Real-Time Bayesian Analysis of Ground Motion Envelopes for Earthquake Early Warning

Current earthquake early warning systems usually make magnitude and location predictions and send out a warning to the users based on those predictions. We describe an algorithm that assesses the validity of the predictions in real-time. Our algorithm monitors the envelopes of horizontal and vertical acceleration, velocity, and displacement. We compare the observed envelopes with the ones predicted by Cua & Heaton's envelope ground motion prediction equations (Cua 2005). We define a "test function" as the logarithm of the ratio between observed and predicted envelopes at every second in real-time. Once the envelopes deviate beyond an acceptable threshold, we declare a misfit. Kurtosis and skewness of a time evolving test function are used to rapidly identify a misfit. Real-time kurtosis and skewness calculations are also inputs to both probabilistic (Logistic Regression and Bayesian Logistic Regression) and nonprobabilistic (Least Squares and Linear Discriminant Analysis) models that ultimately decide if there is an unacceptable level of misfit. This algorithm is designed to work at a wide range of amplitude scales. When tested with synthetic and actual seismic signals from past events, it works for both small and large events.

Development of a Cationic Mucic Acid Polymer-Based Nanoparticle siRNA Delivery System

Cancer chemotherapy has advanced from highly toxic drugs to more targeted treatments in the last 70 years. Chapter 1 opens with an introduction to targeted therapy for cancer. The benefits of using a nanoparticle to deliver therapeutics are discussed. We move on to siRNA in particular, and why it would be advantageous as a therapy. Specific to siRNA delivery are some challenges, such as nuclease degradation, quick clearance from circulation, needing to enter cells, and getting to the cytosol. We propose the development of a nanoparticle delivery system to tackle these challenges so that siRNA can be effective.

Chapter 2 of this thesis discusses the synthesis and analysis of a cationic mucic acid polymer (cMAP) which condenses siRNA to form a nanoparticle. Various methods to add polyethylene glycol (PEG) for stabilizing the nanoparticle in physiologic solutions, including using a boronic acid binding to diols on mucic acid, forming a copolymer of cMAP with PEG, and creating a triblock with mPEG on both ends of cMAP. The goal of these various pegylation strategies was to increase the circulation time of the siRNA nanoparticle in the bloodstream to allow more of the nanoparticle to reach tumor tissue by the enhanced permeation and retention effect. We found that the triblock mPEG-cMAP-PEGm polymer condensed siRNA to form very stable 30-40 nm particles that circulated for the longest time – almost 10% of the formulation remained in the bloodstream of mice 1 h after intravenous injection.

Chapter 3 explores the use of an antibody as a targeting agent for nanoparticles. Some antibodies of the IgG1 subtype are able to recruit natural killer cells that effect antibody dependent cellular cytotoxicity (ADCC) to kill the targeted cell to which the antibody is bound. There is evidence that the ADCC effect remains in antibody-drug conjugates, so we wanted to know whether the ADCC effect is preserved when the antibody is bound to a nanoparticle, which is a much larger and complex entity. We utilized antibodies against epidermal growth factor receptor with similar binding and pharmacokinetics, cetuximab and panitumumab, which differ in that cetuximab is an IgG1 and panitumumab is an IgG2 (which does not cause ADCC). Although a natural killer cell culture model showed that gold nanoparticles with a full antibody targeting agent can elicit target cell lysis, we found that this effect was not preserved in vivo. Whether this is due to the antibody not being accessible to immune cells or whether the natural killer cells are inactivated in a tumor xenograft remains unknown. It is possible that using a full antibody still has value if there are immune functions which are altered in a complex in vivo environment that are intact in an in vitro system, so the value of using a full antibody as a targeting agent versus using an antibody fragment or a protein such as transferrin is still open to further exploration.

In chapter 4, nanoparticle targeting and endosomal escape are further discussed with respect to the cMAP nanoparticle system. A diboronic acid entity, which gives an order of magnitude greater binding (than boronic acid) to cMAP due to the vicinal diols in mucic acid, was synthesized, attached to 5kD or 10kD PEG, and conjugated to either transferrin or cetuximab. A histidine was incorporated into the triblock polymer between cMAP and the PEG blocks to allow for siRNA endosomal escape. Nanoparticle size remained 30-40 nm with a slightly negative ca. -3 mV zeta potential with the triblock polymer containing histidine and when targeting agents were added. Greater mRNA knockdown was seen with the endosomal escape mechanism than without. The nanoparticle formulations were able to knock down the targeted mRNA in vitro. Mixed effects suggesting function were seen in vivo.

Chapter 5 summarizes the project and provides an outlook on siRNA delivery as well as targeted combination therapies for the future of personalized medicine in cancer treatment.

Associação entre práticas de alimentação e ganho de peso intra-hospitalar em recém-nascidos prematuros de muito baixo peso de nascimento.

Este trabalho avaliou [1] os fatores associados à ocorrência de restrição ao ganho de peso observada na alta hospsitalar e [2] a associação entre as práticas de alimentação e o ganho de peso durante a internação, em recém-nascidos prematuros de muito baixo peso de nascimento (501 a 1.499g) na maternidade do Hsopital Geral de Bonsucesso (Rio de Janeiro). Os dados foram coletados de forma retrospectiva para os nascimetnos do período compreendido entre junho de 2002 a junho de 2004. Do total de 247 recém-nascidos incluídos no estudo, 203 tiveram alta hospitalar. As características ao nascimento, asmorbidades e as práticas de alimentação foram levantadas dos prontuários de acordo com um questionário de pesquisa. O menor peso de nascimento, ser pequeno para idade gestacional-percentil 3, o maior escore CRIB e a ocorrência de sepse foram associados à ocorrência de restrição ao ganho de peso extra-uterino na alta. Das cento e cinquenta e oito crianças com peso adequado ao nascimento, sessenta e nova (43,7%) encontravam-se com peso abaixo do 3 percentil na alta. Nesses casos de restrição ao ganho de peso foram preditores: a ocorrência de sepse, de doença metabólica óssea e o maior número de transfusões sanguíneas, embora a capacidade de explicação do modelo tenha sido pequena (14%). Estas situações merecem destaque na prática neonatal, pois podem ser marcadores de um pior desempenho no que diz respeito ao ganho de peso durante a internação. Uma vez que as morbidades explicaram pouco a c]ocorrência de restrição ao ganho de peso extra-uterino, em especial os casos intrahospitalares. Foi analisada a associação entre evolução do peso nos primeiro dois meses de vida e as práticas de alimentação. Utilizando a análise de regressão longitudinal de efeitos mistos foi observado que o número de dias para o início de dieta enteral, de dias para atingir a dieta plena, de dias para início de dieta parenteral e de dias de uso de dieta parenteral, influenciaram a evolução precoce do peso (até 17 dia). O número de dias para início da dieta parenteral não influenciou a evolução do peso após o 17 dia de vida. Os resultados do presente estudo sugerem 1) que o menor peso de nascimento, ser pequeno para idade gestacional, ter maior escore CRIB e a ocorrência de sepse associam-se a ocorrência de restrição ao ganho de peso extra-uterino; 2) dentre os recém-nascidos com peso apropriado ao nascimento, a ocorrência de sepse, de doença metabólica óssea e o maior número de transfusões sanguíneas associaram-se a um pior desempenho ponderal; 3) que as práticas de alimentação decididas precocemente associam-se ao ganho de pseo intra-hospitalar e a revisão destas pode melhorar o desempenho ponderal de recém-nascidos prematuros de muito baixo peso de nascimento.

Predictive techniques for turbulent oscillatory flows

The prediction of turbulent oscillatory flow at around transitional Reynolds numbers is considered for an idealized electronics system. To assess the accuracy of turbulence models, comparison is made with measurements. A stochastic procedure is used to recover instantaneous velocity time traces from predictions. This procedure enables more direct comparison with turbulence intensity measurements which have not been filtered to remove the oscillatory flow component. Normal wall distances, required in some turbulence models, are evaluated using a modified Poisson equation based technique. A range of zero, one and two equation turbulence models are tested, including zonal and a non-linear eddy viscosity models. The non-linear and zonal models showed potential for accuracy improvements.

Transient reflectivity on vertically aligned single-wall carbon nanotubes

One-color transient reflectivity measurements are carried out on two different samples of vertically aligned single-wall carbon nanotube bundles and compared with the response recently published on unaligned bundles. The negative sign of the optical response for both samples indicates that the free electron character revealed on unaligned bundles is only due to the intertube interactions favored by the tube bending. Neither the presence of bundles nor the existence of structural defects in aligned bundles is able to induce a free-electron like behavior of the photoexcited carriers. This result is also confirmed by the presence of non-linear excitonic effects in the transient response of the aligned bundles. © 2013 Elsevier B.V.

InxGa1-xAs/AlyGa1-yAs/AlzGa1-zAs asymmetric step quantum-well middle wavelength infrared detectors

InxGa1-xAs/AlyGa1-yAs/AlzGa1-zAs asymmetric step quantum-well middle wavelength (3-5 mum) infrared detectors are fabricated. The components display photovoltaic-type photocurrent response as well as the bias-controlled modulation of the peak wavelength of the main response, which is ascribed to the Stark shifts of the intersubband transitions from the local ground states to the extended first excited states in the quantum wells, at the 3-5.3 mum infrared atmospheric transmission window. The blackbody detectivity (D-bb*) of the detectors reaches to about 1.0x10(10) cm Hz(1/2)/W at 77 K under bias of +/-7 V. By expanding the electron wave function in terms of normalized plane wave basis within the framework of the effective-mass envelope-function theory, the linear Stark effects of the intersubband transitions between the ground and first excited states in the asymmetric step well are calculated. The obtained results agree well with the corresponding experimental measurements. (C) 2001 American Institute of Physics.

Dynamic and complex microclimate responses to warming and grazing manipulations

Synthesis efforts that identify patterns of ecosystem response to a suite of warming manipulations can make important contributions to climate change science. However, cross-study comparisons are impeded by the paucity of detailed analyses of how passive warming and other manipulations affect microclimate. Here we document the independent and combined effects of a common passive warming manipulation, open-top chambers (OTCs), and a simulated widespread land use, clipping, on microclimate on the Tibetan Plateau. OTCs consistently elevated growing season averaged mean daily air temperature by 1.0-2.0 degrees C, maximum daily air temperature by 2.1-7.3 degrees C and the diurnal air temperature range by 1.9-6.5 degrees C, with mixed effects on minimum daily air temperature, and mean daily soil temperature and moisture. These OTC effects on microclimate differ from reported effects of a common active warming method, infrared heating, which has more consistent effects on soil than on air temperature. There were significant interannual and intragrowing season differences in OTC effects on microclimate. For example, while OTCs had mixed effects on growing season averaged soil temperatures, OTCs consistently elevated soil temperature by approximately 1.0 degrees C early in the growing season. Nonadditive interactions between OTCs and clipping were also present: OTCs in clipped plots generally elevated air and soil temperatures more than OTCs in nonclipped plots. Moreover, site factors dynamically interacted with microclimate and with the efficacy of the OTC manipulations.These findings highlight the need to understand differential microclimate effects between warming methods, within warming method across ecosystem sites, within warming method crossed with other treatments, and within sites over various timescales. Methods, sites and scales are potential explanatory variables and covariables in climate warming experiments. Consideration of this variability among and between experimental warming studies will lead to greater understanding and better prediction of ecosystem response to anthropogenic climate warming.

Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.)

Sk?t, L., Humphreys, J., Humphreys, M. O., Thorogood, D., Gallagher, J. A., Sanderson, R., Armstead, I. P., Thomas, I. D. (2007). Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics, 177 (1), 535-547. Sponsorship: BBSRC RAE2008

Optymalizacja metod analizy Főrsterowskiego rezonansowego przeniesienia energii (FRET) pojedynczych cząsteczek

Wydział Chemii: Zakład Chemii Fizycznej

Sectoral impacts on the diversity of carabid beetles (Coleoptera: Carabidae) and their associated ecosystem service of biocontrol

This thesis aimed to provide an understanding of how human-induced changes in the economic sectors of agriculture and transport affect carabid diversity, potential carabidmediated biocontrol and predator-pest interactions. The research involved both observational and manipulative laboratory and field-based studies. Observational research consisted of two large-scale investigations of (1) the impact of Miscanthus and oilseed rape production (n=45) and (2) the impact of horticultural and ecological based landscaping of roadside verges (n=64). This research is the first record of carabid diversity, potential biocontrol and community assemblage with respect to bioenergy crop production and roadside landscaping in an Irish context and it is also an important addition to the limited knowledge of carabid populations in these ecosystems internationally. Manipulative work involved the examination of the role predator identity, diversity and biomass play in the suppression of pollen beetle larvae (an economically damaging insect pest of oilseed rape in Europe), using a novel experimental design called ‘simplex’. To complement this research, an additional field study on the impact of low and high oilseed rape pesticide management on carabid species richness and abundance, and crop yield, was also conducted. This research is a great contribution to the existing understanding of what constitutes the important components of predator biodiversity and expands the knowledge of the usefulness of carabid predators in the context of pollen beetle larvae control. In particular, the work shows that the abundance or biomass of beetles has an effect that is far larger than the effect of diversity on the capacity of beetles to consume prey. In turn, the field study showed that pesticide applications had little impact on yield, or carabid richness, but that carabid abundance/biomass declined drastically. The work provides compelling evidence that management practices erode the useful components of biodiversity that are essential for the delivery of biocontrol services.

Transport energy demand: techno-economic modelling and scenarios for Irish climate policy

The case for energy policy modelling is strong in Ireland, where stringent EU climate targets are projected to be overshot by 2015. Policy targets aiming to deliver greenhouse gas and renewable energy targets have been made, but it is unclear what savings are to be achieved and from which sectors. Concurrently, the growth of personal mobility has caused an astonishing increase in CO2 emissions from private cars in Ireland, a 37% rise between 2000 and 2008, and while there have been improvements in the efficiency of car technology, there was no decrease in the energy intensity of the car fleet in the same period. This thesis increases the capacity for evidenced-based policymaking in Ireland by developing techno-economic transport energy models and using them to analyse historical trends and to project possible future scenarios. A central focus of this thesis is to understand the effect of the car fleet‘s evolving technical characteristics on energy demand. A car stock model is developed to analyse this question from three angles: Firstly, analysis of car registration and activity data between 2000 and 2008 examines the trends which brought about the surge in energy demand. Secondly, the car stock is modelled into the future and is used to populate a baseline “no new policy” scenario, looking at the impact of recent (2008-2011) policy and purchasing developments on projected energy demand and emissions. Thirdly, a range of technology efficiency, fuel switching and behavioural scenarios are developed up to 2025 in order to indicate the emissions abatement and renewable energy penetration potential from alternative policy packages. In particular, an ambitious car fleet electrification target for Ireland is examined. The car stock model‘s functionality is extended by linking it with other models: LEAP-Ireland, a bottom-up energy demand model for all energy sectors in the country; Irish TIMES, a linear optimisation energy system model; and COPERT, a pollution model. The methodology is also adapted to analyse trends in freight energy demand in a similar way. Finally, this thesis addresses the gap in the representation of travel behaviour in linear energy systems models. A novel methodology is developed and case studies for Ireland and California are presented using the TIMES model. Transport Energy

Bacteria localization and chorion thinning among preterm premature rupture of membranes.

OBJECTIVE: Bacterial colonization of the fetal membranes and its role in pathogenesis of membrane rupture is poorly understood. Prior retrospective work revealed chorion layer thinning in preterm premature rupture of membranes (PPROM) subjects. Our objective was to prospectively examine fetal membrane chorion thinning and to correlate to bacterial presence in PPROM, preterm, and term subjects. STUDY DESIGN: Paired membrane samples (membrane rupture and membrane distant) were prospectively collected from: PPROM = 14, preterm labor (PTL = 8), preterm no labor (PTNL = 8), term labor (TL = 10), and term no labor (TNL = 8), subjects. Sections were probed with cytokeratin to identify fetal trophoblast layer of the chorion using immunohistochemistry. Fluorescence in situ hybridization was performed using broad range 16 s ribosomal RNA probe. Images were evaluated, chorion and choriodecidua were measured, and bacterial fluorescence scored. Chorion thinning and bacterial presence were compared among and between groups using Student's t-test, linear mixed effect model, and Poisson regression model (SAS Cary, NC). RESULTS: In all groups, the fetal chorion cellular layer was thinner at rupture compared to distant site (147.2 vs. 253.7 µm, p<0.0001). Further, chorion thinning was greatest among PPROM subjects compared to all other groups combined, regardless of site sampled [PPROM(114.9) vs. PTL(246.0) vs. PTNL(200.8) vs. TL(217.9) vs. TNL(246.5)]. Bacteria counts were highest among PPROM subjects compared to all other groups regardless of site sampled or histologic infection [PPROM(31) vs. PTL(9) vs. PTNL(7) vs. TL(7) vs. TNL(6)]. Among all subjects at both sites, bacterial counts were inversely correlated with chorion thinning, even excluding histologic chorioamnionitis (p<0.0001 and p = 0.05). CONCLUSIONS: Fetal chorion was uniformly thinner at rupture site compared to distant sites. In PPROM fetal chorion, we demonstrated pronounced global thinning. Although cause or consequence is uncertain, bacterial presence is greatest and inversely correlated with chorion thinning among PPROM subjects.

Increasing Motorcycle Taxi Driver Conspicuity in Tanzania

Motorcycle crash related injuries and deaths are increasing rapidly in many African nations. Utilizing conspicuity measures, such as wearing reflective, fluorescent safety vests, are effective as crash prevention strategies. Furthermore, use of some conspicuity measures is mandated by law among motorcycle-taxi drivers in Tanzania. Nonetheless, uptake remains low. Locally appropriate strategies to improve crash preventative behaviors are needed.

To explore whether use of conspicuity measures could be improved through eliminating cost-barriers, we tested a distribution strategy involving the provision of free motorcycle safety vests among a population of motorcycle-taxi drivers in Moshi, Tanzania. We conducted a cluster randomized controlled trial among 180 motorcycle-taxi drivers in which half of the participants (90) were randomized to the intervention arm and received a free reflective vest. The other half of the participants (90) were randomized to the control arm and did not receive free vests. Whether motorcycle taxi drivers used the reflective vest was then unobtrusively observed on city streets over a period of three months.

Mixed-effects logistic regression was used to estimate differential uptake of the vests between trial arms. At baseline, 3.3% of individuals in both arms used a reflective vest. In three months of follow-up, 79 drivers in the intervention arm and 82 drivers in the control arm were able to be observed. In the intervention arm the average proportion of observations during which drivers were observed to be using a reflective vest was 9.5%, compared to 2.0% in the control arm (odds ratio: 5.5, 95% confidence interval: 1.1-26.9, p-value: 0.04). Distribution of free reflective vests did lead to an increase in vest usage, however, the increase was minimal. Removing economic barriers alone appears insufficient to adequately improve adherence to conspicuity measures.

Basking sharks and oceanographic fronts: quantifying associations in the north‐east Atlantic

Understanding the mechanisms linking oceanographic processes and marine vertebrate habitat use is critical to effective management of populations of conservation concern. The basking shark Cetorhinus maximus has been shown to associate with oceanographic fronts – physical interfaces at the transitions between water masses – to exploit foraging opportunities resulting from aggregation of zooplankton. However, the scale, significance and variability of these observed associations have not yet been established. Here, we quantify the influence of mesoscale (10s – 100s km) frontal activity on habitat use over timescales of weeks to months. We use animal-mounted archival tracking with composite front mapping via Earth Observation (EO) remote sensing to provide an oceanographic context to individual shark movements. We investigate levels of association with fronts occurring over two spatio-temporal scales, (i) broad-scale seasonally persistent frontal zones and (ii) contemporaneous mesoscale thermal and chl-a fronts. Using random walk simulations and logistic regression within an iterative generalised linear mixed modelling (GLMM) framework, we find that seasonal front frequency is a significant predictor of shark presence. Temporally-matched oceanographic metrics also indicate that sharks demonstrate a preference for productive regions, and associate with contemporaneous thermal and chl-a fronts more frequently than could be expected at random. Moreover, we highlight the importance of cross-frontal temperature change and persistence, which appear to interact to affect the degree of prey aggregation along thermal fronts. These insights have clear implications for understanding the preferred habitats of basking sharks in the context of anthropogenic threat management and marine spatial planning in the northeast Atlantic.

Basking sharks and oceanographic fronts: quantifying associations in the north-east Atlantic

Understanding the mechanisms linking oceanographic processes and marine vertebrate habitat use is critical to effective management of populations of conservation concern. The basking shark Cetorhinus maximus has been shown to associate with oceanographic fronts – physical interfaces at the transitions between water masses – to exploit foraging opportunities resulting from aggregation of zooplankton. However, the scale, significance and variability of these observed associations have not yet been established. Here, we quantify the influence of mesoscale (10s – 100s km) frontal activity on habitat use over timescales of weeks to months. We use animal-mounted archival tracking with composite front mapping via Earth Observation (EO) remote sensing to provide an oceanographic context to individual shark movements. We investigate levels of association with fronts occurring over two spatio-temporal scales, (i) broad-scale seasonally persistent frontal zones and (ii) contemporaneous mesoscale thermal and chl-a fronts. Using random walk simulations and logistic regression within an iterative generalised linear mixed modelling (GLMM) framework, we find that seasonal front frequency is a significant predictor of shark presence. Temporally-matched oceanographic metrics also indicate that sharks demonstrate a preference for productive regions, and associate with contemporaneous thermal and chl-a fronts more frequently than could be expected at random. Moreover, we highlight the importance of cross-frontal temperature change and persistence, which appear to interact to affect the degree of prey aggregation along thermal fronts. These insights have clear implications for understanding the preferred habitats of basking sharks in the context of anthropogenic threat management and marine spatial planning in the northeast Atlantic.