Coral reef habitat maps derived from a high-spatial-resolution multi-spectral satellite image using object based image analysis

Coral reef maps at various spatial scales and extents are needed for mapping, monitoring, modelling, and management of these environments. High spatial resolution satellite imagery, pixel <10 m, integrated with field survey data and processed with various mapping approaches, can provide these maps. These approaches have been accurately applied to single reefs (10-100 km**2), covering one high spatial resolution scene from which a single thematic layer (e.g. benthic community) is mapped. This article demonstrates how a hierarchical mapping approach can be applied to coral reefs from individual reef to reef-system scales (10-1000 km**2) using object-based image classification of high spatial resolution images guided by ecological and geomorphological principles. The approach is demonstrated for three individual reefs (10-35 km**2) in Australia, Fiji, and Palau; and for three complex reef systems (300-600 km**2) one in the Solomon Islands and two in Fiji. Archived high spatial resolution images were pre-processed and mosaics were created for the reef systems. Georeferenced benthic photo transect surveys were used to acquire cover information. Field and image data were integrated using an object-based image analysis approach that resulted in a hierarchically structured classification. Objects were assigned class labels based on the dominant benthic cover type, or location-relevant ecological and geomorphological principles, or a combination thereof. This generated a hierarchical sequence of reef maps with an increasing complexity in benthic thematic information that included: 'reef', 'reef type', 'geomorphic zone', and 'benthic community'. The overall accuracy of the 'geomorphic zone' classification for each of the six study sites was 76-82% using 6-10 mapping categories. For 'benthic community' classification, the overall accuracy was 52-75% with individual reefs having 14-17 categories and reef systems 20-30 categories. We show that an object-based classification of high spatial resolution imagery, guided by field data and ecological and geomorphological principles, can produce consistent, accurate benthic maps at four hierarchical spatial scales for coral reefs of various sizes and complexities.

Análise da variabilidade da marcha de indivíduos com comprometimento articular unilateral do quadril por meio de sensores inerciais

Data variability analysis has been the focus of a number of studies seeking to capture differences of patterns generated by biological systems. Although several studies related to gait employ the analysis of variability in their observations, we noticed a lack of such information for subjects with unilateral coxarthrosis undergoing total hip arthroplasty (THA). To tackle this deficiency of information, we conducted a study of the gait on a treadmill with10 healthy subjects (30.7 ± 6.75 years old) from G1 and 24 subjects (65 ± 8.5 years old) with unilateral THA from G2. Thus, by means of two inertial measurement units (IMUs) positioned in the pelvis, we have developed a detection method of the step and stride for calculating these intervals and extract the signal characteristics. The variability analysis (coefficient of variation) was performed, taking into consideration the extracted features and the step and stride times. The average and the 95% confidence interval estimate for the average of the step and stride times to each group were in agreement with literature. The mean coefficient of variation for the step and stride times was calculated and compared among groups by the Kruskal-Wallis test with 95% confidence interval. Each component X, Y and Z of the two IMUs (accelerometer, magnetometer and gyroscope) corresponded to a variable. The resultants of each sensor, the linear velocity (accelerometers) and the instantaneous angular displacement (gyroscopes) completed the set of variables. The characteristics were extracted from the signals of these variables to check the variability in the G1 and G2 groups . There were significant differences (p <0.05) between G1 and G2 for the average of the step and stride times. The variability of the step and stride, as well as the variability of all other evaluated characteristics were higher for the group G2 (p <0.05). The method proposed in this study proved to be suitable for the measuring of variability of biomechanical parameters related to the extracted features. All the extracted features categorized the groups. The G2 group showed greater variability, so it is possible that the age and the pathological condition of the hip both contributed to this result.

Mode-locking via dissipative Faraday instability

Emergence of coherent structures and patterns at the nonlinear stage of modulation instability of a uniform state is an inherent feature of many biological, physical and engineering systems. There are several well-studied classical modulation instabilities, such as Benjamin-Feir, Turing and Faraday instability, which play a critical role in the self-organization of energy and matter in non-equilibrium physical, chemical and biological systems. Here we experimentally demonstrate the dissipative Faraday instability induced by spatially periodic zig-zag modulation of a dissipative parameter of the system - spectrally dependent losses - achieving generation of temporal patterns and high-harmonic mode-locking in a fibre laser. We demonstrate features of this instability that distinguish it from both the Benjamin-Feir and the purely dispersive Faraday instability. Our results open the possibilities for new designs of mode-locked lasers and can be extended to other fields of physics and engineering.

Oxygen tension, H2S, and NO bioavailability:is there an interaction?

Molecular oxygen (O2) is an essential component for survival and development. Variation in O2 levels leads to changes in molecular signaling and ultimately affects the physiological functions of many organisms. Nitric oxide (NO) and hydrogen sulfide (H2S) are two gaseous cellular signaling molecules that play key roles in several physiological functions involved in maintaining vascular homeostasis including vasodilation, anti-inflammation, and vascular growth. Apart from the aforementioned functions, NO and H2S are believed to mediate hypoxic responses and serve as O2 chemosensors in biological systems. In this literature review, we briefly discuss NO and H2S and their roles during hypoxia.

Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding

Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.

Determination of Biomolecular Interdomain Motions using Nuclear Magnetic Resonance

Biological macromolecules can rearrange interdomain orientations when binding to various partners. Interdomain dynamics serve as a molecular mechanism to guide the transitions between orientations. However, our understanding of interdomain dynamics is limited because a useful description of interdomain motions requires an estimate of the probabilities of interdomain conformations, increasing complexity of the problem.

Staphylococcal protein A (SpA) has five tandem protein-binding domains and four interdomain linkers. The domains enable Staphylococcus aureus to evade the host immune system by binding to multiple host proteins including antibodies. Here, I present a study of the interdomain motions of two adjacent domains in SpA. NMR spin relaxation experiments identified a 6-residue flexible interdomain linker and interdomain motions. To quantify the anisotropy of the distribution of interdomain orientations, we measured residual dipolar couplings (RDCs) from the two domains with multiple alignments. The N-terminal domain was directly aligned by a lanthanide ion and not influenced by interdomain motions, so it acted as a reference frame to achieve motional decoupling. We also applied {\it de novo} methods to extract spatial dynamic information from RDCs and represent interdomain motions as a continuous distribution on the 3D rotational space. Significant anisotropy was observed in the distribution, indicating the motion populates some interdomain orientations more than others. Statistical thermodynamic analysis of the observed orientational distribution suggests that it is among the energetically most favorable orientational distributions for binding to antibodies. Thus, the affinity is enhanced by a pre-posed distribution of interdomain orientations while maintaining the flexibility required for function.

The protocol described above can be applied to other biological systems in general. Protein molecule calmodulin and RNA molecule trans-activation response element (TAR) also have intensive interdomain motions with relative small intradomain dynamics. Their interdomain motions were studied using our method based on published RDC data. Our results were consistent with literature results in general. The differences could be due to previous studies' use of physical models, which contain assumptions about potential energy and thus introduced non-experimental information into the interpretations.

Building resilience for social-ecological sustainability in Atlantic Europe

This thesis argues that complex adaptive social–ecological systems (SES) theory has important implications for the design of integrated ocean and coastal governance in the EU. Traditional systems of governance have struggled to deal with the global changes, complexity and uncertainties that challenge a transition towards sustainability in Europe’s maritime macro-regions. There is an apparent disconnect between governance strategies for sustainability in Europe’s maritime macro-regions and a sound theoretical basis for them. My premise is that the design of governance architecture for maritime regional sustainability should be informed by SES theory. Therefore, the aim of this research was to gain insight into a multilevel adaptive governance architecture that combines notions of sustainability and development in the context of the Atlantic Europe maritime macro-region. The central research question asked whether it is possible to achieve this insight by using a SES as a framework and analytical tool. This research adopted social ecology and sustainability science as a foundation for understanding society–nature relations. Concepts from complex adaptive systems, SES and resilience theories were integrated into a conceptual framework that guided the investigation and analysis. A study was conducted to conceptualise the European Atlantic social–ecological system (EASES). This was used to represent and understand the Atlantic Europe macro-region as a SES. The study examined the proposition that governance can be focused on building SES resilience to help achieve maritime regional sustainability. A workbook method was developed and used to elicit expert opinion regarding EASES. The study identified sources of resilience and resilience dynamics that require management in the context of multilevel adaptive governance. This research found that the Atlantic Europe macro-region is a key focal level for multilevel adaptive governance architecture. The majority of the findings are specific to Atlantic Europe and not generalisable to other maritime macro-regions in Europe.

Synthetic Studies of Azulenyl and Pseudoazulenyl Nitrones

Free radicals have been implicated in various pathological conditions such as, stroke, aging and ischemic heart disease (IHD), as well as neurodegenerative diseases like Alzheimer’s, Parkinson’s, and Huntington’s disease. The role of antioxidants in protection from the harmful effects of free radicals has long been recognized. Trapping extremely reactive free radicals and eliminating them from circulation has been shown to be effective in animal models. Nitrone-based free radical traps have been extensively explored in biological systems. Examples include nitrones such as PBN, NXY-059, MDL-101,002, DMPO and EMPO. However, these nitrones have extremely high oxidation potentials as compared to natural antioxidants such as Vitamin E (á-tocopherol), and glutathione. Becker et al. (1995) synthesized novel azulenyl nitrones, which were shown to have oxidation potentials much lower than that of any of the previously reported nitrone based spin traps. Another azulenyl nitrone derivative, stilbazulenyl nitrone (STAZN), was shown to have an even lower oxidation potential within the range of natural antioxidants. STAZN, a second generation free radical trap, was found to be markedly superior than the two most studied nitrones, PBN and NXY-059, in animal models of cerebral ischemia and in an in vitro assay of lipid peroxidation. In this study, a third generation azulenyl nitrone was synthesized with an electron donating group on the previously synthesized STAZN derivative with the aim to lower the oxidation potential even more. Pseudoazulenes, because of the presence of an annular heteroatom, have been reported to possess even lower oxidation potential than that of the azulenyl counterpart. Therefore, pseudoazulenyl nitrones were synthesized for the first time by extracting and elaborating valtrate from the roots of Centranthus ruber (Red valerian or Jupiter’s beard). Several pseudoazulenyl nitrones were synthesized by using a facile experimental protocol. The physical and biological properties of these pseudoazulenyl nitrones can be easily modified by simply changing the substituent on the heteroatom. Cyclic voltammetry experiments have shown that these pseudoazulenyl nitrones do indeed have low oxidation potentials. The oxidation potential of these nitrones was lowered even more by preparing derivatives bearing an electron donating group at the 3-position of the five membered ring of the pseudoazulenyl nitrone.

ENVIRONMENTAL INFLUENCES AND EPIGENETIC MECHANISMS IN RISK FOR DEPRESSION

Genetic and environmental factors interact to influence vulnerability for internalizing psychopathology, including Major Depressive Disorder (MDD). The mechanisms that account for how environmental stress can alter biological systems are not yet well understood yet are critical to develop more accurate models of vulnerability and targeted interventions. Epigenetic influences, and more specifically, DNA methylation, may provide a mechanism by which stress could program gene expression, thereby altering key systems implicated in depression, such as frontal-limbic circuitry and its critical role in emotion regulation. This thesis investigated the role of environmental factors from infancy and throughout the lifespan affecting the serotonergic (5-HT) system in the vulnerability to and treatment of depression and anxiety and potential underlying DNA methylation processes. First, we investigated the contributions of additive genetic vs. environmental factors on an early trait phenotype for depression (negative emotionality) in infants and their stability over time in the first 2 years of life. We provided evidence of the substantial contributions of both genetic and shared environmental factors to this trait, as well as genetically- and environmentally- mediated stability and innovation. Second, we studied how childhood environmental stress is associated with peripheral DNA methylation of the serotonin transporter gene, SLC6A4, as well as long-term trajectories of internalizing behaviours. There was a relationship between childhood psychosocial adversity and SLC6A4 methylation in males, as well as between SLC6A4 methylation and internalizing trajectory in both sexes. Third, we investigated changes in emotion processing and epigenetic modification of the SLC6A4 gene in depressed adolescents before and after Mindfulness-Based Cognitive Therapy (MBCT). The alterations from pre- to post-treatment in connectivity between the ACC and other network regions and SLC6A4 methylation suggested that MBCT may work to optimize the connectivity of brain networks involved in cognitive control of emotion as well as also normalize the relationship between SLC6A4 methylation and activation patterns in frontal-limbic circuitry. Our results from these three studies strengthen the theory that environmental influences are critical in establishing early vulnerability factors for MDD, driving epigenetic processes, and altering brain processes as an individual undergoes treatment, or experiences relapse.

A hierarchical approach to defining marine heatwaves

Marine heatwaves (MHWs) have been observed around the world and are expected to increase in intensity and frequency under anthropogenic climate change. A variety of impacts have been associated with these anomalous events, including shifts in species ranges, local extinctions and economic impacts on seafood industries through declines in important fishery species and impacts on aquaculture. Extreme temperatures are increasingly seen as important influences on biological systems, yet a consistent definition of MHWs does not exist. A clear definition will facilitate retrospective comparisons between MHWs, enabling the synthesis and a mechanistic understanding of the role of MHWs in marine ecosystems. Building on research into atmospheric heatwaves, we propose both a general and specific definition for MHWs, based on a hierarchy of metrics that allow for different data sets to be used in identifying MHWs. We generally define a MHW as a prolonged discrete anomalously warm water event that can be described by its duration, intensity, rate of evolution, and spatial extent. Specifically, we consider an anomalously warm event to be a MHW if it lasts for five or more days, with temperatures warmer than the 90th percentile based on a 30-year historical baseline period. This structure provides flexibility with regard to the description of MHWs and transparency in communicating MHWs to a general audience. The use of these metrics is illustrated for three 21st century MHWs; the northern Mediterranean event in 2003, the Western Australia ‘Ningaloo Niño’ in 2011, and the northwest Atlantic event in 2012. We recommend a specific quantitative definition for MHWs to facilitate global comparisons and to advance our understanding of these phenomena.

A hierarchical approach to defining marine heatwaves

Marine heatwaves (MHWs) have been observed around the world and are expected to increase in intensity and frequency under anthropogenic climate change. A variety of impacts have been associated with these anomalous events, including shifts in species ranges, local extinctions and economic impacts on seafood industries through declines in important fishery species and impacts on aquaculture. Extreme temperatures are increasingly seen as important influences on biological systems, yet a consistent definition of MHWs does not exist. A clear definition will facilitate retrospective comparisons between MHWs, enabling the synthesis and a mechanistic understanding of the role of MHWs in marine ecosystems. Building on research into atmospheric heatwaves, we propose both a general and specific definition for MHWs, based on a hierarchy of metrics that allow for different data sets to be used in identifying MHWs. We generally define a MHW as a prolonged discrete anomalously warm water event that can be described by its duration, intensity, rate of evolution, and spatial extent. Specifically, we consider an anomalously warm event to be a MHW if it lasts for five or more days, with temperatures warmer than the 90th percentile based on a 30-year historical baseline period. This structure provides flexibility with regard to the description of MHWs and transparency in communicating MHWs to a general audience. The use of these metrics is illustrated for three 21st century MHWs; the northern Mediterranean event in 2003, the Western Australia ‘Ningaloo Niño’ in 2011, and the northwest Atlantic event in 2012. We recommend a specific quantitative definition for MHWs to facilitate global comparisons and to advance our understanding of these phenomena.

Of Marx and Makers: an Historical Perspective on Generative Justice

In Marxist frameworks “distributive justice” depends on extracting value through a centralized state. Many new social movements—peer to peer economy, maker activism, community agriculture, queer ecology, etc.—take the opposite approach, keeping value in its unalienated form and allowing it to freely circulate from the bottom up. Unlike Marxism, there is no general theory for bottom-up, unalienated value circulation. This paper examines the concept of “generative justice” through an historical contrast between Marx’s writings and the indigenous cultures that he drew upon. Marx erroneously concluded that while indigenous cultures had unalienated forms of production, only centralized value extraction could allow the productivity needed for a high quality of life. To the contrary, indigenous cultures now provide a robust model for the “gift economy” that underpins open source technological production, agroecology, and restorative approaches to civil rights. Expanding Marx’s concept of unalienated labor value to include unalienated ecological (nonhuman) value, as well as the domain of freedom in speech, sexual orientation, spirituality and other forms of “expressive” value, we arrive at an historically informed perspective for generative justice. 

Transition metal complexes of some N4-phenylsemicarbazones: crystal structures and spectral studies

The work embodied in this thesis was carried out by the author in the Department of Applied Chemistry, CUSAT, Kochi, during the period 2009-2012. The thesis is an introduction to our attempts to evaluate the coordination behavior of some compounds of our interest. The biological activities of semicarbazones and their metal complexes have been an active area of research during the past years because of their significant role in naturally occurring biological systems. Tridentate NNO and ONO semicarbazone systems formed from heterocyclic and aromatic carbonyl compounds and their transition metal complexes are wellauthenticated compounds in this field and their synthesis, crystal structures and spectral studies are well desirable. Hence, we decided to develop a research program aimed at the syntheses, crystal structures and spectral studies of new N4- phenylsemicarbazones derived from 2-formylpyridine and 3-ethoxysalicylaldehyde and their transition metal complexes and new transition metal complexes of 2- benzoylpyridine-N4-phenylsemicarbazone. In addition to various physicochemical methods of analysis, single crystal X-ray diffraction studies were also used for the characterization of the complexes.

L'apport de la théorie des systèmes dynamiques complexes à l'ontologie du droit international dans la crise- Analyse de l'action normative du Conseil de sécurité

Cette thèse est une réflexion originale sur le droit international dans la crise, car elle aborde le droit international grâce à une théorie peu connue en droit, celle des systèmes dynamiques complexes. L’étude du cas particulier de la gestion normative de la crise par le Conseil de sécurité illustre les intérêts de l’utilisation d’une théorie novatrice en droit. La théorie des systèmes dynamiques complexes offre les outils d’une réflexion sur le droit, fondée sur les interactions du droit avec le contexte particulier dans lequel il intervient, la crise, et ses acteurs. La mise en lumière de ces interactions favorise une lecture critique du droit international dans la crise et permet de renouveler l’ontologie de ce droit. Les dynamiques complexes appréhendées et définies par cette théorie sont utiles lorsqu’il s’agit d’expliquer les atouts et les limites de l’action normative du Conseil. Par ailleurs en renouvellant l’ontologie du droit, la théorie des systèmes dynamiques complexes facilite une lecture prospective de l’action normative du Conseil et insiste sur le rôle institutionnel du droit.

Den offentliga sektorns komplexa adaptiva system : En kvalitativ studie om medarbetarpolicys i praktiken

Intresset för hur HR och ledning kan påverka medarbetarnas beteendemönster och den sociala strukturen inom organisationer har gett upphov till denna undersökning. Med utgångspunkt i teorier om komplexa adaptiva system som perspektiv har jag försökt fånga medarbetarnas förutsättningar att nå organisationers vision och därmed förverkliga medarbetarpolicyn i praktiken. Tillsammans med kontaktpersoner från den undersökta kommunen har jag gjort en djupdykning i en offentlig organisation i syfte att förklara byråkratins inverkan på beteendemönstret hos medarbetarna och hur de tillsammans skapar en social struktur vilken speglar organisationens vision. Syftet med studien är att undersöka hur det adaptiva systemet fungerar i en byråkratisk organisation och vad det betyder för medarbetarnas möjligheter att förverkliga organisationens vision och medarbetarpolicy. Undersökningen har genomförts på en socialförvaltning i en kommun i mellan Sverige och med en kvalitativ metod och semistrukturerade intervjuer har sex respondenter deltagit i undersökningen. Samtliga respondenter har olika befattningar inom organisationen och bidrar därmed med olika perspektiv på samma fenomen. Undersökningens resultat visar att den offentliga verksamhetens byråkratiska organisationsstruktur bidrar till att det bildas olika adaptiva system inom organisationen, där medarbetarnas beteendemönster bildar en social struktur som leder till att visionen och medarbetarpolicyn inte förverkligas. Undersökningen visar även att de adaptiva systemen inom organisationen inte påverkar varandra, då de inte interagerar med varandra inom organisationen. Det som ligger till grund för hur medarbetarnas beteendemönster etableras inom organisationen är kraven från omvärlden, hög arbetsbelastning och avsaknaden av stabilitet i den organisatoriska och sociala arbetsmiljön och inte vad tidigare forskning visat; att det skulle vara hög regelstyrning som ligger till grund för beteendemönstret inom den offentliga sektorn. Slutsatsen är att för att medarbetarna ska kunna förverkliga organisationens vision och medarbetarpolicy kräver det att HR, ledning och medarbetare alla ingår i samma adaptiva system. För att det ska vara möjligt behöver HR upprätta strategier för hur samtliga inom organisationen ska interagera med varandra i det dagliga arbetet. Ledningen och medarbetarna behöver även ha goda möjligheter att kommunicera med varandra regelbundet i en större omfattning än vad de gör idag. Konkreta åtgärder för hur det lämpligen bör genomföras presenteras under diskussionen.