A Survey of Ocean Simulation and Rendering Techniques in Computer Graphics

This paper presents a survey of ocean simulation and rendering methods in computer graphics. To model and animate the ocean's surface, these methods mainly rely on two main approaches: on the one hand, those which approximate ocean dynamics with parametric, spectral or hybrid models and use empirical laws from oceanographic research. We will see that this type of methods essentially allows the simulation of ocean scenes in the deep water domain, without breaking waves. On the other hand, physically-based methods use Navier-Stokes Equations (NSE) to represent breaking waves and more generally ocean surface near the shore. We also describe ocean rendering methods in computer graphics, with a special interest in the simulation of phenomena such as foam and spray, and light's interaction with the ocean surface

Stability of salts and complexes of humic acids

Základem práce je studium vlivu přítomnosti kovů inkorporovaných do struktury huminových látek při tepelné zátěži za přítomnosti vzdušného kyslíku. Pro tyto účely byla použita lignitická huminová kyselina, u které byl nejprve retitračně-vodivostní metodou stanoven počet vazných míst, tj. karboxylových skupin. Smícháním s roztoky sodných a měďnatých iontů byly získány koncové produkty s různými stupni nasycení zjištěných vazných míst. Pro zhodnocení termooxidační stability byla provedena termogravimetrická analýza a diferenční kompenzační kalorimetrie. Výsledky přinášejí nový pohled na reaktivitu huminové kyseliny s kovovými ionty v kapalné fázi, poukazují na možný vznik „porézní“ struktury sodných humátů a jejich schopnost retence vody.The ground of this work lies in the study of influence of metal ions incorporated onto the structure of humic substances during thermal stress in the presence of air oxygen. For these purposes, lignitic humic acid was used. The amount of binding sites, i.e. carboxylic groups, was determined by retitration-conductometric method. Mixing the humic acid with solutions of sodium and cupric ions gave the final products with different saturation degrees of detected binding sites. For the evaluation of thermooxidative stability, thermogravimetric analysis and differential scanning calorimetry were performed. The results bring new view upon the reactivity of humic acid with metal ions in the liquid state, indicate possible formation of “porous” structure of sodium humates and their water-retention ability.

Freshwaters: which NOM matters?

One of the difficulties encountered in the study of natural organic matter (NOM) in aquatic environments concerns terminology: a large number of different names and acronyms are used. In fact, this diversity merely reflects the variety of approaches applied to the study of NOM, leading to the definition and measurement of different operationally-defined fractions. As a result, the choice of the ‘best' method to use and of the ‘best' fraction to work on in a particular case is far from straightforward. This has as a consequence that often very simple methods for NOM characterisation are used in applied environmental studies and surveys. This study includes, first, a review of the most widely applied terminology, as described in over 500 articles, and, second, a first attempt at assessing how the panoply of methods available is really used in applied environmental studie

Development of innovative analytical methodologies, mainly focused on X-ray fluorescence spectrometry, to characterise building materials and their degradation processes based on the study performed in the historical building Punta Begoña Galleries (Getxo, Basque Country, Spain)

282 p.The characterisation and preservation of Cultural Heritage is of great importance in order to understand and preserve human evolution and history. Mortars are usually the main material employed in the construction of buildings belonging to Cultural Heritage. These building materials are multi-layered complex systems, often characterised by an inhomogeneous structure with a composition varying surprisingly depending on their geographical location and time period. The characterisation of the original composition and the definition of the degradation reactions of mortars can give assistance to restorers and can lead to propose new ways for future conservation (e.g. preventive conservation). In this PhD. Thesis, new Analytical Methodologies have been developed for the characterisation of mortars and the diagnosis of pathologies present on them, trying to encompass some of the most important facts present in the current evolution of the science dedicated to Cultural Heritage. Portable devices based on elemental and molecular spectroscopic techniques have been demonstrated as powerful tools to extract reliable conclusions without extracting any sample, which is of high importance when dealing with objects belonging to Cultural Heritage. On the one hand, different new easy and cost-effective natural and artificial passive samplers useful for the characterisation of the increasing atmospheric Particulate Matter in the current atmosphere are proposed in order to study the effect of its deposition over the building materials. On the other hand, the advantages of the increasing in situ non-destructive analytical techniques are also shown as well as the development of new X-ray fluorescence based quantification methodologies as an easy, cost effective and Green Analytical Chemistry option to other more traditionally employed techniques for the characterisation of building materials and their degradation products. At the time of starting the project of this PhD. Thesis, the University of the Basque Country UPV/EHU and the City Council of Getxo (Basque Country, Spain) signed an agreement to recover a highly degraded historical building, the Punta Begoña Galleries. The proposed methodologies have been developed based on the materials from this building and the degradation processes that are suffering

Monitoring of the impact of the extraction of marine aggregates, in casu sand, in the zone of the Hinder Banks

The far offshore Hinder Banks are targeted for exploitation of huge quantities of sand, mainly for coastal defence works. Here, up to 2.9 million m³ can be taken over 3 months, with a maximum of 35 million m³ over a period of 10 years. Large vessels can be used extracting 12500 m³ per run. South of the Hinder Banks concession, a Habitat Directive area is present, hosting ecologically valuable gravel beds. For these, it is critical to assess the effect of multiple and frequent depositions of fine material from dredging-induced sediment plumes.A monitoring strategy was set-up, tailored for assessing the importance and extent of physical perturbations that are created by the extraction activities. The monitoring design focuses on hydrodynamics and sediment transport with feedback loops between both modelling and field studies. Main targets are assessing changes in seafloor integrity and hydrographic conditions, two key descriptors of marine environmental status within Europe’sMarine Strategy Framework Directive. Seafloor integrity relates to the functions that the seabed provides to the ecosystem (e.g., structure; oxygen and nutrient supply), whilst hydrographic conditions refer to currents and/orother oceanographic parameters of which changes could adversely impact on benthic ecosystems.State-of-the-art instrumentation (from RV Belgica) has been used, to measure the 3D current structure, turbidity, depth, backscatter and particle size of the material in the water column, both in-situ and whilst sailing transectsover the sandbanks. In the Habitat Directive Area, gravel bed integrity (i.e., epifauna; sand/gravel ratio; patchiness) was measured as well. Most innovatively, an autonomous underwater vehicle was deployed (Wave Glider®, Liquid Robotics Inc.), resulting in quasi 22 days of current, turbidity and other oceanographic data.From a first data-model integration, and analyses against hydrometeorological databases, main results showed: (1) high spatial and temporal variability of turbidity, both current- and wave-induced; (2) important topography-induced resuspension over the sandbanks, especially under wave agitation; (3) spreading and deposition of dredging-induced sediment plumes; and (4) competitiveness of ebb and flood, meaning that deposition of fine sediments on the gravel beds is realistic. Field data on currents were used for the validation of a three-imensional hydrodynamic model. Results confirmed good model predictions of current magnitude and current directions in zone 4, critical for future impact assessment.Data will be integrated with results from the morphological and biological monitoring, respectively carried out by the Continental Shelf Service of FPS Economy and the Institute for Agricultural and Fisheries Research

Development of innovative analytical methodologies, mainly focused on X-ray fluorescence spectrometry, to characterise building materials and their degradation processes based on the study performed in the historical building Punta Begoña Galleries (Getxo, Basque Country, Spain)

282 p.The characterisation and preservation of Cultural Heritage is of great importance in order to understand and preserve human evolution and history. Mortars are usually the main material employed in the construction of buildings belonging to Cultural Heritage. These building materials are multi-layered complex systems, often characterised by an inhomogeneous structure with a composition varying surprisingly depending on their geographical location and time period. The characterisation of the original composition and the definition of the degradation reactions of mortars can give assistance to restorers and can lead to propose new ways for future conservation (e.g. preventive conservation). In this PhD. Thesis, new Analytical Methodologies have been developed for the characterisation of mortars and the diagnosis of pathologies present on them, trying to encompass some of the most important facts present in the current evolution of the science dedicated to Cultural Heritage. Portable devices based on elemental and molecular spectroscopic techniques have been demonstrated as powerful tools to extract reliable conclusions without extracting any sample, which is of high importance when dealing with objects belonging to Cultural Heritage. On the one hand, different new easy and cost-effective natural and artificial passive samplers useful for the characterisation of the increasing atmospheric Particulate Matter in the current atmosphere are proposed in order to study the effect of its deposition over the building materials. On the other hand, the advantages of the increasing in situ non-destructive analytical techniques are also shown as well as the development of new X-ray fluorescence based quantification methodologies as an easy, cost effective and Green Analytical Chemistry option to other more traditionally employed techniques for the characterisation of building materials and their degradation products. At the time of starting the project of this PhD. Thesis, the University of the Basque Country UPV/EHU and the City Council of Getxo (Basque Country, Spain) signed an agreement to recover a highly degraded historical building, the Punta Begoña Galleries. The proposed methodologies have been developed based on the materials from this building and the degradation processes that are suffering

Statistical Models for Single Molecule Localization Microscopy

Single-molecule localization microscopy (SMLM) has revolutionized the field of cell biology. It allowed scientists to break the Abbe diffraction limit for fluorescence microscopy and got it closer to the electron microscopy resolution but still it faced some serious challenges. Two of the most important of these are the sample drift and the measurement noise problems that result in lower resolution images. Both of these problems are generally unavoidable where the sample drift is a natural mechanical phenomenon that occurs during the long time of image acquisition required for SMLM (Geisler et al. 2012) while the measurement noise, which arises from combining localization uncertainty and counting error, is related to the number of photons collected from the fluorophore and affects the precision in locating the centroids of single molecules (Thompson, Larson, and Webb 2002). Previous work has tried to devise methods to deal with the sample drift problem but unfortunately, these methods either add too much complexity to the experimental setup or are just inefficient in correctly estimating the drift at the single frame level (Wang et al. 2014). As for measurement noise, all current regular image rendering algorithms treat every detection of the fluorophore as a separate event and hence, the localization uncertainty of every detection of the same molecule would give offset coordinates from the other detections leading to a distorted final image. In this thesis, I demonstrate two novel approaches based on statistical concepts to address each of these two problems. The algorithm for solving the sample drift problem is based on Bayesian inference and it showed efficiency in estimating drift at the single-frame level and proved superior and more straightforward than the available methods. The algorithm for addressing the measurement noise problem is based on Gibbs sampling and not only did it enhance resolution, but it also offers for the first time a means to quantify resolution uncertainty as well as uncertainty in cluster size measurement for clustering proteins. Therefore, this work offers a significant advancement in the field of SMLM and more generally, cell biology

3-Amino-2-Piperidinequinoline A Novel Natural Product-Inspiried Synthetic Compound with Antimalarial Activity

Malaria afflicts about 500 million people worldwide thus causing significant global economic toll. The drugs available to treat the disease are rapidly losing their efficacy because of widespread prevalence of drug resistant parasites. Thus there is an urgent need to discover novel malaria therapeutics. This research is focused on to study the properties of a novel naturallike synthetic scaffold and analyze its selectivity, and cellular mechanism of action in Plasmodium falciparum. We have identified a novel compound, 3-amino-2-piperidinequinoline (APQ), which we termed UCF401. APQ demonstrated IC[sub50] at submicromolar concentrations against Plasmodium falciparum using the SYBR Green-I fluorescence assay measuring cellular proliferation. This compound also demonstrated low cytotoxicity against the NIH3T3 and HEPG2 cells using MTS assays, showing an IC50 of 174 [micro]M and 125 [micro]M respectively, suggesting of excellent selectivity. We evaluated the compliance of APQ with Lipinski\u27s parameters and determined the in vitro physicochemical profiles of the compound. Our results show that APQ is a Lipinski parameter compliant and has good physicochemical properties. The cellular mechanism of action of APQ was characterized through the assessment of the effects of the compound at different stages of the parasite\u27s intraerythrocytic life cycle. This assay was done by treating a synchronized cell line with the compound at 5X the IC50 value and then imaging the cells at 12-hour intervals. We found that APQ arrests parasite development at the trophozoite stage. In addition we determined that APQ is parasitocidal after a 96 h exposure. These results demonstrate that APQ can be considered as a validated hit and/or early lead