On the remote sensing of oceanic and atmospheric convection in the Greenland Sea by synthetic aperture radar

In this paper we discuss characteristic properties of radar signatures of oceanic and atmospheric convection features in the Greenland Sea. If the water surface is clean (no surface films or ice coverage), oceanic and atmospheric features can become visible in radar images via a modulation of the surface roughness, and their radar signatures can be very similar. For an unambiguous interpretation and for the retrieval of quantitative information on current and wind variations from radar imagery with such signatures, theoretical models of current and wind phenomena and their radar imaging mechanisms must be utilized. We demonstrate this approach with the analysis of some synthetic aperture radar (SAR) images acquired by the satellites ERS-2 and RADARSAT-1. In once case, an ERS-2 SAR image an a RADARSAT-1 ScanSAR image exhibit pronounced cell-like signatures with length scales on the order of 10-20 km and modulation depths of about 5-6 dB and 9-10 dB, respectively. Simulations with a numerical SAR imagaing model and various input current and wind fields reveal that the signatures in both images can be expained consistently by wind variations on the order of±2.5 ms, but not by surface current variations on realistic orders of magnitude. Accordingly, the observed features must be atmospheric convection cells. This is confirmed by visible typical cloud patterns in a NOAA AVHRR image of the test scenario. In another case, the presence of an oceanic convective chimney is obvious from in situ data, but no signatures of it are visible in an ERS-2 SAR image. We show by numerical simulations with an oceanic convection model and our SAR imaging model that this is consistent with theoretical predictions, since the current gradients associated with the observed chimney are not sufficiently strong to give rise to significant signatures in an ERS-2 SAR image under the given conditions. Further model results indicate that it should be generally difficult to observe oceanic convection features in the Greenland Sea with ERS-2 or RADARSAT-1 SAR, since their signatures resulting from pure wave-current interaction will be too weak to become visible in the noisy SAR images in most cases. This situation will improve with the availability of future high-resolution SARs such as RADARSAT-2 SAR in fine resolution mode (2004) and TerraSAR-X (2005) which will offer significantly reduced speckle noise fluctuations at comparable spatial resolutions and thus a much better visibility of small image variations on spatial scales on the order of a few hundred meters

Offshore oil seepage visible from space : a Synthetic Aperture Radar (SAR) based automatic detection, mapping and quantification system

Offshore oil seepage is believed to be the largest source of marine oil, yet very few of their locations and seepage fluxes have been discovered and reported. Natural oil seep sites are important as they serve as potential energy sources and because they are hosts to a very varied marine ecosystem. These seeps can also be associated with gas hydrates and methane emissions and hence, locating natural oil seeps can provide locations where the sources of greenhouse gases could be studied and quantified. A quantification of the amount of crude oil released from natural oil seeps is important as it can be used to set a background against which the excess anthropogenic sources of marine oil can be checked. This will provide an estimate of the 'contamination' of marine waters from anthropogenic sources. Until the onset of remote sensing techniques, field measurements and techniques like hydroacoustic measurements or piston core analysis were used to obtain knowledge about the geological settings of the seeps. The remote sensing techniques either involved manual or semi-automatic image analysis. An automatic algorithm that could quantitatively and qualitatively estimate the locations of oil seeps around the world would reduce the time and costs involved by a considerable margin. Synthetic Aperture Radar (SAR) sensors provide an illumination and weather independent source of ocean images that can be used to detect offshore oil seeps. Oil slicks on the ocean surface dampen the small wind driven waves present on the ocean surface and appear darker against the brighter ocean surface. They can, hence, be detected in SAR image. With the launch of the latest Sentinel-1 satellite aimed at providing free SAR data, an algorithm that detects oil slicks and estimates seep location is very beneficial. The global data coverage and the reduction of processing times for the large amounts of SAR data would be unmatchable. The aim of this thesis was to create such an algorithm that could automatically detect oil slicks in SAR images, map the location of the estimated oil seeps and quantify their seepage fluxes. The thesis consists of three studies that are compiled into one of more manuscripts that are published, accepted for publication or ready for submission. The first study of this thesis involves the creation of the Automatic Seep Location Estimator (ASLE) which detects oil slicks in marine SAR images and estimates offshore oil seepage sites. This, the first fully automatic oil seep location estimation algorithm, has been implemented in the programming language Python and has been tested and validated on ENVISAT images of the Black Sea. The second study reported in this thesis focuses on the optimisation of the created ASLE and comparison of the ASLE with other existing algorithms. It also describes the efficiency of the ASLE with respect to other existing algorithms and the results show that the ASLE can successfully detect seeps of active seepages. The third study aimed to provide the status of the offshore seepage in the southern Gulf of Mexico estimated from the ASLE using SAR images from ENVISAT and RADARSAT-1. The ASLE was used to detect natural oil slicks from SAR images and estimate the locations of feeding seeps. The estimated seep locations and the slicks contributing to these estimations were then analysed to quantify their seepage fluxes and rates. The three case studies illustrate that an automatic offshore seepage detection and estimation system such as the Automatic Seep Location Estimator (ASLE) is very beneficial in order to locate global oil seeps and estimate global seepage fluxes. It provides a technique to detect offshore seeps and their seepage fluxes in a fast and highly efficient manner by using Synthetic Aperture Radar images. This allows global accessibility of offshore oil seepage sites. The availability of large amounts of historic SAR datasets, the presence of 5 active SAR satellites and the latest launch of the European Space Agency satellite Sentinel-1, which provides free data, shows that there is no shortage in the availability of SAR data. The result of the work done in this thesis provides a means to utilise this large SAR dataset for the purpose of offshore oil seepage detection and offshore seepage related geophysical applications. The created system will be an important tool in the future not just to estimate offshore seepage in local seas but in global oceans that are otherwise challenging for field analysis

Monitoreo de derrames de hidrocarburos en cuerpos de agua mediante técnicas de sensado remoto

Dentro de un panorama de aumento constante en la demanda de energía, es notoria la creciente exploración de cuencas hidrocarburíferas sujetas a duras condiciones climáticas y antes consideradas remotas. En este contexto, las técnicas de sensado remoto pueden ser utilizadas para dar soporte a la detección y monitoreo de vertidos accidentales o productos de la propia operatoria, siendo entre ellas la tecnología SAR una de las que dispone de mayor potencial de aplicación. Desde el presente trabajo, se hace una introducción al estado del arte en la materia, a las capacidades de estas técnicas, como así también a sus limitaciones y herramientas para superarlas. Se detallan un conjunto de características que potencialmente explican al objeto detectado y que posteriormente ingresadas a un proceso de clasificación de redes neuronales de reconocimiento de patrones serán de de utilidad para establecer, con un cierto grado de confiabilidad, si éste objeto esta relacionado a una falsa alarma o a un real derrame de hidrocarburos. Se entrenó a la red neural con escenas extraídas de imágenes Envisat-ASAR, de las que se obtuvieron alrededor de 230 manchas, alcanzando un 81,3% de casos de correcta clasificación en el caso de derrames reales y un 100% en el caso de falsas alarmas. Los resultados alcanzados, en conjunto con una futura implementación de una aplicación automatizada de alerta y monitoreo, dan pautas claras de la potencialidad de esta técnica aplicable sobre zonas de interés ecológico, socioeconómico o geopolítico

Study of the aryl hydrocarbon receptor mediated effects through in silico modeling and in vitro bioassays

The aryl hydrocarbon receptor (AhR) is a cytoplasmatic sensor of diverse endogenous and exogenous substances. In a toxicological context, the former known as “dioxin receptor” has been investigated as a xenobiotic chemoreceptor and due to its roles in mediating carcinogenesis, endocrine disruption, among other immunological, hepatic, cardiovascular, and dermal toxicity mechanisms. The deep physiological implications of AhR in cellular proliferation, adhesion, division, differentiation, as well as in the reproductive, immunological and cardiovascular homeostasis have opened a new field of research in order to harness AhR’s pharmacological potential. Hence, AhR has become a therapeutic target of inflammatory, infectious, malignant, and immunological conditions. Toxicological and pharmacological fields could benefit from discovering novel AhR modulators to elucidate further on the chemical-biological implications of this crucial transcription factor. In this Thesis, the following objective was proposed in order to contribute to such understanding. General Objective: Evaluate diverse chemical compounds as modulators of AhR by means of in silico and in vitro methods. The general objective was concretized in specific aims distributed in the five Chapters of this Thesis as follow: Chapter 1. Review the literature on AhR mediated effects and the existing theoretical and experimental methods employed to study the structural and functional aspects of the receptor. Chapter 2. Develop and experimentally validate QSAR models to predict the AhR agonist activity of chemical compounds. Chapter 3. Analyze the dual effects of a set of benzothiazoles as AhR modulators and antimicrobial agents. Chapter 4. Evaluate a novel set of triarylmethane compounds as AhR ligands. Chapter 5. Study the AhR antagonism discovered in potentially harmful substances using computational methods.The aryl hydrocarbon receptor (AhR) is a cytoplasmatic sensor of diverse endogenous and exogenous substances. In a toxicological context, the former known as “dioxin receptor” has been investigated as a xenobiotic chemoreceptor and due to its roles in mediating carcinogenesis, endocrine disruption, among other immunological, hepatic, cardiovascular, and dermal toxicity mechanisms. The deep physiological implications of AhR in cellular proliferation, adhesion, division, differentiation, as well as in the reproductive, immunological and cardiovascular homeostasis have opened a new field of research in order to harness AhR’s pharmacological potential. Hence, AhR has become a therapeutic target of inflammatory, infectious, malignant, and immunological conditions. Toxicological and pharmacological fields could benefit from discovering novel AhR modulators to elucidate further on the chemical-biological implications of this crucial transcription factor. In this Thesis, the following objective was proposed in order to contribute to such understanding. General Objective: Evaluate diverse chemical compounds as modulators of AhR by means of in silico and in vitro methods. The general objective was concretized in specific aims distributed in the five Chapters of this Thesis as follow: Chapter 1. Review the literature on AhR mediated effects and the existing theoretical and experimental methods employed to study the structural and functional aspects of the receptor. Chapter 2. Develop and experimentally validate QSAR models to predict the AhR agonist activity of chemical compounds. Chapter 3. Analyze the dual effects of a set of benzothiazoles as AhR modulators and antimicrobial agents. Chapter 4. Evaluate a novel set of triarylmethane compounds as AhR ligands. Chapter 5. Study the AhR antagonism discovered in potentially harmful substances using computational methods

Development of a PET radioligand targeting angiogenesis for oncology applications

All tumours must become vascularised in order to survive and metastasise, and initiate angiogenesis through the dysregulated and uncontrolled release of pro-angiogenic factors. Such uncontrolled angiogenesis leads to highly disordered and abnormal vasculature and is widely recognised as a hallmark of cancer. The major angiogenic pathway hyper-activated in cancer is the VEGF-VEGFR₂ signalling system. Anti-angiogenic therapies have been developed, but there is no accepted way of determining which patients will respond. The development of a molecular imaging probe targeting VEGFR₂ through the use of PET represents one way to achieve this. Currently, there are no PET imaging probes which exhibit the required characteristics. Therefore, the initial focus of this project was to synthesise novel probes based around existing suitable pharmacophores. Initial libraries focusing on urea or indole motifs, lacked either routes to a radiolabelling precursor or selectivity on biological testing, and were abandoned. A third library based around the only known selective VEGFR₂ inhibitor 5-((7-benzyloxyquinazolin-4-yl)amino)-4-fluoro-2-methylphenol 98, ZM323881, was developed. Synthesis of 98 proceeded via the Dimroth rearrangement in three steps, with a shorter synthesis time, use of less toxic reagents and easier purification than published methods. Initial kinase profiling revealed 98 also targeted closely related kinases; VEGFR₁, VEGFR₃, RET, PDGFRα. Known inhibitor 98 and closely related analogue 4-fluoro-5-((7- (4-fluorobenzyl)oxy))quinazoline-4-yl)amino)-2-methylphenol 101 exhibited activity against VEGFR₂, 4.75 nM and 7.5 nM respectively. The quinazoline focused library was selected for radiolabelling. Initial radiolabelling revealed a debenzylation reaction occurring, to produce 4-(2-fluoro-5-hydroxy-4-methylphenyl)amino quinazolin-7-ol 166 during the radiolabelling reaction. Radiolabelling analogue 7-(benzyloxy)-N-(4-bromo—fluorophenyl)quinazolin-4-amine 123, via the Dimroth rearrangement was troublesome and requires more optimisation, due the presence of the de-cyanation by-product. Initial biological testing presented in this thesis does not rule out the quinazoline library from its use as a PET imaging agent and further in vitro characterisation is required

Tyrosine derivatives and their anti-cancer applications

The incorporation of a propargyl group to a natural product target allows for a streamlined approach to the investigation of structure activity relationships (SARs) and target identification in forward chemical genetics programmes using a ‘click’-based approach. To this end, an efficient synthesis of O-propargylated tyrosine derivatives was designed, and these have been used in the construction of peptide motifs both (a) derived from phage display libraries and (b) found in natural products. The L-tyrosine derivative Y* (compound I, X=H, R=H) was incorporated into a peptide sequence, PTTIYY, which is known to prevent the inhibition of p53 by the AG-2 protein. Y* has been included as both the terminal and the internal tyrosine in the peptide sequence. ELISA assays were carried out to determine how the binding of PTTIYY* and PTTIY*Y to AG-2 compared to that of the un-marked PTTIYY sequence. The results of these assays allowed new conclusions to be drawn regarding the important binding features of the peptide and possible sites for further optimisation of the AG-2 binding properties of this peptide through ‘click’ functionalisation of the modified tyrosine. The binding of the peptides incorporating Y* was also assessed using MCF-7 breast cancer cell lysate, known to contain the AG-2 protein. These results confirmed those seen for the purified AG-2 ELISA. The related bromo-D-tyrosine derivative (compound I, X=Br, R=Me) has been prepared and employed towards the synthesis of a bisebromoamide derivative. Bisebromoamide is a newly discovered polypeptide, and a promising anti-cancer agent. The bisebromoamide derivative contains a thiazole unit (Tzl), two N-methylated amino acids, and an oxopropyl pyrrolidine (Opp) moiety, which is unique to bisebromoamide in natural products. The activity of this bisebromoamide derivative will be investigated via ‘click’-based affinity chromatography using a new supported linker recently developed within the Hulme group

New tools for target identification by affinity chromatography

The recovery of the selected biological material in affinity-based separations relies on reversing the biological interaction responsible for the binding. General elution methods which are independent of the bioaffinity interaction have attracted increasing attention. The first three chapters of this thesis describe the development of a novel “click” functionalised azobenzene-based linker for affinity-independent elution protocols and the preliminary affinity studies using this linker. Ligands functionalised with a bioorthogonal propargyl label were readily attached to the terminal azide of the linker using the copper(I) catalysed Huisgen cycloaddition (or "click" reaction). Following separation, the linker was cleaved under mild non-denaturing conditions using Na2S2O4. In the last three chapters a novel approach towards the synthesis of the 4-methyl proline fragment of the cytotoxic natural product bisebromoamide (a potential affinity target) is proposed. For the pyrrolidine ring construction an enamide-olefin ring-closing metathesis (RCM) approach has been attempted. The installation of the required absolute stereochemistry has been achieved using a phase-transfer catalyst for the enantioselective alkylation of Schiff bases derived from glycine esters

Outline of fungi and fungus-like taxa

This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.Fil: Wijayawardene, N. N.. Qujing Normal University; ChinaFil: Hyde, K. D.. Mae Fah Luang University; TailandiaFil: Al-Ani, L. K. T.. University of Baghdad; IraqFil: Tedersoo, L.. University of Tartu; EstoniaFil: Haelewaters, D.. University of South Bohemia; República Checa. Purdue University; Estados Unidos. Universidad Autónoma de Chiriquí; PanamáFil: Becerra, Alejandra Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Schnittler, M.. Ernst Moritz Arndt University Greifswald; AlemaniaFil: Shchepin, O. N.. The Komarov Botanical Institute of the Russian Academy of Sciences; RusiaFil: Novozhilov, Y. K.. The Komarov Botanical Institute of the Russian Academy of Sciences; RusiaFil: Silva-Filho, A.G. S.. Universidade Federal do Rio Grande do Norte; BrasilFil: Gentekaki, E.. Mae Fah Luang University; TailandiaFil: Liu, P.. Jilin Agricultural University; ChinaFil: Cavender, J. C.. Ohio University; Estados UnidosFil: Kang, Y.. Guizhou Medical University; ChinaFil: Mohammad, S.. Iranian Research Organization for Science and Technology; IránFil: Zhang, L. F.. Qujing Normal University; ChinaFil: Xu, R. F.. Qujing Normal University; ChinaFil: Li, Y. M.. Qujing Normal University; ChinaFil: Dayarathne, M. C.. Guizhou University; ChinaFil: Ekanayaka, A. H.. Mae Fah Luang University; TailandiaFil: Wen, T. C.. Guizhou University; ChinaFil: Deng, C. Y.. Guizhou Academy of Science; ChinaFil: Pereira, O. L.. Universidade Federal de Viçosa; BrasilFil: Navathe, S.. Agharkar Research Institute; IndiaFil: Hawksworth, D. L.. The Natural History Museum; Reino UnidoFil: Fan, X. L.. Beijing Forestry University; ChinaFil: Dissanayake, L. S.. Guizhou University; ChinaFil: Kuhnert, E.. Leibniz University Hannover; AlemaniaFil: Grossart, H. P.. Leibnitz Institute of Freshwater Ecology and Inland Fisheries; AlemaniaFil: Thines, M.. Senckenberg Biodiversity and Climate Research Centre; Alemani

Investigation into experimental toxicological properties of plant protection products having a potential link to Parkinson's disease and childhood leukaemia

In 2013, EFSA published a literature review on epidemiological studies linking exposure to pesticides and human health outcome. As a follow up, the EFSA Panel on Plant Protection Products and their residues (PPR Panel) was requested to investigate the plausible involvement of pesticide exposure as a risk factor for Parkinson's disease (PD) and childhood leukaemia (CHL). A systematic literature review on PD and CHL and mode of actions for pesticides was published by EFSA in 2016 and used as background documentation. The Panel used the Adverse Outcome Pathway (AOP) conceptual framework to define the biological plausibility in relation to epidemiological studies by means of identification of specific symptoms of the diseases as AO. The AOP combines multiple information and provides knowledge of biological pathways, highlights species differences and similarities, identifies research needs and supports regulatory decisions. In this context, the AOP approach could help in organising the available experimental knowledge to assess biological plausibility by describing the link between a molecular initiating event (MIE) and the AO through a series of biologically plausible and essential key events (KEs). As the AOP is chemically agnostic, tool chemical compounds were selected to empirically support the response and temporal concordance of the key event relationships (KERs). Three qualitative and one putative AOP were developed by the Panel using the results obtained. The Panel supports the use of the AOP framework to scientifically and transparently explore the biological plausibility of the association between pesticide exposure and human health outcomes, identify data gaps, define a tailored testing strategy and suggests an AOP’s informed Integrated Approach for Testing and Assessment (IATA)

Literature and history in the age of ideas: essays on the French Enlightenment presented to George R. Havens

(print) xix, 414 p. ; 24 cmGEORGES MAY Foreword ix -- Preface xvii -- HUGH M . DAVIDSON Fontenelle, Perrault, and the Realignment of the Arts 3 -- J. H. BRUMFITT Historical Pyrrhonism and Enlightenment Historiography in France 15 -- CHARLES G. S. WILLIAMS The Diamond of Courtoisie and the Dragonnades of 1681: Valincour's Vie de François de Lorraine 31 -- ALESSANDRO S. CRISAFULLI The Journal des Sçavans and the Lettres Persanes 59 -- HARCOURT BROWN From London to Lapland: Maupertuis, Johann Bernoulli I, and La Terre applatie, 1728-1738 69 -- IRA O. WADE Notes on the Making of a Philosophe: Cuenz and Bouhier 97 -- JEAN SAREIL Sur les Mémoires de Voltaire 125 -- JEANNE R. MONTY Voltaire's Debt to the Encyclopédie in the Opinion en Alphabet 153 -- ROBERT D. COTTRELL Ulcerated Hearts: Love in Voltaire's La Mort de César 169 -- VIRGIL W. TOPAZIO A Réévaluation of Rousseau's Political Doctrine 179 -- JAMES F. HAMILTON Literature and the "Natural Man" in Rousseau's Emile 195 -- RICHARD A. BROOKS Rousseau's Antifeminism in the Lettre à d'Alembert and Emile 209 -- OTIS FELLOWS Diderot's Supplément as Pendant for La Religieuse 229 -- DOUGLAS BONNEVILLE Diderot's Artist: Puppet and Poet 245 -- GEORGES MAY Une certaine Madame Madin 255 -- DIANA GUIRAGOSSIAN Subterfuges et stratagèmes, ou les romanciers malgré eux 273 -- EDWARD P. SHAW Censorship and Subterfuge in Eighteenth-Century France 287 -- THEODORE BESTERMAN Bibliographie Notes on the Beaumarchais-Goezman Lawsuit 311 -- ARNOLD AGES Lamartine and the Philosophes 321 -- GITA MAY Stendhal and the Age of Ideas 343 -- PAUL M. SPURLIN Readership in the American Enlightenment 359 -- DOROTHY M. MCGHEE Encyclopedism and Its Conscience: Evolution and Revolution 377 -- A Bibliography of the Writings of George R. Havens 387 -- Notes on the Contributors 401 -- Index 40