Dissertations / Theses on the topic 'Degraders'

A series of three experiments were conducted to determine the diversity of indigenous chlorobenzoate (CB) degraders in soil and to investigate the use of different methods of bioaugmentation for remediation of contaminated soil. In the first study, soil was amended with either 500 or 1000 μg of 3-CB g⁻¹ and was either uninoculated or inoculated with the 3-CB degrader Comamonas testosteroni BR60. Bioaugmentation with C. testosteroni BR60 increased 3-CB degradation at both contaminant levels, and the increase was more pronounced at the higher level due to contaminant inhibition of indigenous 3-CB degraders. Bioaugmentation also appeared to reduce the deleterious effects that 3-CB contamination had on indigenous soil microbial populations as evidenced by changes in culturable heterotrophic bacterial populations. In the second study, two similar pristine soils were contaminated with 500 μg of 2-, 3-, or 4-CB g⁻¹ . The two soils differed in their ability to degrade the compounds with one degrading 2- and 4-CB and the other degrading 3- and 4-CB. Several hundred degraders were isolated, grouped according to DNA fingerprints, and selected degraders were identified by 16S rDNA sequences. The identity of the CB degraders differed between the two soils. The results indicated that the development of 2-, 3-, and 4-CB degrader populations was site-specific even for the soils that developed under similar soil-forming conditions. The third study also used the two soils from the second study. This project investigated the potential for use of activated soil, which contained an indigenous degrader population, as a bioaugmentation inoculant. An aliquot of a given soil that contained an indigenous 2-, 3-, or 4-CB degrader population was added to a soil that did not have an indigenous degrader population for the same contaminant. The study found that bioaugmentation with activated soil increased degradation of each 2-, 3-, and 4-CB but only if the activated soil was pre-exposed to the contaminant prior to use for bioaugmentation. The results from these three studies indicate that CB degrader populations are diverse and variable in pristine soils and, if not present in contaminated soils, appropriate degrader populations may be established via different bioaugmentation strategies.

Isoprene (2-methyl 1, 3-butadiene) is the most abundant non-methane BVOC (biogenic volatile organic compound) released into the atmosphere. Terrestrial plants are the primary producers of isoprene and release 500-750 million tonnes of isoprene per year, to protect themselves from abiotic environmental stresses such as heat and reactive oxygen species. Many studies have explored isoprene production but very little is known about consumption of isoprene by microbes. Cleveland and Yavitt in 1998 (Cleveland and Yavitt 1998), and more recently Khawand et al. 2016 (Khawand et al. 2016), demonstrated that microbes isolated from terrestrial environments are capable of using isoprene as sole carbon and energy source. By applying cultivation-dependent and cultivation-independent techniques, such as DNA Stable Isotope Probing (Dumont and Murrell 2005), my objective was to determine the distribution, diversity and activity of isoprene-degrading bacteria in the terrestrial environment. Isoprene-degrading microbes were enriched by adding 13 to 50 ppm isoprene to microcosms using topsoil from a willow tree and topsoil/leaves from an oil palm tree. DNA stable isotope probing, using 13C-labelled isoprene, assisted in revealing the diversity of active isoprene degraders by labelling organisms that incorporated the isoprene, directly or indirectly. PCR retrieval of partial 16S rRNA genes from this DNA revealed labelled members of the genera Ramlibacter, Variovorax, Rhodococcus and Methylibium, for willow soil, and Rhodococcus, Gordonia, Aquabacterium, Aquincola, Methylobacterium and members from the Sphingomonadaceae family, for the oil palm tree. Using cultivation-dependent methods I isolated seven phylogenetically different isoprene-utilizing bacteria of the genera Rhodococcus, Nocardioides and Variovorax from willow soil environment; another four phylogenetically different bacteria belonging to the genera Gordonia, Sphingopyxis and Sphingobacterium from the oil palm tree. Results suggest Rhodococcus is a cosmopolitan isoprene-degrader, present in a variety of environments, and different isoprene-degrading bacteria were found associated to willow and oil palm trees.

The thesis consists of two main projects: a) the development of a novel strategy to gain genetic control with spatiotemporal precision, and b) the optimisation of inhibitors of the protein kinase p38α, which has a major role in the homeostasis of tumours and in the regulation of metastasis, invasion and proliferation, amongst other processes in cancer. a) Guaymoxifen is a molecule that is inactive with respect to the Cre method for genetic modification, but can be cleaved by a xeno-enzyme (LigF, artificially expressed in the metastatic cells of our mouse model, but not in the innate cells of the model) to liberate the active compound hydroxytamoxifen (4OHT). When guaymoxifen is administered to a CreER-GFP mouse (which has the potential to express green fluorescent protein upon exposure to 4OHT) that possesses LigF metastatic tumours, 4OHT will only be released around these metastatic tumour cells. Therefore, genetic modification (expression of GFP in this case) will only occur in the cells surrounding the tumour sites (stroma), allowing visualisation and isolation of key stromal cells during tumour development. A drawback was that the liver of the mouse was also capable of cleaving guaymoxifen and releasing 4OHT, which caused genetic recombination to occur away from the stroma and thus generated background noise, which limited the use of this technique in vivo. In order to address this problem, we developed a family of compounds based on guaymoxifen that would be more resistant to oxidative metabolism in the liver, by substitution of the beta- ether bond. Initial biological testing of these compounds identified 2 analogues that were more resistant to liver cleavage, yet could still be effectively cleaved by LigF in vitro. Ongoing work will complete the data needed for proof of concept of this strategy. 4OHT, (the active part), possesses a double bond with four distinct substituents, which leads to the existence of 2 stereoisomers. Only the Z stereoisomer is active against CreER, and furthermore, the proZ isomer of guaymoxifen is preferentially cleaved by LigF over the proE isomer. We therefore synthesised a modified analogue of 4OHT: 2Me-4OHT which favours the formation of the active isomer due to steric repulsion from the additional methyl group. This analogue was demonstrated to have comparable activity to 4OHT in CreER assays and in vivo. We therefore prepared the corresponding compound including the guaiacol moiety and observed that it could be cleaved by LigF to liberate active 2Me-4OHT in vitro. The liberated compound possessed a Z:E isomer ratio that was approximately 8x higher than that of 4OHT. In vivo examination is ongoing to determine the performance of these compounds in the complete mouse models. b) Our objective was to design and synthesise a new family of compounds based on the existing p38α inhibitor PH-797804 (PH), developed by Pfizer. We incorporated a variety of functional groups at different lengths distant from a crucial amide moiety of the molecule, which could be modified without adversely affecting the affinity for the target protein. The added functionalities were amenable to conjugation to moieties for the accumulation in tumour cells, such as peptide sequences or gold nanoparticles. The selective accumulation of these drug conjugates in the tumour cells would avoid the side effects associated with p38α inhibitors, such as skin rash and liver toxicity, identified in a number of phase II clinical trials. Our free analogues, before incorporation of the directing groups, were tested in a number of biological assays and in vivo. They maintained the activity of PH, and in the case of 4-13a even displayed superior activity. A new series of conjugates bound to RGD (an integrin recognition fragment) and analogues of somatostatin (a ligand for somatostatin receptor) were synthesised and shown to possess activity in vitro and preliminary in vivo tests. The conjugates were predicted to have an affinity for the corresponding receptors, which are overexpressed on the surface of many types of tumour cells and would thereby cause the accumulation of the conjugates in tumours. Endosomic assisted internalisation and cleavage would then release the active analogues within the tumour cells. Ongoing testing aims to establish the therapeutic benefit of these conjugates. We also designed a PROTAC (“Proteolysis Targeting Chimera”) using PH as the warhead. After screening of appropriate ligands for E3 ubiquitin ligase and optimisation of the linker, we obtained a family of compounds that induced the ubiquitination and degradation of p38α and p38 in cellular assays at nanomolar concentrations. The degradation took less than 8 hours and was maintained for over 48 hours, in a range of cell lines. These PROTACs were also effective in vivo, whereby p38α was degraded in lung tissue after 16 h when administered intratracheally, but not in nearby tissues such as heart or lung. Ongoing optimisation to improve the solubility and bioavailability of this PROTAC hopes to achieve a novel therapy for use against cancer.
La tesis consiste en dos proyectos principales: a) desarrollo de una estrategia novedosa para la modificación genética con control espaciotemporal, y b) mejora de inhibidores de la proteína p38α, que tiene un papel muy importante en la homeostasis de tumores y en la regulación de la metástasis, invasión y proliferación, etc. a) Una molécula (que denominamos Guaymoxifen) inactiva respeto al método “Cre” de modificar genes, que mediante la acción de una xeno-enzima (LigF, sólo expresada en bacterias, no en las células humanas), se parte y libera hydroxytamoxifen (4OHT, la parte activa). Cuando se administra guaymoxifen a un ratón con tumores que expresan LigF, libera 4OHT sólo alrededor de las células tumorales, y entonces solo se modifica la genética de dichas células. El problema es que en el hígado también se libera 4OHT y causa ruido de fondo en los datos. Para afrontar ésta problema del metabolismo en el hígado, desarrollamos una familia de nuevos análogos de guaymoxifen que fueron más resistentes. Las pruebas biológicas identificaron dos análogos más resistentes, pero 4OHTam todavía fue liberado por la enzima LigF. También sintetizamos un nuevo análogo de 4OHT (la parte activa): 2Me-4OHT, que favorece la formación del estereoisómero activo debido a la repulsión estérica del grupo metilo añadido. Esté análogo tenía una actividad en los ensayos Cre-ER parecido a 4OHT. Preparamos el compuesto correspondiente incluyendo la parte “guay” y vimos en los ensayos de escisión que LigF rompe la molécula, liberando 2Me-4OHT. Así pues, cuando tenga lugar la isomerización se generará una mezcla enriquecida en el isómero activo. b) Nuestro objetivo es diseñar y sintetizar una nueva familia de compuestos basada en un inhibidor ya existente, PH-797804 (PH), desarrollado por Pfizer. Hemos incorporado una variedad de grupos funcionales en estos análogos para que pudiéramos unir grupos directores, como por ejemplo nanopartículas de oro, o secuencias peptídicas, para direccionar el inhibidor al tumor con más especificidad. Así ganaríamos más eficacia y superaríamos los efectos secundarios asociados con los inhibidores de p38α ya descritos. Nuestros análogos, antes de incorporar los grupos directores, fueron probados en ensayos celulares y también in vivo en tumores implantados en ratones y mantuvieron la actividad de la inhibición de p38α, o incluso más alta que la del PH. Una nueva serie de análogos fue sintetizada con nuestros análogos enlazado covalentemente a RGD, y a análogos de somatostatina. El mismo análogo de la serie también fue modificado para incluir un iniciador de “E3 ubiquitin ligase”, para obtener un PROTAC (“Proteolysis Targeting Chimera”) con capacidad de degradar p38α. Después de un programa de optimización de los iniciadores de E3 ubiquitin ligase y optimización del “linker,” conseguimos una familia de compuestos “PROTAC” que degradaban eficazmente la proteína. Estas son las primeras moléculas pequeñas con capacidad para degradar únicamente p38α y p38beta descritas hasta el momento. La degradación fue probada en una variedad de líneas células y también in vivo.

Les hydrocarbures aromatiques polycycliques (HAP) sont des polluants organiques, ubiquistes, potentiellement toxiques et cancérigènes. Dans les sols, la dégradation des HAP est principalement due à l'activité microbienne. Certaines études ont montré que la biodégradation des HAP pouvait être augmentée dans la rhizosphère des plantes où le nombre et l'activité microbienne sont stimulés, grâce aux exsudats racinaires. Cependant les bénéfices des plantes ne sont pas toujours observés, et les exsudats pourraient aussi modifier la biodisponibilité des HAP. Les objectifs de ce travail ont été de mieux comprendre ces interactions sol-plante-microorganismes qui conditionnent le devenir des HAP dans la rhizosphère en suivant notamment (i) les bactéries possédant les gènes codant une HAP-dioxygènase, (ii) les espèces bactériennes impliquées dans la dégradation du phénanthrène, et (iii) la disponibilité et la biodégradation des HAP dans des terres industrielles historiquement contaminées.Les expériences ont été conduites dans des dispositifs à compartiments, lesquels permettent une diffusion des exsudats racinaires dans le sol tout en retenant physiquement les racines, puis en microcosmes avec un ajout d'exsudats racinaires naturels produits à partir d'une culture hydroponique de ray-grass (Lolium perenne, L). Les expériences ont été réalisées dans un premier temps avec du sable en ajoutant du phénanthrène (PHE) et un inoculum bactérien issu d'un sol d'une ancienne cokerie puis directement avec des sols historiquement contaminés en HAP. Les nombres de copies de gènes codant pour l'ADNr 16S et pour des HAP-dioxygènases ont été quantifiés par PCR en temps réel pour estimer la proportion de bactéries dégradantes. Les structures des communautés ont été comparées par électrophorèses (TTGE). En plus de l'analyse des 16 HAP totaux, une extraction non exhaustive des HAP a été réalisée à la cyclodextrine pour en estimer la disponibilité. L'utilisation de la méthode SIP (stable isotope probing) avec du 13C-phénanthrène a permis d'identifier les bactéries directement impliqués sa dégradation dans un sol historiquement contaminé. Les expériences en dispositifs à compartiments ont confirmé que la dissipation du phénanthrène est plus importante lorsque la distance aux racines est plus faible, et montrent que le nombre de copies de gène 16S et de gène de HAP-dioxygénase varie avec l'âge des plantes et du temps de contact des compartiments latéraux avec le tapis racinaire. Mais elles montrent aussi que la dissipation du phénanthrène n'est pas plus importante dans les pots plantés, tandis que dans les expériences en microcosmes une inhibition de la dissipation du PHE a même été observée en présence d'exsudats. La présence d'exsudats racinaires a profondément modifié la structure des communautés dégradant les HAP, et l'expérience SIP a permis d'identifier les bactéries directement impliquées dans la dégradation du 13C-phénanthrène et de montrer qu'elles étaient différentes en présence ou non d'exsudats. En présence d'exsudats, la proportion des bactéries dégradantes dans la population totale est passée de 1 % dans la terre d'origine et dans les traitements sans exsudats à plus de 10 %. Même si les exsudats racinaires ralentissent la dissipation du phénanthrène, en fournissant une source de carbone plus facilement métabolisable, ils ont augmenté la quantité de HAP extractibles à la cyclodextrine dans deux des trois sols historiquement contaminés, suggérant un effet de ceux-ci sur la biodisponibilité des HAP
Polycyclic Aromatic Hydrocarbons (PAH) are organics pollutants, ubiquitous, toxics and potentially carcinogenic. In soil, PAH degradation is mainly attributed to microbial organism. Several studies have thus reported enhanced PAH degradation in soil in the presence of plants. Rhizospheric soil increase the number et the activity of microorganisms in soil by the release of roots exudates. However, bene?cial effects of plants in the remediation are not always observed and roots exudates could be limited PAH biodegradation. The object of this study was to investigate the fate of PAHs in rhizosphere, following (i) the PAH-dioxygenase genes DNA to quantify the PAH-degrading bacteria, (ii) species implicated in phenanthrene biodegradation, and (iii) PAH availability and biodegradation from industrial soils.Different experimental devices have been designed to study detailed processes in the rhizosphere. First is a compartments devices were a nylon mesh permits diffusion of plant soluble substances towards the adjacent root free compartment as a rhizosphere. Secondly microcosms were enriched with natural roots exudates from hydroponic culture of ray-grass (Lolium perenne L.). In first time, experiments were conducted using sand and bacterial inoculum from an industrially PAH-contaminated soil and then directly with a soil historically contaminated by PAH. The Real-Time PCR quantification of 16S rRNA gene copy and of functional PAH-RHD? genes permitted to assess the proportion of a degrading bacteria. Bacterial community structure was approached from Temporal Thermal Gradient gel Electrophoresis (TTGE) fingerprinting, and bands sequencing. Nonexhaustive cyclodextrin-based extraction technique provided a estimate of the ?labile? or available pool of PAH in soil. Use of stable isotope probing (SIP) technique with [13C]phenanthrene allowed a bacterial identification of directly implicated in industrial soil.The presence of exudates modified microbial community of PAH-degrading bacteria. SIP experiment showed that 13C-labelled PHE-degrading bacteria was different depending on the exudates input. Many species having to degrade phenanthrene were able to use exudates. Presence of root exudates increased the proportion of PAH-RHD? genes compared to the bulk soil at the beginning and in microcosms without exudates (respectively 10% and 1 %). However, phenanthene dissipation in sand or soil were weaker with root exudates and aged PAH concentrations has not shifted during incubation time. Nevertheless, the root exudates increased the PAH labile fraction extract with cyclodextrin solution into two in three soils historically contaminated

Bodies Degraded by Friction is a collection of poetry existing in finite spaces. The first section, “A Moment and a Moment and a Moment," attempts to capture in words small passages of time as simple as clicking through a Facebook photo album and as destructive as new love. The second section, “It’s Complicated," is a manuscript in progress detailing a year in the life of an “other woman" negotiating an interpersonal relationship role underrepresented in self-help books and mass media. Several themes run throughout the book: the consequences of the use of technology-mediated communication as digital isolationist mechanisms, the collisions of real/virtual identity and real/virtual place, disruption as a poetic device, and the idea that love is a fleeting and ultimately impermanent state.
Master of Fine Arts

La segmentation des caracteres degrades est un probleme tres complique. Les caracteres coupes et les caracteres colles sont deux types de degradation que nous rencontrons frequemment dans les vieux documents. Beaucoup de systemes de reconnaissance de caracteres restent obsoletes devant ce probleme. Ces systemes peuvent actuellement, reconnaitre des documents complexes : texte et images en nivaux de gris, disposition complique du texte, colonnes, etc. Mais, ces systemes sont incapables de reconnaitre les documents tres degrades. Des milliards de pages sont a scanner et reconnaitre une fois le probleme des caracteres coupes, colles et sous-echantillonnes sera resolu. Nous proposons donc dans cette these des techniques tres efficaces pour resoudre le probleme de segmentation et reconnaissance des caracteres coupes et ceux qui sont colles basees sur la cooperation segmentation/reconnaissance. Ces techniques utilisent plusieurs outils mathematiques comme la logique floue ou les statistiques. Un algorithme regroupant toutes ces techniques est ensuite expose. Il reussit a traiter les chaines de caracteres constituees d'un certain nombre de caracteres coupes ou colles sans une connaissance a priori de la largeur des caracteres ni de leur nombre. Le taux de reconnaissance est de 75% pour les caracteres colles, et de 87% pour les caracteres coupes. Un post-traitement base sur des contraintes lexicales permet facilement de ramener ces taux a 94% pour les caracteres colles et 98% pour les caracteres coupes.

The degradation of soil quality due to anthropogenic causes is globally important, both in terms of ecosystem services and ecological biodiversity. Soil quality reduction is stated to be detrimental for population densities and species diversity of soil invertebrates, including the mesofauna (Acari and Collembola). Within the soil food web, mesofauna occupy several trophic levels and as such facilitate nutrient turnover, fulfilling vital ecosystem functions and services. Understanding soil invertebrate population dynamics not only during degradation, but equally upon ecosystem restoration, is vital to identify possible losses or benefits to healthy ecosystem functioning. Prior to this investigation the Highfield site, Rothamsted Research, had been divided and maintained as grassland, arable cropping or bare fallow for 50 years. The latter resulted in a soil that had low soil organic matter levels, poor structure, low bacterial biomass and virtually no invertebrate population. Investigations into the invertebrate population changes, within both the experimental plots and surrounding land, upon alteration of the existing management strategies was completed over a two year period. Changes to mesofaunal populations were detected across all treatments following conversion. Generally, new fallow and arable management strategies produced low density fluctuating populations affected by the physical disturbance of ploughing and lack of soil organic matter as a basal food resource. Grassland management produced increased species diversity and abundance within a more stable soil food web. Each of the new management strategies developed towards its equivalent management strategy within the control treatments. Although it was apparent that the mesofaunal populations were re-establishing under more favourable environmental conditions, there was no definitive conclusion as to the source of the population increases. An attempt to identify the physical mode of invertebrate movement was completed, utilising a prototype mesocosm to act as a physical barrier, this showed promise for future use in such studies.

Aquesta tesi pretén contribuir a donar resposta a les necessitats que es plantegen des de la pràctica de la restauració ecològica d’espais degradats, així com des de la gestió sostenible dels residus urbans. En un primer treball es valida la utilitat del protocol OCDE-217, basat en l’activitat respiratòria del sòl, per estudiar la toxicitat d’alguns dels metalls pesants habitualment presents en major proporció a les esmenes orgàniques utilitzades en restauració, especialment als fangs de depuradora urbana. En aquest sentit, el protocol OCDE-217 ha estat una metodologia vàlida per a la detecció d’efectes adversos dels tres metalls estudiats, Cr, Zn i Cu, sobre la respiració del sòl induïda per substrat. La magnitud dels efectes inhibidors observats és coherent amb les referències consultades, essent el Cu el metall més tòxic després de 28 dies d’exposició. També s’ha comprovat que l’adició de matèria orgànica fresca emmascara l’efecte dels metalls pesants sobre la respiració del sòl ja que incrementa la biomassa microbiana, així com l’adsorció i la immobilització dels metalls. En un segon treball de la tesi s’entra en la caracterització de diferents tipus d’esmenes orgàniques procedents de residus urbans, així com en l’avaluació dels seus efectes sobre el sòl i la vegetació quan són usats en la construcció de tecnosols per a la restauració de pedreres, abocadors o talussos de carretera. Així s’avaluen els efectes de l’aplicació de fangs de depuradora urbana a curt (2 anys) i mitjà termini (10 anys), en una selecció de tipus d’actuacions de rehabilitació representatives de les realitzades en pedreres de roca calcària. S’ha demostrat que l’ús de fangs de depuradora permet millorar els resultats de la rehabilitació de sòls degradats, a la vegada que es valoritzen residus orgànics i minerals. La construcció de tecnosols amb fangs de depuradora facilita una ràpida revegetació, especialment pel que fa a espècies herbàcies, fet que permet l’estabilització ràpida de talussos i controla l’escorrentiu, la qual cosa redueix també l’erosió superficial, que és un objectiu prioritari en talussos de fort pendent com els que trobem en activitats extractives, infraestructures de transport o abocadors. A mitjà termini (una dècada), els sòls esmenats amb fangs de depuradora afavoreixen l’enriquiment del sòl en matèria orgànica i el segrest de carboni, ja que hem comprovat que contenen fins a cinc vegades més de carboni orgànic que els sòls homòlegs no esmenats. Aquest enriquiment és el resultat de l’augment de la producció primària a causa dels nutrients aportats pels fangs, que encara és evident després de deu anys. Aquest augment de la producció primària es tradueix també en un major recobriment vegetal que protegeix el sòl de l’erosió. Pel que fa als bioestabilitzats, resultants de l’estabilització aeròbica de la fracció orgànica de residus municipals, s’ha constatat que existeix una important heterogeneïtat en relació als principals paràmetres estudiats. Els digests, procedents de la digestió anaeròbica de la matèria orgànica obtinguda per la separació mecànica de la fracció resta dels residus urbans, presenten un contingut baix d’impureses i una major concentració de N que els bioestabilitzats, la qual cosa els fa més adequats per a ser aplicats al sòl. L’últim treball de la tesi es dedica a l’establiment i validació d’un protocol per a l’avaluació de la restauració d’activitats extractives, anomenat RESTOQUARRY. El protocol RESTOQUARRY permet identificar problemes crítics que posen en risc l’èxit de la restauració i que requereixen de canvis profunds en el disseny i l’execució dels treballs. La major part de les restauracions avaluades amb RESTOQUARRY requereixen de mesures correctores per a millorar alguns aspectes de la restauració.
Esta tesis pretende contribuir a dar respuesta a las necesidades que se plantean desde la práctica de la restauración ecológica de espacios degradados, así como desde la gestión sostenible de los residuos urbanos. En un primer trabajo se valida la utilidad del protocolo OCDE-217, basado en la actividad respiratoria del suelo, para estudiar la toxicidad de algunos de los metales pesados habitualmente presentes en mayor proporción en algunas de las enmiendas orgánicas utilizadas en restauración, especialmente los lodos de depuradora urbana. En este sentido, el protocolo OCDE-217 ha sido una metodología válida para la detección de efectos adversos (y también beneficiosos) de los tres metales estudiados, Cr, Zn y Cu, sobre la respiración del suelo inducida por sustrato. La magnitud de los efectos inhibidores observados es coherente con las referencias consultadas, siendo el Cu el metal más tóxico después de 28 días de exposición. También se ha comprobado que la adición de materia orgánica fresca enmascara el efecto de los metales pesados sobre la respiración del suelo ya que incrementa la biomasa microbiana, así como la adsorción y la inmovilización de los metales. En un segundo trabajo de la tesis se entra en la caracterización de diferentes tipos de enmiendas orgánicas procedentes de residuos urbanos, así como en la evaluación de sus efectos sobre el suelo y la vegetación cuando son usados en la construcción de tecnosoles para la restauración de canteras, vertederos o taludes de carretera. Así se evalúan los efectos de la aplicación de lodos de depuradora urbana a corto (2 años) y medio plazo (10 años), en una selección de tipos de actuaciones de rehabilitación representativas. Se ha demostrado que el uso de lodos de depuradora permite mejorar los resultados de la rehabilitación de suelos degradados, a la vez que se valorizan residuos orgánicos y minerales. A medio plazo (una década), los suelos enmendados con lodos de depuradora favorecen el enriquecimiento del suelo en materia orgánica y el secuestro de carbono, ya que hemos comprobado que contienen hasta cinco veces más carbono orgánico que los suelos homólogos no enmendados. Este enriquecimiento es el resultado del aumento de la producción primaria debido a los nutrientes aportados por los lodos, que todavía es evidente después de diez años. Este aumento de la producción primaria se traduce también en una mayor cobertura vegetal que protege el suelo de la erosión. En cuanto a los bioestabilizados, resultantes de la estabilización aeróbica de la fracción orgánica de residuos municipales, se ha constatado que existe una importante heterogeneidad en relación a los principales parámetros estudiados. Esta heterogeneidad se da entre diferentes plantas de tratamiento de residuos, pero también entre diferentes lotes de una misma planta, lo que supone una importante restricción a la hora de hacer generalizaciones para su uso. Los digestatos, procedentes de la digestión anaeróbica de la materia orgánica obtenida por la separación mecánica de la fracción resto de los residuos urbanos, presentan un contenido bajo de impurezas y una mayor concentración de N que los bioestabilizados, lo que los hace más adecuados para a ser aplicados al suelo. El último trabajo de la tesis se dedica al establecimiento y validación de un protocolo para la evaluación de la restauración de actividades extractivas, llamado RESTOQUARRY. El protocolo RESTOQUARRY permite identificar problemas críticos que ponen en riesgo el éxito de la restauración y que requieren de cambios profundos en el diseño y la ejecución de los trabajos. La mayor parte de las restauraciones evaluadas con RESTOQUARRY requieren de medidas correctoras para mejorar algún aspecto de la restauración.
This thesis aims to contribute to respond to the needs that arise from the practice of ecological restoration, as well as from the sustainable management of urban waste. In a first study, the usefulness of the OECD-217 protocol is validated for studying the toxicity of some of the heavy metals usually present in a greater proportion in some of the organic amendments used in restoration, especially sewage sludge. In this sense, the OECD-217 protocol has been a valid methodology for the detection of adverse (and also beneficial) effects of the three metals studied, Cr, Zn and Cu, on substrate-induced soil respiration. The magnitude of the inhibitory effects observed is consistent with the references consulted, with Cu being the most toxic metal after 28 days of exposure. The addition of fresh organic matter has also been shown to mask the effect of heavy metals on soil respiration as it increases microbial biomass, as well as the adsorption and immobilization of metals. A second thesis work is focused on the characterization of different types of organic amendments from urban waste, as well as the evaluation of their effects on the soil and vegetation when used in the construction of technosols for the restoration of quarries, landfills or road slopes. Thus, the effects of the application of urban sewage sludge in the short (2 years) and medium term (10 years) are evaluated, in a selection of representative types of rehabilitation actions. The use of sewage sludge has been shown to improve the results of the rehabilitation of degraded soils, at the same time that organic and mineral wastes are valorized. In the medium term (one decade), soils amended with sewage sludge favor the enrichment of the soil in organic matter, and consequently carbon sequestration, since we have found that they contain up to five times more organic carbon than non-amended homologous soils. This enrichment is the result of the increase in primary production due to the nutrients provided by the sludge, which is still evident after ten years. This increase in primary production also translates into greater plant cover that protects the soil from erosion. As for the biostabilized (Compost-Like-Output), resulting from the aerobic stabilization of the organic fraction of municipal waste, it has been found that there is significant heterogeneity in relation to the main parameters studied. This heterogeneity occurs between different waste treatment plants, but also between different batches of the same plant, which is an important restriction when making generalizations for its use. The digestates, derived from the anaerobic digestion of organic matter obtained by the mechanical separation of the remaining fraction of urban waste, have a low content of impurities and a higher concentration of N than the biostabilized, which makes them more suitable for being applied to the soil. The last work of the thesis is devoted to the establishment and validation of a protocol for the evaluation of the restoration of extractive activities, called RESTOQUARRY. The RESTOQUARRY protocol allows the identification of critical problems that put the success of the restoration at risk and that require profound changes in the design and execution of the work. Most of the restorations evaluated with RESTOQUARRY require corrective measures to improve some aspects of the restoration.

Thesis (M.S. Operations Research) Naval Postgraduate School, September 1999.
"September 1999". Thesis advisor(s): William K. Krebs, Jason McCarley. DTIC Descriptor(s): Image Processing, Target Recognition, Night Vision Devices, Forward Looking Infrared Systems, Theses, Color Displays, Pattern Recognition, Visual Perception, Man Machine Systems, Multispectral. Includes bibliographical references (p. 83-88). Also available online.

Desizing wastewater is largely responsible for the chemical oxygen demand (COD) load in the textile industry wastewater. A larger portion of COD comes from degraded starch in desizing wastewater. Removing the starch from the wastewater by an ultrafiltration process may reduce the environmental problem caused by the textile factory. If the treatment is made in such a way that all starch components are removed from the wastewater, the treated water can be reused by the factory. If the starch in the concentrate is stable, it can also be reused as a sizing agent. This will give the factory an economic advantage.

In this thesis we have studied the fouling mechanisms involved in the ultrafiltration of solution with partially degraded starch in order to find the treatibility of such solutions. The work has mainly been directed to uncover how the different fouling mechanisms depend on the operating parameters, and to find the performance of selected membranes. In addition, different models were evaluated for their validity in predicting the performance of the membranes and the data was fitted to the model that give the best prediction and are physically more meaningful. In addition, the starch solution was concentrated, and the flux, concentration, retention and rejection profiles as a function of concentrating time were investigated.

For the study, we used a partially degraded starch solution as a model solution. The solution was prepared in the laboratory by enzymatic degradation of potato starch to different levels. In order to evaluate the reproducibility of the degraded starch, three replicates were prepared. The reproducibility was determined by comparing the molar mass distribution from HPLSEC analysis and the concentration of reducing sugar from a DNS test for the replicates. The analyses show very good reproducibility. Three starch model solutions with three different degradation levels were chosen for our ultrafiltration experiments to investigate the effect of average molar mass of the starch.

For the ultrafiltration of the solution ES625 (from PCI) and MPT-U20 (from KOCH) membranes were used. Both membranes were used in the investigation of the contribution of different fouling mechanisms to the flux decline during ultrafiltration of the solution. In the evaluation of the performance of ultrafiltration of the starch solution, however, only the ES625 membrane was used. According to the manufacturers, both membranes have nearly equal pure water flux and MWCO. But in our test, we observed a higher and different pure water flux for each type of membrane. The ES625 had a lower flux (higher retention) than the MPTU20 membrane.

In the ultrafiltration of partially degraded starch solution the permeate flux declines very fast and, for a low feed concentration, it reaches a steady state in a very short time. The steady state time was observed to increase with concentration, molar mass and transmembrane pressure drop, and to decrease with cross flow velocity. All the three fouling mechanisms (concentration polarization, adsorption and deposition) were responsible for the flux decline. The major observed contributors are, however, adsorption and deposition. Adsorption is largely responsible at low-pressure operation while the deposition fouling effect is dominant at higher pressures, near or beyond the limiting flux.

For the ES625 membrane, the contribution of adsorptive fouling increases with concentration and decreases with molar mass of the starch, temperature and pH at a given transmembrane pressure and cross flow velocity. The effect of the operating parameters on the depositional fouling is in line with literature. It increases with pressure, concentration, molar mass and temperature, and decreases with cross flow velocity. Its dependence on pressure can be expressed by a power function with exponent larger than 1.0. This seems to due to an increase in thickness and compaction of the starch gel/deposit at the membrane surface as the transmembrane pressure drop is increased. The contribution of the concentration polarization is also dependent on concentration, cross flow velocity and pressure. Its relative contribution increases with concentration while it decreases with an increase in cross flow velocity. In the turbulent flow regime the relation between the resistance contributed by concentration polarization increases almost linearly with transmembrane pressure drop. In the laminar flow regime, however, the relative contribution of the resistance due to concentration polarization increases for the lower range of pressure and decreases for the higher range of pressure. Its relative contribution also increases with temperature and decreases with increasing molar mass. But the overall fouling resistance in the ultrafiltration of the starch solution increases with feed concentration, molar mass of the starch and transmembrane pressure drop and decreases with cross flow velocity and temperature.

The trend of the flux loss due to all fouling mechanisms for MPT-U20 membrane is similar to ES625 membrane except for adsorption and concentration polarization with changes in concentration and molar mass. The difference could be a result of the difference in morphological properties between the two membranes and the experimental procedures used in determining flux data that used for calculating the contributions. From the pure water flux and the retention data, the ES625 membrane seemed to have a smaller pore size than the MPT-U20 membrane.

Among the ultrafiltration models, the resistances-in-series model was chosen for its provision to include all the fouling mechanisms into the model. When our permeate flux data was fitted to the model, it gives a good fit. However, the model fails to give realistic estimates of the contribution of the individual fouling mechanisms. In order to improve this problem, the model was modified by introducing osmotic pressure across the membrane in such a way that the effect of concentration polarization is accounted for. This modified model is more physically meaningful and gives a realistic estimate of the contribution the reversible and irreversible fraction of the overall resistance.

In concentrating mode operation, the permeate was continuously withdrawn and hence, the concentration of starch in the feed tank was increased. At an early stage of ultrafiltration, the permeate flux appeared to increase slightly, which seems, a result a shear thinning of the starch solution when the solution was pumped through the system. For the rest of the operation, the flux was decreasing, the retention was increasing and the rejection of the membrane was shifted to a lower molar mass as the solution in the feed tank got more concentrated as expected. The shift of rejection to the lower molar mass region is due to the fouling layer that reduces the accessibility of the pores of the membrane.

Generally, the flux we obtained in ultrafiltration of a partially degraded starch solution with the ES625 tubular membrane is equal or better than the reported values from an existing ultrafiltration plant that has been used in the textile industry to recover a synthetic sizing agent (PVA) from the desizing wastewater. The retention is, however, rather low. Two or more stages of treatment are needed to get all starch components removed from the wastewater and make the treated water reusable (recycled).

An experiment was set up at Alfred College, in Eastern Ontario, to investigate methods of correcting the negative effects of deep compaction of fine textured soils.
The site was divided into two fields of four treatments with three replicates of each. Treatment 1 was control, treatment 2 subsoiled, treatment 3 compacted and treatment 4 compacted then subsoiled. In year 1 barley was sown in both fields, underseeded with alfalfa in Field 1. The following year alfalfa was grown in Field 1 and corn using minimum tillage in field 2.
Measurements included cone penetration resistance, dry bulk density, and crop yields.
It was found that compaction had a significant effect on lowering yields. However, due to the experiment methodology in the measuring of cone penetration resistance and dry bulk density plus a blocking effect in the corn field, the results were inconclusive statistically as to whether the subsoiling in combination with minimum tillage and alfalfa had an effect of decompacting the soil profile.

One of the lasting concerns in audiology is the unexplained individual differences in speech perception performance even for individuals with similar audiograms. One proposal is that there are cognitive/perceptual individual differences underlying this vulnerability and that these differences are present in normal hearing (NH) individuals but do not reveal themselves in studies that use clear speech produced in quiet (because of a ceiling effect). However, previous studies have failed to uncover cognitive/perceptual variables that explain much of the variance in NH performance on more challenging degraded speech tasks. This lack of strong correlations may be due to either examining the wrong measures (e.g., working memory capacity) or to there being no reliable differences in degraded speech performance in NH listeners (i.e., variability in performance is due to measurement noise). The proposed project has 3 aims; the first, is to establish whether there are reliable individual differences in degraded speech performance for NH listeners that are sustained both across degradation types (speech in noise, compressed speech, noise-vocoded speech) and across multiple testing sessions. The second aim is to establish whether there are reliable differences in NH listeners' ability to adapt their phonetic categories based on short-term statistics both across tasks and across sessions; and finally, to determine whether performance on degraded speech perception tasks are correlated with performance on phonetic adaptability tasks, thus establishing a possible explanatory variable for individual differences in speech perception for NH and hearing impaired listeners.

Thesis (Honors)--Ohio State University, 2006.
Title from first page of PDF file. Document formatted into pages: contains 35 p.; also includes graphics. Includes bibliographical references (p. 28-29). Available online via Ohio State University's Knowledge Bank.

New generation military helicopters are required to fly Nap-of-the-Earth (NoE) roles at night and in poor weather conditions. In these situations the pilot must guide the aircraft through obstacle cluttered environments, retain sufficient stabilised ' control, while at the same time coping with a range of degraded visual conditions. The Useable Cue Environment (UCE) procedures provide a means of assessing handling qualities as a function of available visual information, subsequently suggesting minimum control requirements (Response Types) in order to aid the pilot with the stabilisation of the aircraft. While the UCE procedures are' the preferred industry standard for quantifying and maintaining good levels of handling qualities in DVE, there is no direct appreciation of the difficulties encountered with guiding the aircraft or avoiding obstacles. The aim of this study was to develop the UCE approach by incorporating the guidance function of piloting, subsequently enriching the 'Helicopter Handling Qualities in Degraded Visual Environments' analysis procedures. To date few investigations have taken place to determine how the pilot guides the aircraft at low level and through cluttered environments. Recent studies in this field, involving the University of Liverpool, have suggested the importance of the movement of objects and textures in the visual scene (optical flow) for such prospective flight control. The most recent incarnation of this theory introduces the importance of a parameter called tau, ' , a natural temporal means of control thought to be exercised by animals and humans. '-theory provided a starting point for this investigation, developing into a series of piloted simulation trials to examine guidance based manoeuvring. Using a few carefully selected visual degradations, this extensive simulation campaign helped to identify the important visual information for guidance, such as the visual flow quality and the temporal range through which the pilot can see in order to plan his way through a cluttered environment. These findings have been translated into new UCE limits and overlaid onto the existing UCE chart. Added to these handling qualities prediction methods, a pilot control strategy for performing each of the manoeuvres has been developed using the principles of ' coupling. The possible use of this ,,-based control has been explained through the conceptual design of a tunnel-in-the-sky type flight director.

The problem of sonar images degraded by wave-induced random ship motion and their restoration by filtering methods is investigated. The nature of the random motion is examined in detail, and a model is set up to describe its power spectrum in terms of the sea spectrum and the ship's receptance. A sonar measurement formula and its approximated form is derived. It is shown that the approximation represents a signal with additive coloured noise process. The signal is the measured seafloor profile and is approximated by a first-order Markov process. Several filters are proposed: Kalman Filter, Recursive Least Squares Interpolating (RLSI) Filter, and Adaptive ARMA Filter. In addition, Fast Estimation Algorithm and Adaptive Algorithm are introduced to determine unknown parameters in the Kalman Filter. Simulation results are generated using these filters. Performances are found to be strongly dependent on both signal and noise characteristics, with the exception of the RLSI Filter, which is relatively independent of wind speed, the main noise parameter. Computational complexities, estimation delay and convergence rates associated with the various filters are also examined. Finally, Extended Kalman Filter and Self-Tuning Filter are proposed as possible candidates for dealing with non-stationary, time-varying degradation problem.
Applied Science, Faculty of
Electrical and Computer Engineering, Department of
Graduate

Les performances des systèmes de reconnaissances basés sur l'iris sont très négativement affectées par les relâchements des contraintes lors de l'acquisition des images (sujet mobile ou faiblement coopératif, image acquise loin du capteur…). L’objectif de cette thèse est de proposer une amélioration des algorithmes de segmentation traditionnels afin de pouvoir travailler dans de telles conditions. Nous avons identifié et traité quarte modules qui permettent de limiter l'impact des dégradations des images sur les performances du système de reconnaissance global : • Une localisation précise et robuste de la pupille dans l'image l'œil. Pour cela, nous avons développé une méthode qui supprime les cils et les sourcils de l'image pour faciliter la détection de la pupille. • Une segmentation précise de la texture de l'iris dans l'image. Nous avons étudié plusieurs méthodes de la littérature des Contours Actifs et comparé l'impact de ces méthodes sur les performances de reconnaissances du système complet. • Une estimation précise et robuste des contours anatomique de l'iris indépendamment des occlusions dans l'image. Pour cela, nous avons dérivé les équations des Contours Actifs explicitement pour des cercles et des ellipses. Nous avons par ailleurs proposé une méthodologie efficace pour rendre la détection moins sensible aux minimas locaux. • Une méthode de détection des erreurs de segmentation. Il est en effet important de pouvoir avertir le système de reconnaissance global qu'une erreur s’est produite. Pour cela nous avons développé plusieurs critères d'évaluation de la qualité de segmentation. Nous avons ensuite fusionnés ces mesures en utilisant un algorithme de type <> (SVR) pour former une mesure de qualité globale évaluant la qualité de la segmentation
This thesis is focused on the development of robust segmentation algorithms for iris recognition systems working in degraded acquisition conditions. In controlled acquisition scenarios, iris segmentation is well handled by simple segmentation schemes, which modeled the iris borders by circles and assumed that the iris can only be occluded by eyelids. However, such simple models tend to fail when the iris is strongly occluded or off-angle, or when the iris borders are not sharp enough. In this thesis, we propose a complete segmentation system working efficiently despite the above-mentioned degradations of the input data. After a study of the recent state of the art in iris recognition, we identified four key issues that an iris segmentation system should handle when being confronted to images of poor quality, leading this way to four key modules for the complete system: • The system should be able locate the pupil in the image in order to initialize more complex algorithms. To address this problem, we propose an original and effective way to first segment dark elements in the image that can lead to mistakes of the pupil localization process. This rough segmentation detects high frequency areas of the image and then the system uses the pupil homogeneity as a criterion to identify the pupil area among other dark regions of the image. • Accurate segmentation of the iris texture in the eye image is a core task of iris segmentation systems. We propose to segment the iris texture by Active Contours because they meet both the requirement in robustness and accuracy required to perform segmentation on large databases of degraded images. We studied several Active Contours that varies in speed, robustness, accuracy and in the features they use to model the iris region. We make a comparative evaluation of the algorithms’ influence on the system performance. • A complete segmentation system must also accurately estimate the iris shape in occluded regions, in order to format the iris texture for recognition. We propose a robust and accurate scheme based on a variational formulation to fit an elliptic model on the iris borders. We explicitly derive evolution equations for ellipses using the Active Contours formalism. We also propose an effective way to limit the sensitivity of this process to initial conditions. This part of our work is currently under review for final acceptance in the international journal Computer Vision and Image Understanding (CVIU). • Finally, we address the main issue of automatic detection of segmentation failures of the system. Few works in the literature address measuring the quality of a segmentation algorithm, critical task for an operational system. We propose in this thesis a set of novel quality measures for segmentation and show a correlation between each of them with the intrinsic recognition performance of the segmented images. We perform fusion of the individual quality measures via a Support Vector Regression (SVR) algorithm, in order to propose a more robust global segmentation quality score

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, February 1999.
Includes bibliographical references (leaves 50-52).
Thermo-oxidative aging produces a non-uniform degradation state in PMR-15 resin. A surface layer, usually attributed to oxidative degradation, forms. This surface layer has different properties from the inner material. A set of material tests was designed to separate the properties of the oxidized surface layer from the properties of interior material. Test specimens were aged at 316°C in either air or nitrogen, for durations of up to 800 hours. The thickness of the oxidized surface layer in air aged specimens, and the shrinkage and coefficient of thermal expansion (CTE) of nitrogen aged specimens were measured directly. The nitrogen-aged specimens were assumed to have the same properties as the interior material in the air-aged specimens. Four-point-bend tests were performed to determine modulus of both the oxidized surface layer and the interior material. Bimaterial strip specimens consisting of oxidized surface material and unoxidized interior material were constructed and used to determine surface layer shrinkage and CTE. Results confirm that the surface layer and core materials have substantially different properties.
by Luis C. Tsuji.
S.M.

Inland waters including streams, rivers, reservoirs and lakes are regarded as a significant site of Organic Carbon (OC) cycling, and greenhouse gas production. As a result, there has been significant recent interest in the rates and fate of fluvial carbon exported from organic soils, such as peatlands. Additionally, peatlands can be subject to substantial degradation resulting in high rates of fluvial OC export, and this has led to efforts to repair degraded peatlands through restoration programmes. As a consequence, the study of degraded areas is useful to quantify the upper values of carbon release, understand processes of transformation, and evaluate the success of restoration programmes. Importantly peatlands are also collection areas for drinking water, which has implications for treatment, and requires better understanding of carbon cycling upstream of treatment works, in headwater rivers, reservoirs and pipes. UK upland blanket peat catchments are a key location in which to consider global questions surrounding fluvial carbon export and transformations, as they are highly degraded, provide a source of drinking water supply, and are currently undergoing pioneering methods of landscape scale restoration. This thesis considers Kinder Scout, an area of highly degraded and gullied blanket peatland in the South Pennines, UK. Using analysis of water samples collected over several years in the Kinder reservoir catchment and plateau, this thesis presents three novel contributions to global questions concerning OC cycling and peatlands. Firstly it provides (to date), the only carbon budget for a reservoir in a peat dominated catchment with high Particulate Organic Carbon (POC) export, which demonstrates that reservoirs may be net sources of Dissolved Organic Carbon (DOC), with the implication that POC-DOC interactions are important OC transformation mechanism in degraded systems. Secondly through use of a unique integrated combination of methods, it considers changes in carbon flux and composition in both river, lake and pipe locations, providing detailed understanding of the relative roles of river reaches, reservoirs and supply pipes, in controlling fluvial carbon cycling in peatland systems, and upstream of water treatment works. An important implication here, is that rate and direction of change in water treatability varies through a catchment. Finally, it includes results from the first widespread monitoring of the catchment scale effects of a new method of peatland revegetation. This restoration approach is being applied at landscape scale and the findings here, are that despite fears to the contrary, it does not lead to short term increases in fluvial carbon loss, which is an important piece of evidence supporting practical conservation approaches in these systems. To further enhance this research, a combination of field and laboratory investigations into carbon transformation processes, and ongoing restoration mentoring should be undertaken.

The use of digital images of handwritten historical documents has increased in recent years. This has been possible through the Internet, which allows users to access a vast collection of historical documents and makes historical and data research more attainable. However, the insurmountable number of images available in these digital libraries is cumbersome for a single user to read and process. Computers could help read these images through methods known as Optical Character Recognition (OCR), which have had significant success for printed materials but only limited success for handwritten ones. Most of these OCR methods work well only when the images have been preprocessed by getting rid of anything in the image that is not text. This preprocessing step is usually known as binarization. The binarization of images of historical documents that have been affected by degradation and that are of poor image quality is difficult and continues to be a focus of research in the field of image processing. We propose two novel approaches to attempt to solve this problem. One combines recursive Otsu thresholding and selective bilateral filtering to allow automatic binarization and segmentation of handwritten text images. The other adds background normalization and a post-processing step to the algorithm to make it more robust and to work even for images that present bleed-through artifacts. Our results show that these techniques help segment the text in historical documents better than traditional binarization techniques.

Thesis (Ph. D.) -- University of Maryland, College Park, 2005.
Thesis research directed by: Marine-Estuarine-Environmental Sciences. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

Past studies of object recognition in vision and language have shown that (1) identification of the larger structure of an object is possible even if its component units are ambiguous or missing, and (2) contexts often influence the perception of the component units. The present study asked whether a similar case could be found in audition, investigating (1) whether melody recognition would be possible with uncertain pitch cues, and (2) whether adding contextual information would enhance pitch perception. Sixteen musically trained listeners attempted to identify, on a piano keyboard, pitches of tones in three different context conditions: (1) single tones, (2) pairs of tones, and (3) familiar melodies. The pitch cues were weakened using bandpass filtered noises of varying bandwidths. With increasing bandwidth, listeners were less able to identify the pitches of the tones. However, they were able to name the melodies despite their inability to identify the individual notes. There was no effect of context; whether or not listeners heard single tones, pairs of tones, or melodies did not influence their pitch identification of the tones. Several possible explanations were discussed regarding types of information that listeners had access to, since they could not have relied on detailed features of the melodies.

Heavy reliance on GPS is preventing unmanned air systems (UAS) from being fully inte- grated for many of their numerous applications. In the absence of GPS, GPS-reliant UAS have difficulty estimating vehicle states resulting in vehicle failures. Additionally, naively using erro- neous measurements when GPS is available can result in significant state inaccuracies. We present a simultaneous localization and mapping (SLAM) solution to GPS-degraded navigation that al- lows vehicle state estimation and control independent of global information. Optionally, a global map can be constructed from odometry measurements and can be updated with GPS measurements while maintaining robustness against outliers.We detail a relative navigation SLAM framework that distinguishes a relative front end and global back end. It decouples the front-end flight critical processes, such as state estimation and control, from back-end global map construction and optimization. Components of the front end function relative to a locally-established coordinate frame, completely independent from global state information. The approach maintains state estimation continuity in the absence of GPS mea- surements or when there are jumps in the global state, such as after map optimization. A global graph-based SLAM back end complements the relative front end by constructing and refining a global map using odometry measurements provided by the front end.Unlike typical approaches that use GPS in the front end to estimate global states, our unique back end uses a virtual zero and virtual constraint to allow intermittent GPS measurements to be applied directly to the map. Methods are presented to reduce the scale of GPS induced costs and refine the map’s initial orientation prior to optimization, both of which facilitate convergence to a globally consistent map. The approach uses a state-of-the-art robust least-squares optimization algorithm called dynamic covariance scaling (DCS) to identify and reject outlying GPS measure- ments and loop closures. We demonstrate our system’s ability to generate globally consistent and aligned maps in GPS-degraded environments through simulation, hand-carried, and flight test re- sults.

Parmi les diverses modalités biométriques qui permettent l'identification des personnes, l'iris est considéré comme très fiable, avec un taux d'erreur remarquablement faible. Toutefois, ce niveau élevé de performances est obtenu en contrôlant la qualité des images acquises et en imposant de fortes contraintes à la personne (être statique et à proximité de la caméra). Cependant, dans de nombreuses applications de sécurité comme les contrôles d'accès, ces contraintes ne sont plus adaptées. Les images résultantes souffrent alors de diverses dégradations (manque de résolution, artefacts...) qui affectent négativement les taux de reconnaissance. Pour contourner ce problème, il est possible d’exploiter la redondance de l’information découlant de la disponibilité de plusieurs images du même œil dans la séquence enregistrée. Cette thèse se concentre sur la façon de fusionner ces informations, afin d'améliorer les performances. Dans la littérature, diverses méthodes de fusion ont été proposées. Cependant, elles s’accordent sur le fait que la qualité des images utilisées dans la fusion est un facteur crucial pour sa réussite. Plusieurs facteurs de qualité doivent être pris en considération et différentes méthodes ont été proposées pour les quantifier. Ces mesures de qualité sont généralement combinées pour obtenir une valeur unique et globale. Cependant, il n'existe pas de méthode de combinaison universelle et des connaissances a priori doivent être utilisées, ce qui rend le problème non trivial. Pour faire face à ces limites, nous proposons une nouvelle manière de mesurer et d'intégrer des mesures de qualité dans un schéma de fusion d'images, basé sur une approche de super-résolution. Cette stratégie permet de remédier à deux problèmes courants en reconnaissance par l'iris: le manque de résolution et la présence d’artefacts dans les images d'iris. La première partie de la thèse consiste en l’élaboration d’une mesure de qualité pertinente pour quantifier la qualité d’image d’iris. Elle repose sur une mesure statistique locale de la texture de l’iris grâce à un modèle de mélange de Gaussienne. L'intérêt de notre mesure est 1) sa simplicité, 2) son calcul ne nécessite pas d'identifier a priori les types de dégradations, 3) son unicité, évitant ainsi l’estimation de plusieurs facteurs de qualité et un schéma de combinaison associé et 4) sa capacité à prendre en compte la qualité intrinsèque des images mais aussi, et surtout, les défauts liés à une mauvaise segmentation de la zone d’iris. Dans la deuxième partie de la thèse, nous proposons de nouvelles approches de fusion basées sur des mesures de qualité. Tout d’abord, notre métrique est utilisée comme une mesure de qualité globale de deux façons différentes: 1) comme outil de sélection pour détecter les meilleures images de la séquence et 2) comme facteur de pondération au niveau pixel dans le schéma de super-résolution pour donner plus d'importance aux images de bonnes qualités. Puis, profitant du caractère local de notre mesure de qualité, nous proposons un schéma de fusion original basé sur une pondération locale au niveau pixel, permettant ainsi de prendre en compte le fait que les dégradations peuvent varier d’une sous partie à une autre. Ainsi, les zones de bonne qualité contribueront davantage à la reconstruction de l'image fusionnée que les zones présentant des artéfacts. Par conséquent, l'image résultante sera de meilleure qualité et pourra donc permettre d'assurer de meilleures performances en reconnaissance. L'efficacité des approches proposées est démontrée sur plusieurs bases de données couramment utilisées: MBGC, Casia-Iris-Thousand et QFIRE à trois distances différentes. Nous étudions séparément l'amélioration apportée par la super-résolution, la qualité globale, puis locale dans le processus de fusion. Les résultats montrent une amélioration importante apportée par l'utilisation de la qualité globale, amélioration qui est encore augmentée en utilisant la qualité locale
Among the large number of biometric modalities, iris is considered as a very reliable biometrics with a remarkably low error rate. The excellent performance of iris recognition systems are obtained by controlling the quality of the captured images and by imposing certain constraints on users, such as standing at a close fixed distance from the camera. However, in many real-world applications such as control access and airport boarding these constraints are no longer suitable. In such non ideal conditions, the resulting iris images suffer from diverse degradations which have a negative impact on the recognition rate. One way to try to circumvent this bad situation is to use some redundancy arising from the availability of several images of the same eye in the recorded sequence. Therefore, this thesis focuses on how to fuse the information available in the sequence in order to improve the performance. In the literature, diverse schemes of fusion have been proposed. However, they agree on the fact that the quality of the used images in the fusion process is an important factor for its success in increasing the recognition rate. Therefore, researchers concentrated their efforts in the estimation of image quality to weight each image in the fusion process according to its quality. There are various iris quality factors to be considered and diverse methods have been proposed for quantifying these criteria. These quality measures are generally combined to one unique value: a global quality. However, there is no universal combination scheme to do so and some a priori knowledge has to be inserted, which is not a trivial task. To deal with these drawbacks, in this thesis we propose of a novel way of measuring and integrating quality measures in a super-resolution approach, aiming at improving the performance. This strategy can handle two types of issues for iris recognition: the lack of resolution and the presence of various artifacts in the captured iris images. The first part of the doctoral work consists in elaborating a relevant quality metric able to quantify locally the quality of the iris images. Our measure relies on a Gaussian Mixture Model estimation of clean iris texture distribution. The interest of our quality measure is 1) its simplicity, 2) its computation does not require identifying in advance the type of degradations that can occur in the iris image, 3) its uniqueness, avoiding thus the computation of several quality metrics and associated combination rule and 4) its ability to measure the intrinsic quality and to specially detect segmentation errors. In the second part of the thesis, we propose two novel quality-based fusion schemes. Firstly, we suggest using our quality metric as a global measure in the fusion process in two ways: as a selection tool for detecting the best images and as a weighting factor at the pixel-level in the super-resolution scheme. In the last case, the contribution of each image of the sequence in final fused image will only depend on its overall quality. Secondly, taking advantage of the localness of our quality measure, we propose an original fusion scheme based on a local weighting at the pixel-level, allowing us to take into account the fact that degradations can be different in diverse parts of the iris image. This means that regions free from occlusions will contribute more in the image reconstruction than regions with artefacts. Thus, the quality of the fused image will be optimized in order to improve the performance. The effectiveness of the proposed approaches is shown on several databases commonly used: MBGC, Casia-Iris-Thousand and QFIRE at three different distances: 5, 7 and 11 feet. We separately investigate the improvement brought by the super-resolution, the global quality and the local quality in the fusion process. In particular, the results show the important improvement brought by the use of the global quality, improvement that is even increased using the local quality

The Srivastava Lab is focused on the identification and characterization of genes that play a role in basement membrane remodeling. Previously, we identified putative basement membrane degraders through a genetic screen. One such gene has been suggested to play a role in the maintenance of the stem cell niche in Drosophila melanogaster, but no other information about the role this gene plays in development or disease has been published. Here, data are presented from experiments utilizing Drosophila genetics and immunohistochemistry that provide important insights on the biological role of this gene. Collagenase activity was up-regulated upon overexpression of this gene, confirming it as a basement membrane degrader. Additionally, RNA in-situ hybridization experiment results showed expression in the developing imaginal discs of the 3rd instar larva tissues. Overexpression and knockdown studies further demonstrated morphological defects in a number of tissues, including the wing and the eye, and are suggestive of apoptosis. Acridine orange staining confirmed that cell death occurred when the gene was overexpressed and a cleaved caspase antibody staining indicated that process to be caspase-mediated apoptosis.

The ubiquitin-proteasome pathway plays vital roles in multiple cellular processes including protein turnover and transcription regulation. The fate of a ubiquitinated protein is determined by the number of ubiquitin molecules added and the site to which they are added. Monoubiquitinated proteins are stabilized and often activated, while polyubiquitinated proteins are rapidly targeted for degradation. Major histocompatibility complex class II (MHC II) molecules are a vital part of the immune response and are responsible for presenting antigens to CD4+ T cells. The class II transactivator (CIITA) is the master regulator of MHC II transcription and has been shown to have increased transactivity when monoubiquitinated. The focus of this thesis is on the impact of ubiquitination on CIITA stability and MHC II gene expression through the identification of an E3 ligase that targets and ubiquitinates CIITA.

Il muco è un colloide viscoso che costituisce una barriera fisica in tutte le superfici epiteliali del corpo umano, inclusi il tratto gastrointestinale, respiratorio, riproduttivo e urinario (Alemao et al., 2020; Bansil & Turner, 2018). É secreto dalle cellule mucipare che producono uno strato protettivo completo già dopo pochi giorni dalla nascita (Bunesova et al., 2018). La barriera mucosa è coinvolta in più funzioni come ad esempio l’assorbimento di cofattori e nutrienti, la lubrificazione ed inoltre svolge un ruolo fondamentale in correlazione con il sistema immunitario (Anthony P. Corfield, 2015). Le mucine sono glicoproteine e sono le maggiori costituenti del muco (Bansil & Turner, 2018). Queste ultime sono caratterizzate da un alto livello di glicosilazione, sono composte da oligosaccaridi quali N-acetilglucosammina (GlcNAc), N-acetilgalattosamina (GalNAc), fucosio, galattosio e acido sialico, i quali rappresentano fino all’80% della massa molecolare (Bansil & Turner, 2006). Lo scopo di questo lavoro è stato quello di identificare, attraverso un approccio cultura dipendente e indipendente, la popolazione batterica intestinale isolata in soggetti sani che fosse in grado di degradare la mucina. Le feci di cinque adulti sani sono state sottoposte a tre step successivi di arricchimento in un terreno di crescita contenente la mucina come unica fonte di carbonio e azoto. La popolazione batterica è stata confrontata prima e dopo l’arricchimento mediante la metodica del 16S rRNA gene profiling. Sono state isolate solamente tre specie di anaerobi capaci di sviluppare su mucina: Clostridium celatum, Clostridium tertium e Paraclostridium bifermentans. Di queste tre specie è stata effettuata l’analisi genomica e in parallelo un’analisi comparativa con altri genomi presenti nella banca dati NCBI GenBank, in modo da approfondire gli aspetti funzionali e metabolici, oltre che determinare la loro capacità di utilizzo della mucina. In tutti i genomi analizzati, sono stati identificati geni codificanti glicosidasi (GH) coinvolte nella degradazione della mucina, con un massimo di 25 GH riscontrate nel genoma di C. celatum. I geni coinvolti nei pathway di utilizzo dei singoli monosaccaridi quali Gal, GlcNAc and GalNAc, sono stati riscontrati in tutti i tre genomi, mentre solo C. celatum è in grado di utilizzare il fucosio. I tre ceppi oggetto di studio sono stati inoltre caratterizzati dal punto di vista fisiologico. In tutti i ceppi è stata registrata crescita batterica in un intervallo di pH fra 5.5 e 8, con un optimum di crescita di pH 6.5-7, producendo etanolo, acido acetico, propionico, formico e idrogeno. È stata osservata una propensione a formare biofilm solamente in C. celatum e P. bifermentans. Come altri membri della classe Clostridia, i tre clostridi sono in grado di produrre spore, attraverso le quali resistere a condizioni di stress. Per testare se la formazione di spore aumentasse la sopravvivenza, sono stati effettuati dei trattamenti di esposizione all’ossigeno e alle alte temperature. In seguito all’esposizione all’ossigeno tutti i ceppi sono stati in grado di ripristinare lo sviluppo delle cellule vegetative, sebbene in C. celatum sia stata osservata una maggiore sensibilità allo stress indotto da ossigeno. Diversamente, il trattamento con temperature fino a 80°C ha causato una riduzione massima di circa un ordine logaritmico in tutte le specie analizzate. Infine, sono in corso test in vivo su modelli murini Balb/c, per testare la capacità dei tre isolati di colonizzare la mucosa intestinale e di produrre effetti sul sistema immunitario. Per determinare il loro impatto sul modello murino a seguito del trattamento, verrà valutata l’espressione di interleuchine come IL-1β e IL-10.
Mucus is a viscoelastic gel barrier that covers wet epithelial surfaces throughout the body including gastrointestinal (GI), respiratory, reproductive, and urinary tracts (Alemao et al., 2020; Bansil & Turner, 2018). It is secreted by goblet and mucous cells and achieves a complete layer already several days after birth (Bunesova et al., 2018). Different roles and functions are carried out by mucus barrier such as gaseous exchange, nutrient and cofactor adsorption, lubrification, chemical sensing and an important relationship with the immune system (Anthony P. Corfield, 2015). The major building block of mucus are represented by mucins glycoproteins (Bansil & Turner, 2018). Mucins are characterised by an high level of glycosylation, oligosaccharides such as N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GalNAc), fucose, galactose and sialic acidic, constitute up to 80% of their molecular mass (Bansil & Turner, 2006). The aim of this study was to investigate gut mucin degraders of healthy subjects through a culture dependent and independent approach. The faeces of five healthy adults were subjected to three steps of enrichment in a medium with only mucins as carbon and nitrogen sources. The bacterial community was compared before and after the enrichment by 16S rRNA gene profiling. Only three species of strict anaerobes able to grow on mucin were isolated: Clostridium celatum, Clostridium tertium, and Paraclostridium bifermentans. Genome analysis of the strains was carried out and compared with other available genome present on NCBI GenBank database to better understand their metabolic and functional potential, and to determine their ability to use mucin. Genes coding for glycoside hydrolases (GHs) involved in mucin degradation were found in all the genomes, with a higher abundance in C. celatum that possess at least 25 GHs. The distribution of genes required for utilization of Gal, GlcNAc and GalNAc were widespread among all the strains, while only C. celatum degrades fucose. The three strains were investigated also in terms of physiological characterization and functional properties. They all were able to grow in a pH range between 5.5 and 8, with an optimum of pH 6.5-7, producing ethanol, acetic, propionic, formic acids, and hydrogen. Biofilm-forming ability was observed in C. celatum and P. bifermentans. Like other members of Clostridia class, the three clostridia produced spore that resisted to stress conditions. To evaluate whether spore formation improve survival, tolerance to oxygen and high temperature exposure were checked. The three strains were able to resume vegetative growth after exposure to oxygen, albeit C. celatum resulted more susceptible to oxygen stress, whereas heat treatment up to 80°C caused a decrease of maximum one Log. In vivo experiment on Balb/c mice are in progress, to test the ability of the three strains to colonize intestinal mucus and to exert some effect on immune system. To assess their impact, the expression of IL-1β and IL-10 will be measured after the treatment.

1. The blanket bogs of the southern Pennines and Peak District are severely degraded, attributed to centuries of poor land management, wildfire and atmospheric pollution. Restoration efforts have focussed on the revegetation of bare and eroding peat surfaces, with considerable success. 2. Sphagnum mosses provide the form and function of blanket bog, with their remains making up the majority of the peat body. These species were lost from the region and remain largely absent, despite restoration efforts. 3. As a keystone species of peatlands, their return is essential to the continued provision of ecosystem services derived from these uplands. Hence, their reintroduction is of great importance. 4. Preliminary trials determined Sphagnum can be reintroduced to numerous degraded conditions found on blanket peat, with S. fallax the best performing species. Water availability was strongly implicated as a significant factor, with drought proving fatal to propagules. In areas of dense vegetation, flailing has the potential to increase establishment, but requires further verification. 5. Growth trials indicated the legacy of atmospheric pollution was still exerting influence upon the growth of Sphagnum. Peat from the southern Pennines region was shown to contain elevated concentration of numerous pollutant heavy metals and nutrients. A comparative study of some UK bogs demonstrated the consequences of biogeochemical characteristics, whilst further implicating the importance of water availability in degraded sites. 6. The potential of Sphagnum reintroduction to degraded sites was demonstrated, within the constraints of shorter time scales. Over longer periods, with increased experimentation and subsequent monitoring, further understanding will undoubtedly be gathered. It is essential this knowledge is shared, updated and applied by conservation agencies and parties conducting such work.

Photo-oxidatative degradation in isotactic polypropylene (PP) has been examined in samples made by both injection and compression moulding and using different moulding conditions. Samples were exposed to ultraviolet (UV) radiation in the laboratory for periods up to 48 weeks. The specimens were tested in tension and the fracture surfaces were inspected by scanning electron microscopy. The extent of chemical degradation was assessed by gel permeation chromatography and Fourier transform infrared spectroscopy. The structural characterization of the as-moulded and UV-exposed materials was conducted by differential scanning calorimetry, X-ray diffraction, pole figure analysis, and polarized light microscopy. Filled grades of PP containing talc were also investigated. The mechanical properties of degraded PP were shown to be highly dependent on aspects like the extent and depth-profile of degradation, the character of the polymer physical structure, and the presence of filler and nucleating agent. Injection moulded bars containing weld lines were also investigated, and their mechanical properties were generally poorer than those for equivalent samples without weld regions. With most samples studied here a partial recovery in tensile properties was observed after 6-9 weeks exposure. Analysis of the fracture surfaces indicated that in the specimens with better properties the surface cracks did not propagate into the undegraded interior. An increase in the polymer crystallinity was observed during exposure, caused by rearrangement of molecule segments released by oxidative scission in the non-crystalline region. This process, called chemi-crystallization, continues until a large number of chemical defects is present within the molecules, and it results in surface cracks formed spontaneously during exposure. In injection moulded samples the pattern of surface cracks featured circular arcs radiating from the injection gate and they were correlated with the flow lines generated during mould filling. The concentration of surface cracks in these samples varied with the location in the test bar, according to local variations in crystal orientation. The crystallization of photodegraded PP from the melt was investigated under isothermal and non-isothermal conditions. The kinetics of crystallization, degree of crystallinity, and morphology were shown to depend on the molecular weight and on the presence of chemical impurities within the molecules. The crystal y-phase was formed in specimens exposed for more than 18 weeks. Double peaks were normally observed in DSC heating experiments of unfilled polypropylene and were assigned to crystal re-organization during heating. The existence of different molecule species was detected by DSC and light microscopy, and might also have contributed to the melting behaviour.

Estimation of the acoustic parameters Signal-to-Noise Ratio (SNR), Reverberation Time (T60), Direct-to-Reverberant Ratio (DRR), and clipping level from degraded speech are open research questions. These parameters are important for determining speech quality and intelligibility, and they are widely applicable to speech enhancement and speech recognition systems. Whilst SNR, T60, and DRR are useful priors for dereverberation schemes, indications of clipping and the clipping level are useful for signal restoration. This thesis investigates how accurately and robustly to noise and, in the case of clipping detection, robustness to the coding and decoding process it is possible to estimate these parameters non-intrusively from degraded speech in real-time or near real-time, and introduces a range of novel algorithms. Alongside the algorithms, an international research challenge was staged for which a novel noisy reverberant speech corpus was developed to determine the state-of-the-art in T60 and DRR estimation. In tests, the algorithms presented in this thesis were highly competitive, being able to estimate T60 with Pearson correlation coefficient, ρ = 0.608 and DRR with ρ = 0.314. Both algorithms achieved very low computational complexity with Real-Time Factors (RTFs) of 0.0164 and 0.0589 respectively. The clipping detection algorithms achieved F1 approximately 0.6 for Global System For Mobile Communications (GSM) 06.10 decoded speech, babble noise at 20 dB SNR clipping levels in the range -5 to -20dBFS, and also produce an estimate of the original unclipped signal level.

Cognitive resources, specifically working memory capacity are used for listening to speech, especially in noise. Cognitive resources are limited, and if listeners allocate a greater share of these resources to recovering the input signal in noise, fewer resources are available for interpreting and encoding its linguistic content. Although the importance of CSC for individual success in communicative situations has been acknowledged, this concept has not hitherto been explored experimentally. In this thesis, a CSC test (CSCT) was developed and administered to young adults with normal hearing and older adults with age-related hearing loss. CSCT required executive processing of speech at different memory loads with and without visual cues in different noise conditions. A free recall task using the same material was administered for comparison purposes and a battery of cognitive tests was administered to understand the relation between CSC and established cognitive concepts. The aims of the thesis were to investigate how CSC is influenced by 1) different executive demands and memory loads; 2) background noise; 3) visual cues; 4) aging and concomitant hearing loss. The results showed that 1) CSC was sensitive to memory load, and updating demands reduced CSC more than inhibition demands; 2) CSC was reduced in background noise compared to quiet; 3) visual cues enhanced CSC especially in noise; 4) CSC was reduced with ageing and concomitant hearing loss especially when visual cues were absent, memory demands were  increased and background noise was speech-like. The main finding of this thesis was that visual cues enhanced CSC for older individuals with hearing loss, specifically in adverse listening conditions. This demonstrates the importance of audiovisual testing in audiological assessment. Further, specific cognitive resources depleted during listening in noise were at least partially compensated by other cognitive functions. This thesis is the first step towards a theoretical understanding of CSC and in future, tests of CSC may play a crucial role in planning rehabilitation of persons with hearing loss.
Kognitiva resurser, speciellt arbetsminneskapacitet, förbrukas när vi lyssnar på tal, framförallt i bakgrundsbrus. De kognitiva resurserna är begränsade och ju större del som används till att rekonstruera en inkommande signal, desto färre finns fortsatt tillgängliga för att koda in och tolka dess språkliga innehåll. Trots att betydelsen av kognitiv reservkapacitet för framgångrik kommunikation är erkänd har kognitiv reservkapacitet hittills inte blivit undersökt experimentellt. I detta avhandlingsarbete utvecklades CSCT som ett test av kognitiv reservkapacitet. CSCT administrerades till unga vuxna med normal hörsel och äldre individer med åldersrelaterad hörselnedsättning. CSCT kräver exekutiv bearbetning av talat språk under olika minnesbelastningar, med och utan tillgång till visuell information och med och utan bakgrundsbrus. En fri återgivningsuppgift, baserad på samma material som i CSCT, administrerades för att kunna göra jämförelser. Slutligen administrerades ett kognitivt testbatteri för att förstå relationen mellan kognitiv reservkapacitet och andra kognitiva funktioner. Avhandlingens syfte var att undersöka hur kognitiv reservkapacitet påverkas av 1) olika krav på de exekutiva förmågorna och olika grad av minnesbelastning; 2) bakgrundsbrus; 3) tillgång till visuell information; 4) åldrande och åldersrelaterad hörselnedsättning. Resultaten visade att kognitiv reservkapacitet 1) var känsligt för minnesbelastning och reducerades mer av uppdaterings- än inhibitionskrav; 2) reducerades av bakgrundsbrus; 3) ökade med tillgång till visuell information, framförallt i bakgrundsbrus; 4) var reducerad hos äldre med åldersrelaterad hörselnedsättning, speciellt när visuell information saknades, minnesbelastningen ökades och bakgrundsbruset bestod av talspråk. Huvudfyndet var att visuell information frigjorde kognitiv reservkapacitet hos äldre individer med nedsatt hörsel, speciellt när lyssningssituationen var ogynnsam. Detta visar på betydelsen av audiovisuell testning vid audiologisk bedömning. Resultaten visade vidare att när specifika kognitiva resurser förbrukades under ogynnsamma lyssningsförhållanden kunde andra kognitiva funktioner kompensera för detta. Denna avhandling utgör det första steget mot en teoretisk förståelse av kognitiv reservkapacitet. På sikt kan utvärdering av kognitiv reservkapacitet spela en avgörande roll för planering av rehabilitering i samband med hörselnedsättning.

Biodiversity loss is occurring at an unprecedented rate and most of this loss is due to human induced pressure. This loss in biodiversity had led to concerns that the provision of ecosystem services that humans depend upon might be negatively affected. As such much modern conservation science focusses on preserving biodiversity whilst protecting priority ecosystem services. However, there may be spatial and temporal trade-offs between these services and the biodiversity that is considered important. Characterisation of such the relationships between biodiversity and ecosystem services is vital in order to improve management and policies which aim to protect and restore both biodiversity and ecosystem services. The broad aims of the thesis were to explore biodiversity-ecosystem service relationships in (1) ecosystems invaded by non-native plant species and (2) tropical forests affected by human exploitation and disturbance. Specifically this thesis aimed to answer the questions: 1. What effect do non-native plant invasions have on aboveground carbon storage, belowground carbon storage, carbon sequestration, water quality and water provision? 2. How do changes in species richness affect this ecosystem service provision? 3. How do these changes relate to the woodiness and traits of invasive and native dominant species, and the type of ecosystem invaded? 4. What factors drive differences in residual stand damage, biomass loss and species richness change following selective logging? 5. After deforestation how long do carbon stocks and plant biodiversity take to recover in tropical forests? 6. Do carbon and plant biodiversity differ in their recovery rates? 7. Which areas are priorities for restoration of tropical carbon? All chapters in this thesis make use of large datasets that I collated from the literature and other authors in order to draw broad conclusions about trade-offs and relationships between services and biodiversity In the section concentrating on invasive species my results suggest that non-native invasive plants generally increase the storage of carbon, whilst reducing water quality and availability. This may indicate a fundamental trade-off between services where increased biomass of plants results in higher evapotranspiration and thus water loss, while also enhancing the carbon cycle and nitrogen production of microorganisms. In addition my results suggest that aboveground carbon storage increases as species richness is reduced, showing the opposite relationship to that shown in many biodiversity ecosystem functioning experiments. This is the first time any such relationship has been found between community change and ecosystem level impacts in the context of species invasions. However, it seems likely that this relationship depends on the identity and traits of the species, with invasions in open habitats by woody species likely to drive a negative relationship between richness change and biomass change with the opposite true when grassy species invade woodlands. This result presents a trade-off between conservation priorities that managers will need to consider. In Chapter 3 I investigated the possibility of predicting the impact of non-native invasive plant impacts on ecosystem services by using characteristics and functional traits of both invasive and native species. This work suggested that aboveground carbon storage is most easily predicted by traits and characteristics of native and non-native species, with few other ecosystem services well explained by models. Results suggested that transition from woody to non-woody dominant species resulted in most dramatic changes in aboveground carbon storage. However, interestingly aboveground carbon storage also tended to increase where native species were replaced by species of similar woodiness. Similarly, given that woodiness and size of species are related, there was a positive relationship between the invasive species height and increases in aboveground carbon storage. However, all other ecosystem services were poorly predicted by species traits and characteristics. This work suggests that the most dramatic changes in carbon storage may result from shifts in ecosystems that resemble regime shifts. Future work addressing invasive species from this perspective is warranted as many invasions resemble such shifts. In Chapter 4 I investigated the relationships between logging intensity and methods and residual stem damage, biomass loss and species richness change in tropical logged forests. Many syntheses of the logging literature have made little distinction between logged sites, and only one has explored any of the mechanisms that may drive heterogeneity in logging impacts. This is particularly surprising given that Reduced Impact Logging (RIL) has been implemented relatively widely principally to reduce carbon loss from logged forests. My results from this chapter suggest that the principal driver of logging impacts is the intensity at which logging is carried out, showing broadly negative relationships with biomass and tree species richness change and a positive relationship with residual stem damage. Interestingly, RIL appeared to reduce residual stem damage slightly but evidence for this effect was weaker in other analyses. These analyses also suggest a slight increase in tree species richness at low logging intensities, showing some similarities to intermediate disturbance hypothesis type relationships. This is suggestive of a complex relationship between tree species richness and biomass changes during logging that deviated substantially from that suggested in grassland biodiversity-ecosystem function experiments. This is as far as I know the first time this relationship has been suggested in the context of logged forests. The result from this chapter also suggest that there is weak support that RIL reduces logging damage at low intensities but little evidence that this is reflected by changes in biomass. Further studies are needed to discern the effect of RIL over a wide range of logging intensities. Chapter 5 investigates tropical forest recovery following agricultural clearance. In this chapter I aimed to identify the recovery times of different above and belowground carbon pools and tree and epiphyte species richness as well as tree species composition using studies that had paired mature forest sites as comparators. Surprisingly this chapter represents the first attempt to generalise about this recovery rate. The results suggest that following clearance carbon and species richness of plants recovers relatively quickly (<100 years), but species indicative of old forests are rarely present in recovering forests and show few signs of recovery. Thus, while carbon recovery goals may be achievable full recovery of plant biodiversity may require centuries. This slow recovery may be aided by active restoration. Finally in Chapter 6 I investigated which areas should be considered as priorities when restoring tropical forests for carbon storage and bird biodiversity. In this chapter I found evidence of spatial trade-offs between carbon storage and bird species recovery. Empirical models suggested that carbon is accumulated most rapidly in forests with long growing seasons, while probability of bird species presence was primarily driven by habitat specificity, range size and forest cover. Model projections suggested that areas that should be considered a priority for restoration targeting carbon storage are found in the wet tropics while priorities for restoration of bird biodiversity are found in mountainous areas. These analyses indicated that there was no relationship between the two goals, but that by using model projections it was possible to identify areas that maximised both. In summary work in this thesis provides the best synthesis of the relationships between biodiversity and ecosystem services in the context of non-native invasive plants, and selective logging and recovery from tropical forest clearance to date. This is of particular value because such relationships have rarely been explored in these contexts despite widespread and of global importance for conservation.

Intensive agricultural practices and increasing mining activities, driven by increasing world pollution and rapid economic development in the past decades, have resulted in a significant increase in degraded lands on a global scale. The key features of these degraded lands include high availability of heavy metals, low concentrations of organic matter and nutrients [e.g. nitrogen (N)], high alkalinity, salinity and sodicity, high acidity, soil erosion and soil structural decline. One of examples is the increasing deposition of bauxite-processing residue from bauxite ore refineries, with the current global storage of bauxite residue of about 3 Gt and the estimated annual world production of bauxite-processing residue of 120 Mt. The rehabilitation of bauxite residue storage areas is essentially required but frequently retarded by the hostile conditions such as high alkalinity and sodicity, low fertility and high hydraulic conductivity. To deal with these environmental issues, effective mitigation and remediation strategies are needed. One of remediation options is the amendment of different organic (biosolids, composts, biochars etc.) and inorganic materials (lime, fertilizers etc.) to improve soil chemical, physical and biological properties in degraded lands. Biochar, as a carbon-rich material, can be produced under pyrolytic conditions, wildfires or prescribed burning for fire management. Biochars have long-term stability and are considered to be able to improve soil health and plant productivity by reducing concentrations of available heavy metals and increasing nutrient (e.g. N) and water retention. However, properties of biochars vary with their feedstock materials and production (e.g. pyrolysis) conditions. Consequently the effectiveness of biochar amendments is different as a result of interactions of different biochar’s properties and soil properties.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
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Biocatalysis continues to be a powerful tool for the efficient synthesis of optically pure pharmaceuticals that are difficult to access via conventional chemistry. The efficient application of biocatalysis requires the availability of suitable enzymes with high activity and stability under process conditions. However, the borderline stability of biocatalysts in many types of reaction media has often prevented or delayed their implementation for industrial-scale syntheses of fine chemicals and pharmaceuticals. Consequently, there is great interest in understanding the effects of solution conditions on protein stability, as well as in developing strategies to improve enzyme stability and activity in desired reaction media. The enzyme transketolase (TK; E.C. 2.2.1.1) from Escherichia coli is an important biocatalyst in stereo-specific carbon-carbon bond synethesis. The power of transketolase is further augmented when the bioconversion takes place in a multi-step biotransformation in which transketolase and transaminases are employed in series to create chiral amino alcohols from achiral substrates. These compounds are synthetically very useful in the production of a range of compounds with pharmaceutical application. Although many useful reactions have been reported for TK, many of the substrates and products are unstable or insoluble at the pH or temperature range for which the enzyme has optimum activity in aqueous media. Understanding the activity and structural stability of transketolase under bioprocess conditions will Biocatalysis continues to be a powerful tool for the efficient synthesis of optically pure pharmaceuticals that are difficult to access via conventional chemistry. The efficient application of biocatalysis requires the availability of suitable enzymes with high activity and stability under process conditions. However, the borderline stability of biocatalysts in many types of reaction media has often prevented or delayed their implementation for industrial-scale syntheses of fine chemicals and pharmaceuticals. Consequently, there is great interest in understanding the effects of solution conditions on protein stability, as well as in developing strategies to improve enzyme stability and activity in desired reaction media. The enzyme transketolase (TK; E.C. 2.2.1.1) from Escherichia coli is an important biocatalyst in stereo-specific carbon-carbon bond synethesis. The power of transketolase is further augmented when the bioconversion takes place in a multi-step biotransformation in which transketolase and transaminases are employed in series to create chiral amino alcohols from achiral substrates. These compounds are synthetically very useful in the production of a range of compounds with pharmaceutical application. Although many useful reactions have been reported for TK, many of the substrates and products are unstable or insoluble at the pH or temperature range for which the enzyme has optimum activity in aqueous media. Understanding the activity and structural stability of transketolase under bioprocess conditions will improve our capacity to comprehend and ultimately to engineer it to make it work at a broader range of pHs and temperatures, and also in the presence of organic co-solvents. This will potentially help to reduce process development times and also increase the stability and solubility of substrates and products. To provide further insight into the underlying causes of TK deactivation in process conditions, the effects of temperature, pH and organic solvents on the structure, stability, aggregation and activity of Escherichia coli transketolase were characterized in Chapters 3 and 4. The results provided useful information for the engineering of TK enzymes with improved thermostability or extreme pH tolerance and in organic solvent mixtures. For thermostability and tolerance to low pH, mutations may be usefully targeted towards regions of protein sequence predicted to have a high propensity for aggregation. For the retention of biocatalytic activity at high pH or temperatures, stabilisation of the cofactor binding loops were found to be an attractive target. By contrast, the results in aqueous-solvent mixtures instead implied that the solvent dependence of catalytic activity cannot be simply explained by only one mechanism such as active-site binding or the replacement of water molecules, and that the effect of different solvents on protein structure penetration, denaturation and aggregation must also be considered. In the final Chapter, mutagenesis was targeted to the cofactor binding loops to further evaluate their impact on thermal stability. one mutant was found that successfully improved the stability of E. coli transketolase at elevated temperatures, giving a 3 fold specific activity increase at 60 oC compared to wild-type TK.

We investigate the use of noise degraded facial images in the application of facial expression recognition. In particular, we trained Gabor+SVMclassifiers to recognize facial expressions images with various types of noise. We applied Gaussian noise, Poisson noise, varying levels of salt and pepper noise, and speckle noise to noiseless facial images. Classifiers were trained with images without noise and then tested on the images with noise. Next, the classifiers were trained using images with noise, and then on tested both images that had noise, and images that were noiseless. Finally, classifiers were tested on images while increasing the levels of salt and pepper in the test set. Our results reflected distinct degradation of recognition accuracy. We also discovered that certain types of noise, particularly Gaussian and Poisson noise, boost recognition rates to levels greater than would be achieved by normal, noiseless images. We attribute this effect to the Gaussian envelope component of Gabor filters being sympathetic to Gaussian-like noise, which is similar in variance to that of the Gabor filters. Finally, using linear regression, we mapped a mathematical model to this degradation and used it to suggest how recognition rates would degrade further should more noise be added to the images.