Mg/Ca and Sr/Ca in calcites and estimated distribution coefficients in marine sediments (Table 2)

Recrystallization processes in marine sediments can alter the extent to which biogenic calcite composition serves as a proxy of oceanic chemical and isotopic history. Models of calcite recrystallization developed to date have resulted in significant insights into these processes, but are not completely adequate to describe the conditions of recrystallization. Marine sediments frequently have concentration gradients in interstitial dissolved calcium, magnesium, and strontium which have probably evolved during sediment accumulation. Realistic, albeit simplified, models of the temporal evolution of interstitial water profiles of Ca, Mg, and Sr were used with several patterns of recrystallization rate variation to predict the composition of recrystallized inorganic calcite. Comparison of predictions with measured Mg/Ca and Sr/Ca ratios in severely altered calcite samples from several Deep Sea Drilling Project sites demonstrates that models incorporating temporal variation in interstitial water composition more successfully predict observed calcite compositions than do models which rely solely on present-day interstitial water chemistry. Temporal changes in interstitial composition are particularly important in interpreting Mg/Ca ratios in conjunction with Sr/Ca ratios. Estimates of Mg distribution coefficients from previous observations in marine sediments, much lower than those in laboratory studies of inorganic calcite, are confirmed by these results. Evaluation of the effects of diagenetic alteration of biogenic calcium carbonate sediment must be a site-specific process, taking into account accumulation history, present interstitial chemistry and its variation in the past, and sample depths and ages.

Statistically robust representation and comparison of mortality profiles in archaeozoology

Archaeozoological mortality profiles have been used to infer site-specific subsistence strategies. There is however no common agreement on the best way to present these profiles and confidence intervals around age class proportions. In order to deal with these issues, we propose the use of the Dirichlet distribution and present a new approach to perform age-at-death multivariate graphical comparisons. We demonstrate the efficiency of this approach using domestic sheep/goat dental remains from 10 Cardial sites (Early Neolithic) located in South France and the Iberian Peninsula. We show that the Dirichlet distribution in age-at-death analysis can be used: (i) to generate Bayesian credible intervals around each age class of a mortality profile, even when not all age classes are observed; and (ii) to create 95% kernel density contours around each age-at-death frequency distribution when multiple sites are compared using correspondence analysis. The statistical procedure we present is applicable to the analysis of any categorical count data and particularly well-suited to archaeological data (e.g. potsherds, arrow heads) where sample sizes are typically small.

Sound Art and Public Engagement in the Built Environment: Reflections from an Architecture Center

This article explores the deployment of sound in architectural-curatorial and community engagement contexts through the work of PLACE, a multidisciplinary not-for-profit architecture center in Belfast, Northern Ireland. The author, who worked with PLACE and contributed to the projects discussed here, contextualizes architecture centers and their relationship with sound before examining the specific case of sound and sound art in Northern Ireland and case studies of projects delivered by PLACE. Specifically, the article evaluates two sound installation artworks and three community engagement projects for young audiences. As a means of curating urbanism and architecture, sound-art-as-public-art affords useful strategies to examine, describe or critique the environment as alternatives to traditional architecture exhibition formats. Sound’s temporality and materiality allow sound art works to exist as temporary sculptural interventions in the urban sphere, with attendant implications for public art procurement and urban acoustics. Rich territories of engagement are opened when using sound in a community participatory context.

Modelling the effectiveness of grass buffer strips in managing muddy floods under a changing climate

Muddy floods occur when rainfall generates runoff on agricultural land, detaching and transporting sediment into the surrounding natural and built environment. In the Belgian Loess Belt, muddy floods occur regularly and lead to considerable economic costs associated with damage to property and infrastructure. Mitigation measures designed to manage the problem have been tested in a pilot area within Flanders and were found to be cost-effective within three years. This study assesses whether these mitigation measures will remain effective under a changing climate. To test this, the Water Erosion Prediction Project (WEPP) model was used to examine muddy flooding diagnostics (precipitation, runoff, soil loss and sediment yield) for a case study hillslope in Flanders where grass buffer strips are currently used as a mitigation measure. The model was run for present day conditions and then under 33 future site-specific climate scenarios. These future scenarios were generated from three earth system models driven by four representative concentration pathways and downscaled using quantile mapping and the weather generator CLIGEN. Results reveal that under the majority of future scenarios, muddy flooding diagnostics are projected to increase, mostly as a consequence of large scale precipitation events rather than mean changes. The magnitude of muddy flood events for a given return period is also generally projected to increase. These findings indicate that present day mitigation measures may have a reduced capacity to manage muddy flooding given the changes imposed by a warming climate with an enhanced hydrological cycle. Revisions to the design of existing mitigation measures within existing policy frameworks are considered the most effective way to account for the impacts of climate change in future mitigation planning. 

Ecological effects of flow and temperature regimes on fish communities in temperate rivers

Les organismes aquatiques sont adaptés à une grande variabilité hydrique et thermique des rivières. Malgré ceci, la régulation des eaux suscite des changements aux débits qui peuvent provoquer des impacts négatifs sur la biodiversité et les processus écologiques en rivière. Celle-ci peut aussi causer des modifications au niveau des régimes thermiques et des caractéristiques de l’habitat du poisson. Des données environnementales et biologiques décrivant l’habitat du poisson existent, mais elles sont incomplètes pour plusieurs rivières au Canada et de faible qualité, limitant les relations quantitatives débit-température-poissons à un petit nombre de rivières ou à une région étudiée. La recherche menée dans le cadre de mon doctorat concerne les impacts de la génération d'hydroélectricité sur les rivières; soit les changements aux régimes hydriques et thermiques reliés à la régulation des eaux sur la variation des communautés ichtyologiques qui habitent les rivières régulées et naturelles au Canada. Suite à une comparaison d’échantillonnage de pêche, une méthode constante pour obtenir des bons estimés de poisson (richesse, densité et biomasse des espèces) a été établie pour évaluer la structure de la communauté de poissons pour l’ensemble des rivières ciblées par l’étude. Afin de mieux comprendre ces changements environnementaux, les principales composantes décrivant ces régimes ont été identifiées et l’altération des régimes hydriques pour certaines rivières régulées a été quantifiée. Ces résultats ont servi à établir la relation significative entre le degré de changement biotique et le degré de changement hydrique pour illustrer les différences entre les régimes de régulation. Pour faire un complément aux indices biotiques déjà calculés pour l’ensemble des communautés de poissons (diversité, densité et biomasse des espèces par rivière), les différences au niveau des guildes de poissons ont été quantifiées pour expliquer les divers effets écologiques dus aux changements de régimes hydriques et thermiques provenant de la gestion des barrages. Ces derniers résultats servent à prédire pour quels traits écologiques ou groupes d’espèces de poissons les composantes hydriques et thermiques sont importantes. De plus, ces derniers résultats ont servi à mettre en valeur les variables décrivant les régimes thermiques qui ne sont pas toujours inclues dans les études hydro-écologiques. L’ensemble des résultats de cette thèse ont des retombées importantes sur la gestion des rivières en évaluant, de façon cohérente, l’impact de la régulation des rivières sur les communautés de poissons et en développant des outils de prévision pour la restauration des écosystèmes riverains.

Macroinvertebrate Diversity in Urban and Rural Ponds: Implications for Freshwater Biodiversity Conservation

Ponds are among the most biodiverse freshwater ecosystems, yet face significant threats from removal, habitat degradation and a lack of legislative protection globally. Information regarding the habitat quality and biodiversity of ponds across a range of land uses is vital for the long term conservation and management of ecological resources. In this study we examine the biodiversity and conservation value of macroinvertebrates from 91 lowland ponds across 3 land use types (35 floodplain meadow, 15 arable and 41 urban ponds). A total of 224 macroinvertebrate taxa were recorded across all ponds, with urban ponds and floodplain ponds supporting a greater richness than arable ponds at the landscape scale. However, at the alpha scale, urban ponds supported lower faunal diversity (mean: 22 taxa) than floodplain (mean: 32 taxa) or arable ponds (mean: 30 taxa). Floodplain ponds were found to support taxonomically distinct communities compared to arable and urban ponds. A total of 13 macroinvertebrate taxa with a national conservation designation were recorded across the study area and 12 ponds (11 floodplain and 1 arable pond) supported assemblages of high or very high conservation value. Pond conservation currently relies on the designation of individual ponds based on very high biodiversity or the presence of taxa with specific conservation designations. However, this site specific approach fails to acknowledge the contribution of ponds to freshwater biodiversity at the landscape scale. Ponds are highly appropriate sites outside of protected areas (urban/arable), with which the general public are already familiar, for local and landscape scale conservation of freshwater habitats.

'Scratch' locative audio drama - report to BBC executives on trial at BBC FreeThinking 2008

‘Scratch’ investigates the use of physical space as a representation of narrative and dramatic structure. An audio-drama, it is a world-first in being location-sensitive without being tied to any particular place (preceding attempts by others have emphasised location-specific aspects of the genre). Developed in collaboration with and part-funded by BBC Radio Drama, it builds on research undertaken for ‘Dragons’ (output 4). It uses pre-recorded audio on GPS-enabled mobile devices allowing sounds to be virtually attached to locations in an outdoor space. As participants move, they encounter scenes forming a coherent drama which behave differently if the same place is visited more than once. This translocational approach opens novel artistic possibilities exploited through team expertise in narrative, sound design and advanced interaction. It is also significant in the economics of broadcast media as a more viable proposition than the many experimental locative experiences which have been site-specific: this was of great interest to the BBC. The public performance selected for BBC FreeThinking, 1-2 September 2008 in Liverpool as part of European Capital of Culture was reported in a co-authored 2009 conference presentation at ISEA, Belfast, 26-29 August 2009 and in a co-authored short chapter in Spierling and Szilas (eds.) Interactive Storytelling, Springer 2008. Boyd Davis directed the project and devised and undertook the evaluation with 40 trial listeners, reporting to BBC executives (http://researchonline.rca.ac.uk/1000/) for whom a second trial was also run in London in 2009. The evaluation used interview, video observation and a questionnaire combining an open question at the beginning with more specific questions later, avoiding channelling respondents' reactions immediately after the experience into issues which might not be uppermost in their minds, while also yielding data capable of rigorous analysis. The evaluation was to provide feedback to the makers of the drama and to guide policy at the BBC. [287] Participants were recruited principally through the publicity for FreeThinking 2008 – mainly via the festival website. The average age of participants was 40. The gender of participants was 20 males, 17 females and 3 null returns. The evaluation strategy was to combine an open question at the beginning with more specific questions later. In this way we avoided channeling respondents' initial opinions immediately after the experience into issues which might not be uppermost in their minds, while also yielding data capable of rigorous analysis. The purpose of the evaluation was to provide guidance for ourselves as the makers of the drama and to guide policy at the BBC on locative and other interactive media. The responses are analysed in the report.

Leave a light on – Terracotta lamps from Agia Paraskevi of Arachamitai, from the Classical period until Roman times

This thesis deals with terracotta lamps found at the archaeological site of Agia Paraskevi of Arachamitai during the years 2010–2014. The research questions are: What kind of lamps were used on the site and when? For what purposes were the lamps used? Where were they manufactured? In order to address these questions, a total of fifty lamps have been chosen to form the body of research material. To answer the first research question, a typology for these lamps has been created with twenty-one types and one variant, after examining various lamp typologies and previous publications. The find contexts and distribution of the lamps are both examined to test the dates for the different lamp types gathered from other publications, and to answer the question on what purposes the lamps were used on the site. Visual observation of the clay of the lamps and information on clay materials from other sites are both examined to determine the lamps' origins. The lamps in this study date from the 5th century BC to the 2nd century AD. The find contexts allow the dating of the lamps according to the other publications, but suggestions of more site-specific dates are given to some lamps. The distribution of the lamps indicates that while most were used for everyday lighting at the sanctuary, some may have had ritual connections. Most of the lamps were manufactured locally or at a nearby Arcadian site. Few lamps can be regarded as imports.

megaTAL-mediated Gene Editing at the CCR5 locus

Thesis (Ph.D.)--University of Washington, 2016-08

Theatrical Latency: Walking Katrina Palmer’s The Loss Adjusters

In this article I introduce the term ‘theatrical latency’ as a pleasurable effect experienced when listening to sound in relation to visual perception. Latency refers to both the phenomena of audio delay (in feedback from analogue to digital conversion and the momentary lapses experienced when playing live with recorded music) and a theatrical sensation that comes from the reanimation of visual environments through aural framing. In this configuration, the notion of latency takes on a double meaning as both a recorded phenomenon and the retrieval of something dormant within physical objects, sites or materials. These ideas will be introduced through my experience of walking Katrina Palmer’s site-specific audio work The Loss Adjusters (2015) on the island of Portland (UK). The audio tracks create an extended meditation on Portland, interweaving specific locations and histories with fictional characters and ghosts of the island.

Redefining Urban Alleywalls: Urban Design for Active Public Space in Maynard Alley, Chinatown-International District, Seattle

Thesis (Master's)--University of Washington, 2016-06

Environmental impacts of freshwater use and suspended solids in life cycle assessment

Perturbation of natural ecosystems, namely by increasing freshwater use and its degradative use, as well as topsoil erosion by water of land-use production systems, have been emerging as topics of high environmental concern. Freshwater use has become a focus of attention in the last few years for all stakeholders involved in the production of goods, mainly agro-industrial and forest-based products, which are freshwater-intensive consumers, requiring large inputs of green and blue water. This thesis presents a global review on the available Water Footprint Assessment and Life Cycle Assessment (LCA)-based methods for measuring and assessing the environmental relevance of freshwater resources use, based on a life cycle perspective. Using some of the available midpoint LCA-based methods, the freshwater use-related impacts of a Portuguese wine (white ‘vinho verde’) were assessed. However, the relevance of environmental green water has been neglected because of the absence of a comprehensive impact assessment method associated with green water flows. To overcome this constraint, this thesis helps to improve and enhance the LCA-based methods by providing a midpoint and spatially explicit Life Cycle Impact Assessment (LCIA) method for assessing impacts on terrestrial green water flow and addressing reductions in surface blue water production caused by reductions in surface runoff due to land-use production systems. The applicability of the proposed method is illustrated by a case study on Eucalyptus globulus conducted in Portugal, as the growth of short rotation forestry is largely dependent on local precipitation. Topsoil erosion by water has been characterised as one of the most upsetting problems for rivers. Because of this, this thesis also focuses on the ecosystem impacts caused by suspended solids (SS) from topsoil erosion that reach freshwater systems. A framework to conduct a spatially distributed SS delivery to freshwater streams and a fate and effect LCIA method to derive site-specific characterisation factors (CFs) for endpoint damage on aquatic ecosystem diversity, namely on algae, macrophyte, and macroinvertebrates organisms, were developed. The applicability of this framework, combined with the derived site-specific CFs, is shown by conducting a case study on E. globulus stands located in Portugal as an example of a land use based system. A spatially explicit LCA assessment was shown to be necessary, since the impacts associated with both green water flows and SS vary greatly as a function of spatial location.

Distribuição dos metais nas poeiras colhidas em Estarreja: estudo da mobilidade e impacto potencial dos metais no ambiente

As poeiras urbanas, vulgarmente designadas na literatura por street dusts ou road dusts, são misturas heterogêneas de partículas minerais do solo e partículas resultantes do tráfego, formando um material com características únicas e específicas de cada local. Estas partículas, geralmente enriquecidas com elementos potencialmente tóxicos, quando inaladas ou ingeridas poderão ser um risco para a saúde das populações. Neste trabalho foram recolhidas 21 amostras de poeiras urbanas na cidade de Estarreja assim como amostras representativas de partículas relacionados com o tráfego (poeiras resultante do desgaste dos travões e das marcações dos pavimentos e estradas) com o objetivo de investigar a contribuição relativa destas partículas no comportamento geoquímico dessas amostras e o risco associado para as populações locais. Para a concretização do objetivo proposto caracterizou-se química e mineralogicamente as amostras de poeiras urbanas e as partículas relacionadas com o tráfego e avaliou-se a disponibilidade e bioacessibilidade para três elementos considerados potencialmente tóxicos (Cu, Pb e Zn) usando uma combinação de ensaios: (a) digestão ácida; (b) extração sequencial para identificar o fracionamento do Cu, Pb e Zn nas diferentes fases-suporte dos metais, e (c) bioaccessibilidade oral in vitro. Os resultados da análise química mostram que as poeiras dos travões apresentam concentrações elevadas em Fe, Cu, Zn, Mn, Ba, Sb, Cr e Ni sendo de referir diferenças composicionais significativas entre as amostras estudadas. A amostra de tinta contém teores elevados de Ba, Ca, Ti e Pb e também pode conter outros elementos tais como Co, Cr, Cu, Mn. Mineralogicamente constata-se que as amostras de poeiras dos travões tem uma composição mineralógica semelhante mostrando que são constituídas por uma elevada percentagem de material de baixa cristalinidade, grafite e óxidos/hidróxidos de Fe amorfos. A amostra de tinta de marcação dos pavimentos das estradas é composta por material mais cristalino do que a poeira dos travões e é essencialmente constituída por carbonatos (maioritariamente dolomite) e também por barite (em menor quantidade). Os resultados obtidos nas amostras de poeiras urbanas indicam a existência de associações de elementos que definem claramente a componente geogénica e/ou antropogénica e apontam para diferenças entre essas associações nas duas frações estudadas (250 m e 63 m). A heterogeneidade das poeiras é revelada pela existência de partículas com origem geogénica (por exemplo quartzo e aluminossilicatos), de partículas com características marcadamente antropogénicas (partículas enriquecidas em Fe, Pb, Zn e Cu) ou ainda de partículas com origem mista (óxidos de Fe e Ti). Os resultados da extração química seletiva sequencial permitiu concluir que, nas amostras em estudo, as fases de troca e ácido-solúveis são as fases suporte mais importantes para o Cu, Pb e Zn Os resultados dos ensaios de bioacessibilidade mostraram também que uma percentagem significativa de Cu, Pb e Zn total está disponível para absorção gástrica. Este estudo destaca também a necessidade de se caracterizar em detalhe as propriedades intrínsecas das partículas antrópicas presentes nas poeiras urbanas, de forma a compreender as variações da fração bioacessível nos diferentes elementos estudados assim como nas diferentes frações.

A multitracer approach to assess the spatial contamination pattern of hake (Merluccius merluccius) in the French Mediterranean

Chemical contamination levels and stable isotope ratios provide integrated information about contaminant exposure, trophic position and also biological and environmental influences on marine organisms. By combining these approaches with otolith shape analyses, the aim of the present study was to document the spatial variability of Hg and PCB contamination of the European hake (Merluccius merluccius) in the French Mediterranean, hypothesizing that local contaminant sources, environmental conditions and biological specificities lead to site-specific contamination patterns. High Hg concentrations discriminated Corsica (average: 1.36 ± 0.80 μg g− 1 dm) from the Gulf of Lions (average values < 0.5 μg g− 1 dm), where Rhône River input caused high PCB burdens. CB 153 average concentrations ranged between 4.00 ± 0.64 and 18.39 ± 12.38 ng g− 1 dm in the Gulf of Lions, whatever the sex of the individuals, whereas the highest values in Corsica were 6.75 ± 4.22 ng g− 1 dm. Otolith shape discriminated juveniles and adults, due to their different habitats. The use of combined ecotracers was revealed as a powerful tool to discriminate between fish populations at large and small spatial scale, and to enable understanding of the environmental and biological influences on contamination patterns.

STRUCTURAL ANALYSIS OF RIBOSOME BINDING ELEMENTS OF THE 3´ UTR IN TWO POSITIVE-STRAND PLANT RNA VIRUSES

Turnip crinkle virus (TCV) and Pea enation mosaic virus (PEMV) are two positive (+)-strand RNA viruses that are used to investigate the regulation of translation and replication due to their small size and simple genomes. Both viruses contain cap-independent translation elements (CITEs) within their 3´ untranslated regions (UTRs) that fold into tRNA-shaped structures (TSS) according to nuclear magnetic resonance and small angle x-ray scattering analysis (TCV) and computational prediction (PEMV). Specifically, the TCV TSS can directly associate with ribosomes and participates in RNA-dependent RNA polymerase (RdRp) binding. The PEMV kissing-loop TSS (kl-TSS) can simultaneously bind to ribosomes and associate with the 5´ UTR of the viral genome. Mutational analysis and chemical structure probing methods provide great insight into the function and secondary structure of the two 3´ CITEs. However, lack of 3-D structural information has limited our understanding of their functional dynamics. Here, I report the folding dynamics for the TCV TSS using optical tweezers (OT), a single molecule technique. My study of the unfolding/folding pathways for the TCV TSS has provided an unexpected unfolding pathway, confirmed the presence of Ψ3 and hairpin elements, and suggested an interconnection between the hairpins and pseudoknots. In addition, this study has demonstrated the importance of the adjacent upstream adenylate-rich sequence for the formation of H4a/Ψ3 along with the contribution of magnesium to the stability of the TCV TSS. In my second project, I report on the structural analysis of the PEMV kl-TSS using NMR and SAXS. This study has re-confirmed the base-pair pattern for the PEMV kl-TSS and the proposed interaction of the PEMV kl-TSS with its interacting partner, hairpin 5H2. The molecular envelope of the kl-TSS built from SAXS analysis suggests the kl-TSS has two functional conformations, one of which has a different shape from the previously predicted tRNA-shaped form. Along with applying biophysical methods to study the structural folding dynamics of RNAs, I have also developed a technique that improves the production of large quantities of recombinant RNAs in vivo for NMR study. In this project, I report using the wild-type and mutant E.coli strains to produce cost-effective, site-specific labeled, recombinant RNAs. This technique was validated with four representative RNAs of different sizes and complexity to produce milligram amounts of RNAs. The benefit of using site-specific labeled RNAs made from E.coli was demonstrated with several NMR techniques.