenvalues and eigenfunctions are found analytically in closed form. Our contribution to this methodology is that we numerically compute eigenpairs on arbitrary domains and surfaces. Here we present various examples and demonstrate that mode isolation is straightforward especially for low eigenvalues. Additionally we see that if two or more eigenvalues are in a permissible range then the inhomogeneous steady state can be a linear combination of the respective eigenfunctions. Finally we show an example which suggests that pattern formation is robust on similar surfaces in cases that the surface either has or does not have a boundary.

Apoptosis in experimental cerebral malaria: spatial profile of cleaved caspase-3 and ultrastructural alterations in different disease stages

Cerebral malaria (CM) is associated with high mortality and morbidity as a certain percentage of survivors suffers from persistent neurological sequelae. The mechanisms leading to death and functional impairments are yet not fully understood. This study investigated biochemical and morphological markers of apoptosis in the brains of mice infected with Plasmodium berghei ANKA. Cleaved caspase-3 was detected in the brains of animals with clinical signs of CM and immunoreactivity directly correlated with the clinical severity of the disease. Caudal parts of the brain showed more intense immunoreactivity for cleaved caspase-3. Double-labelling experiments revealed processing of caspase-3 primarily in neurons and oligodendrocytes. These cells also exhibited apoptotic-like morphological profiles in ultrastructural analysis. Further, cleavage of caspase-3 was found in endothelial cells. In contrast to neurons and oligodendrocytes, apoptosis of endothelial cells already occurred in early stages of the disease. Our results are the first to demonstrate processing of caspase-3 in different central nervous system cells of animals with CM. Apoptosis of endothelial cells may represent a critical issue for the development of the disease in the mouse model. Neurological signs and symptoms might be attributable, at least in part, to apoptotic degeneration of neurons and glia in advanced stages of murine CM.

Analysis of foraminifera from the Tagus Estuary, Portugal

The distribution and microhabitat of living benthic fora- minifera (15 calcareous and 6 agglutinated) have been studied in two box cores from the Tagus Prodelta. Stable oxygen and carbon isotopes were analysed for eight different species from six surface samples from the Tagus Prodelta and Estuary. At the two box core stations, most of the living foraminifera were restricted to the oxygenated top cm of the sediment and generally show a shallow infaunal behavior. Those taxa are e.g. Rectuvigerina phlegeri, Stainforthia fusiformis and species of the genus Bolivina, which is the most abundant genus in the Tagus Prodelta. Infaunal species are found down to 10 cm depth, and some infaunal taxa, e.g. Bulimina marginata, Globobulimina auriculata and Nonionella turgida, inhabit the low oxic or anoxic sediments. The deep infaunal species are suggested to feed selectively, on refractory organic matter or on the bacterial stocks, while the opportunistic shallow infaunal species are believed to feed on fresh phytodetritus or labile organic matter. Our data show that there is a close connection between the concentration of foraminifera and the distribution of organic matter in the area. The highest abundance of living benthic foraminifera was found in sediments close to the Tagus river plume, where the sediments have relatively high organic carbon contents. The spatial distribution of the stable isotope values of different benthic foraminifera reflects the distribution of the low salinity and relatively high temperature water with high organic carbon fluxes within the Tagus Estuary.

Spatial distribution of key zooplankton species using continuous plankton recorder (CPR) data from the North Atlantic (2000-2009)

The continuous plankton recorder (CPR) survey is an upper layer plankton monitoring program that has regularly collected samples, at monthly intervals, in the North Atlantic and adjacent seas since 1946. Water from approximately 6 m depth enters the CPR through a small aperture at the front of the sampler and travels down a tunnel where it passes through a silk filtering mesh of 270 µm before exiting at the back of the CPR. The plankton filtered on the silk is analyzed in sections corresponding to 10 nautical miles (approx. 3 m**3 of seawater filtered) and the plankton microscopically identified (Richardson et al., 2006 and reference therein). In the present study we used the CPR data to investigate the current basin scale distribution of C. finmarchicus (C5-C6), C. helgolandicus (C5-C6), C. hyperboreus (C5-C6), Pseudocalanus spp. (C6), Oithona spp. (C1-C6), total Euphausiida, total Thecosomata and the presence/absence of Cnidaria and the Phytoplankton Colour Index (PCI). The PCI, which is a visual assessment of the greenness of the silk, is used as an indicator of the distribution of total phytoplankton biomass across the Atlantic basin (Batten et al., 2003). Monthly data collected between 2000 and 2009 were gridded using the inverse-distance interpolation method, in which the interpolated values were the nodes of a 2 degree by 2 degree grid. The resulting twelve monthly matrices were then averaged within the year and in the case of the zooplankton the data were log-transformed (i.e. log10 (x+1).

Spectral analysis of seabed elevation from the Danish Wadden Sea

Bedforms both reflect and influence shallow water hydrodynamics and sediment dynamics. A correct characterization of their spatial distribution and dimensions is required for the understanding, assessment and prediction of numerous coastal processes. A method to parameterize geometrical characteristics using two-dimensional (2D) spectral analysis is presented and tested on seabed elevation data from the Knudedyb tidal inlet in the Danish Wadden Sea, where large compound bedforms are found. The bathymetric data were divided into 20x20 m areas on which a 2D spectral analysis was applied. The most energetic peak of the 2D spectrum was found and its energy, frequency and direction were calculated. A power-law was fitted to the average of slices taken through the 2D spectrum; its slope and y-intercept were calculated. Using these results the test area was morphologically classified into 4 distinct morphological regions. The most energetic peak and the slope and intercept of the power-law showed high values above the crest of the primary bedforms and scour holes, low values in areas without bedforms, and intermediate values in areas with secondary bedforms. The secondary bedform dimensions and orientations were calculated. An area of 700x700 m was used to determine the characteristics of the primary bedforms. However, they were less distinctively characterized compared to the secondary bedforms due to relatively large variations in their orientations and wavelengths. The method is thus appropriate for morphological classification of the seabed and for bedform characterization, being most efficient in areas characterized by bedforms with regular dimensions and directions.

Analysis of the Hydrogeological Conditions and the Effects of Development on the Hydraulic Head at Redmond Ridge East

Redmond Ridge East (RRE) is a large-scale master plan community in East King County, WA. In this report, I evaluate the spatial variability of the Quaternary Advance Outwash (Qva) at RRE and the time-series data for 16 water wells with the intent to better understand groundwater below the RRE area. I investigate changes between pre- and post-development conditions through the determination of temporal changes in annual water level, annual water level fluctuations, hydraulic head response to precipitation, and ambient drainage of the aquifer. I also perform a basic analysis of the annual aquifer recharge and a determination for the storage through the implementation of the water table fluctuation (WTF) method. Associated Earth Sciences (AESI) was tasked with monitoring the geological and environmental impacts during the development of RRE and collected the data I use in this report. AESI involvement in monitoring began in 1998 and extends to the present. Sixteen wells were identified in the RRE area with adequate temporal data to conduct the analysis. A comparison of the well logs and aquifer testing data allowed local variations in the Qva to be mapped. The WTF was used to determine a range of reasonable specific yield values for locations where the Qva was unconfined. Yearly average of the seasonal water level high and lows, and the fluctuations were quantified. Temporal relationships were established through linear regression. The average water level was found to be increasing in some locations, and the corresponding fluctuations were found to decrease. However, no clear change between pre- and post-development was observed. The response of hydraulic head to precipitation was investigated through an analysis of hydrographs for ten wells. Periods of consistent response and the corresponding precipitation during each period were delineated. A linear relationship between precipitation and water level change was determined. The threshold precipitation under which there is a positive response in the hydraulic head was established. No observable changes were apparent between pre- and post-development conditions. The ambient drainage for the Qva was calculated using recessional periods on the hydrograph. The transmissivity of Qva varies with thickness of the overlying lodgment till and thickness of the Qva, itself. Water level fluctuations observed in the Qva are consistent with regional observations. Localized areas in the Qva display the large 10 foot fluctuations and these anomalies are likely due to a combination of the local variability in the storativity as well as the concentration and channeling of water due to geographical variations in the Qva and the overlying topography. All trends seen in the RRE area remained relatively constant through time. There was no evidence showing an effect of development on the hydraulic head at RRE. This implies that the style and distribution of infiltration has not changed as a result of development, and that any measures in place are properly mitigating the effects of development on the RRE region.

Exploring the spatial variation of tides for seafloor mapping data corrections

Senior thesis written for Oceanography 445

Essays on the Analysis of Dynamic Games

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

A vulnerability analysis of the temperate forests of south central Chile A vulnerability analysis of the temperate forests of south central Chile. Biological Conservation, 122 2005: 9-21.

Areas of the landscape that are priorities for conservation should be those that are both vulnerable to threatening processes and that if lost or degraded, will result in conservation targets being compromised. While much attention is directed towards understanding the patterns of biodiversity, much less is given to determining the areas of the landscape most vulnerable to threats. We assessed the relative vulnerability of remaining areas of native forest to conversion to plantations in the ecologically significant temperate rainforest region of south central Chile. The area of the study region is 4.2 million ha and the extent of plantations is approximately 200000 ha. First, the spatial distribution of native forest conversion to plantations was determined. The variables related to the spatial distribution of this threatening process were identified through the development of a classification tree and the generation of a multivariate. spatially explicit, statistical model. The model of native forest conversion explained 43% of the deviance and the discrimination ability of the model was high. Predictions were made of where native forest conversion is likely to occur in the future. Due to patterns of climate, topography, soils and proximity to infrastructure and towns, remaining forest areas differ in their relative risk of being converted to plantations. Another factor that may increase the vulnerability of remaining native forest in a subset of the study region is the proposed construction of a highway. We found that 90% of the area of existing plantations within this region is within 2.5 km of roads. When the predictions of native forest conversion were recalculated accounting for the construction of this highway, it was found that: approximately 27000 ha of native forest had an increased probability of conversion. The areas of native forest identified to be vulnerable to conversion are outside of the existing reserve network. (C) 2004 Elsevier Ltd. All tights reserved.

Genetic analysis of complex demographic scenarios: Spatially expanding populations of the cane toad, Bufo marinus

Inferring the spatial expansion dynamics of invading species from molecular data is notoriously difficult due to the complexity of the processes involved. For these demographic scenarios, genetic data obtained from highly variable markers may be profitably combined with specific sampling schemes and information from other sources using a Bayesian approach. The geographic range of the introduced toad Bufo marinus is still expanding in eastern and northern Australia, in each case from isolates established around 1960. A large amount of demographic and historical information is available on both expansion areas. In each area, samples were collected along a transect representing populations of different ages and genotyped at 10 microsatellite loci. Five demographic models of expansion, differing in the dispersal pattern for migrants and founders and in the number of founders, were considered. Because the demographic history is complex, we used an approximate Bayesian method, based on a rejection-regression algorithm. to formally test the relative likelihoods of the five models of expansion and to infer demographic parameters. A stepwise migration-foundation model with founder events was statistically better supported than other four models in both expansion areas. Posterior distributions supported different dynamics of expansion in the studied areas. Populations in the eastern expansion area have a lower stable effective population size and have been founded by a smaller number of individuals than those in the northern expansion area. Once demographically stabilized, populations exchange a substantial number of effective migrants per generation in both expansion areas, and such exchanges are larger in northern than in eastern Australia. The effective number of migrants appears to be considerably lower than that of founders in both expansion areas. We found our inferences to be relatively robust to various assumptions on marker. demographic, and historical features. The method presented here is the only robust, model-based method available so far, which allows inferring complex population dynamics over a short time scale. It also provides the basis for investigating the interplay between population dynamics, drift, and selection in invasive species.