Inference and Labeling of Metric-Induced Network Topologies

The development and deployment of distributed network-aware applications and services over the Internet require the ability to compile and maintain a model of the underlying network resources with respect to (one or more) characteristic properties of interest. To be manageable, such models must be compact, and must enable a representation of properties along temporal, spatial, and measurement resolution dimensions. In this paper, we propose a general framework for the construction of such metric-induced models using end-to-end measurements. We instantiate our approach using one such property, packet loss rates, and present an analytical framework for the characterization of Internet loss topologies. From the perspective of a server the loss topology is a logical tree rooted at the server with clients at its leaves, in which edges represent lossy paths between a pair of internal network nodes. We show how end-to-end unicast packet probing techniques could b e used to (1) infer a loss topology and (2) identify the loss rates of links in an existing loss topology. Correct, efficient inference of loss topology information enables new techniques for aggregate congestion control, QoS admission control, connection scheduling and mirror site selection. We report on simulation, implementation, and Internet deployment results that show the effectiveness of our approach and its robustness in terms of its accuracy and convergence over a wide range of network conditions.

Robust Identification of Shared Losses Using End-to-End Unicast Probes

Current Internet transport protocols make end-to-end measurements and maintain per-connection state to regulate the use of shared network resources. When two or more such connections share a common endpoint, there is an opportunity to correlate the end-to-end measurements made by these protocols to better diagnose and control the use of shared resources. We develop packet probing techniques to determine whether a pair of connections experience shared congestion. Correct, efficient diagnoses could enable new techniques for aggregate congestion control, QoS admission control, connection scheduling and mirror site selection. Our extensive simulation results demonstrate that the conditional (Bayesian) probing approach we employ provides superior accuracy, converges faster, and tolerates a wider range of network conditions than recently proposed memoryless (Markovian) probing approaches for addressing this opportunity.

Unicast-based Characterization of Network Loss Topologies

Current Internet transport protocols make end-to-end measurements and maintain per-connection state to regulate the use of shared network resources. When a number of such connections share a common endpoint, that endpoint has the opportunity to correlate these end-to-end measurements to better diagnose and control the use of shared resources. A valuable characterization of such shared resources is the "loss topology". From the perspective of a server with concurrent connections to multiple clients, the loss topology is a logical tree rooted at the server in which edges represent lossy paths between a pair of internal network nodes. We develop an end-to-end unicast packet probing technique and an associated analytical framework to: (1) infer loss topologies, (2) identify loss rates of links in an existing loss topology, and (3) augment a topology to incorporate the arrival of a new connection. Correct, efficient inference of loss topology information enables new techniques for aggregate congestion control, QoS admission control, connection scheduling and mirror site selection. Our extensive simulation results demonstrate that our approach is robust in terms of its accuracy and convergence over a wide range of network conditions.

A novel sub-seabed CO2 release experiment informing monitoring and impact assessment for geological carbon storage

Carbon capture and storage is a mitigation strategy that can be used to aid the reduction of anthropogenic CO2 emissions. This process aims to capture CO2from large point-source emitters and transport it to a long-term storage site. For much of Europe, these deep storage sites are anticipated to be sited below the sea bed on continental shelves. A key operational requirement is an understanding of best practice of monitoring for potential leakage and of the environmental impact that could result from a diffusive leak from a storage complex. Here we describe a controlled CO2release experiment beneath the seabed, which overcomes the limitations of laboratory simulations and natural analogues. The complex processes involved in setting up the experimental facility and ensuring its successful operation are discussed, including site selection, permissions, communications and facility construction. The experimental design and observational strategy are reviewed with respect to scientific outcomes along with lessons learnt in order to facilitate any similar future.

Seed dormancy in Arabidopsis thaliana is controlled by alternative polyadenylation of DOG1

DOG1 is a key regulator of seed dormancy in Arabidopsis and other plants. Interestingly, the C-terminus of DOG1 is either absent or not conserved in many plant species. Here, we show that in Arabidopsis DOG1 transcript is subject to alternative polyadenylation. In line with this, mutants in RNA 3' processing complex display weakened seed dormancy in parallel with defects in DOG1 proximal polyadenylation site selection, suggesting that the short DOG1 transcript, is functional. This is corroborated by the finding that the proximally polyadenylated short DOG1 mRNA is translated in vivo and complements the dog1 mutation. In summary, our findings indicate that the short DOG1 protein isoform produced from the proximally polyadenylated DOG1 mRNA is a key player in the establishment of seed dormancy in Arabidopsis and characterize a set of mutants in RNA 3' processing complex required for production of proximally polyadenylated functional DOG1 transcript.

Next generation Bridge weigh-in-motion using fibre optic sensors

There have been over 3000 bridge weigh-in-motion (B-WIM) installations in 25 countries worldwide, this has led vast improvements in post processing of B-WIM systems since its introduction in the 1970’s. Existing systems are based on electrical resistance strain gauges which can be prohibitive in achieving data for long term monitoring of rural bridges due to power consumption. This paper introduces a new low-power B-WIM system using fibre optic sensors (FOS). The system consisted of a series of FOS which were attached to the soffit of an existing integral bridge with a single span of 19m. The site selection criteria and full installation process has been detailed in the paper. A method of calibration was adopted using live traffic at the bridge site and based on this calibration the accuracy of the system was determined. New methods of axle detection for B-WIM were investigated and verified in the field.

Using particle dispersal models to assist in the conservation and recovery of the overexploited native oyster (Ostrea edulis) in an enclosed sea lough

Oyster populations around the world have seen catastrophic decline which has been largely attributed to overexploitation, disease and pollution. While considerable effort and resources have been implemented into restoring these important environmental engineers, the success of oyster populations is often limited by poor understanding of site-specific dispersal patterns of propagules. Water-borne transport is a key factor controlling or regulating the dispersal of the larval stage of benthic marine invertebrates which have limited mobility. The distribution of the native oyster Ostrea edulis in Strangford Lough, Northern Ireland, together with their densities and population structure at subtidal and intertidal sites has been documented at irregular intervals between 1997 and 2013. This paper revisits this historical data and considers whether different prevailing environmental conditions can be used to explain the distribution, densities and population structure of O. edulis in Strangford Lough. The approach adopted involved comparing predictive 2D hydrodynamic models coupled with particle tracking to simulate the dispersal of oyster larvae with historical and recent field records of the distribution of both subtidal and intertidal, populations since 1995. Results from the models support the hypothesis that commercial stocks of O. edulis introduced into Strangford Lough in the 1990s resulted in the re-establishment of wild populations of oysters in the Northern Basin which in turn provided a potential source of propagules for subtidal populations. These results highlight that strategic site selection (while inadvertent in the case of the introduced population in 1995) for the re-introduction of important shellfish species can significantly accelerate their recovery and restoration.

Feasibility study on multifunctional artificial reefs for the Azores

Tese de Doutoramento, Geografia (Ordenamento do Território), 25 de Novembro de 2013, Universidade dos Açores.

Beach sand and the potential for infectious disease transmission: observations and recommendations

Recent studies suggest that sand can serve as a vehicle for exposure of humans to pathogens at beach sites, resulting in increased health risks. Sampling for microorganisms in sand should therefore be considered for inclusion in regulatory programmes aimed at protecting recreational beach users from infectious disease. Here, we review the literature on pathogen levels in beach sand, and their potential for affecting human health. In an effort to provide specific recommendations for sand sampling programmes, we outline published guidelines for beach monitoring programmes, which are currently focused exclusively on measuring microbial levels in water. We also provide background on spatial distribution and temporal characteristics of microbes in sand, as these factors influence sampling programmes. First steps toward establishing a sand sampling programme include identifying appropriate beach sites and use of initial sanitary assessments to refine site selection. A tiered approach is recommended for monitoring. This approach would include the analysis of samples from many sites for faecal indicator organisms and other conventional analytes, while testing for specific pathogens and unconventional indicators is reserved for high-risk sites. Given the diversity of microbes found in sand, studies are urgently needed to identify the most significant aetiological agent of disease and to relate microbial measurements in sand to human health risk.

Functional and molecular characterization of SR45, a plant-specific factor involved in sugar and stress signaling in Arabidopsis thaliana

Dissertation presented to obtain the Ph.D degree in Molecular Biology

Therapeutic riding : learning and recovery for people with disabilities

The purpose ofthis study was to explore the process oftherapeutic riding as an experiential and holistic approach to learning and recovery for people with disabilities as perceived by the providers oftherapeutic riding. To enhance the connection between theory and practice and to suggest future research, the researcher endeavoured to develop a theory that contributed to the knowledge base oftherapeutic riding, animal-assisted therapy and education, experiential education, and experiential therapy in addition to contributing to connections among them. This topic was investigated because ofthe lack ofresearch about the process of therapeutic riding, particularly from learning and a recovery perspective. Few studies have addressed how therapeutic riding outcomes are achieved or how the therapeutic riding process actually works. This study was identified as grounded theory using qualitative data through interviews and narrative reflections with therapeutic riding providers, a researcher's journal, field notes, and written documents. Grounded theory analysis was used to analyze the qualitative data. This consisted ofdoing open, axial, and selective coding. This study provided detailed descriptions ofthe research approach, researcher's involvement, participant and site selection, data collection and analysis, methodological assumptions and limitations, credibility established, and ethical considerations. The findings ofthe data analysis revealed the theme ofrelationships as central to the learning and recovery process oftherapeutic riding for people with disabilities. The significance ofthe team relationships, the horse and rider relationship, and the providers and rider relationship was found. The essential components ofthe learning and recovery process were presented in a diagram in the selective coding phase. Goals oftherapeutic riding included psycho-education; behavioural and social; physical; and equestrian. Parts ofthe process ofhow outcomes were achieved included motivation; "opens new doors;" risk; task analysis; control; communication; and environmental factors. Outcomes of therapeutic riding included independence and mobility; confidence; and transfer abilities or skills. The implications ofthese findings for theory, practice, and further research were also. explored.

Effect of human disturbance on long-term habitat use and breeding success of the European Nightjar, Caprimulgus europaeus

Land managers often respond to declining numbers of target species by creating additional areas of habitat. If these habitats are also subject to human disturbance, then their efforts may be wasted. The European Nightjar (Caprimulgus europaeus) is a ground-nesting bird that is listed as a species of European Conservation Concern. It appears to be susceptible to human disturbance during the breeding season. We examined habitat use and reproductive success over 10 years in a breeding population on 1335 ha of managed land in Nottinghamshire, England. The study site was divided into a heavily disturbed section and a less disturbed section of equal habitat availability, forming a natural long-term experiment. The site is open to the public, and visitor numbers approximately doubled during the study. We found that overall Nightjar density was significantly lower and there were significantly fewer breeding pairs in the heavily disturbed habitat compared with the less disturbed habitat. However, average breeding success per pair, in terms of eggs and fledglings produced, was not significantly different between the two sections across years. Our findings suggest that human recreational disturbance may drastically alter settlement patterns and nest site selection of arriving females in some migratory ground-nesting species and may reduce the utility of apparently suitable patches of remnant and created habitat. Land managers should bear this in mind when creating new areas of habitat that will also be accessible to the public. Our study also highlights the value of long-term population monitoring, which can detect trends that short-term studies may miss.

Arboreal thorn-dwelling ants use domatia morphology to partition nest sites on the savanna ant-plant, Vachellia erioloba

Nest site selection in arboreal, domatia-dwelling ants, particularly those coexisting on a single host plant, is little understood. To examine this phenomenon we studied the African savannah tree Vachellia erioloba, which hosts ants in swollen-thorn domatia. We found four ant species from different genera (Cataulacus intrudens, Tapinoma subtile, Tetraponera ambigua and an unidentified Crematogaster species). In contrast to other African ant plants, many V. erioloba trees (41 % in our survey) were simultaneously co-occupied by more than one ant species. Our study provides quantitative field data describing: (1) aspects of tree and domatia morphology relevant to supporting a community of mutualist ants, (2) how ant species occupancy varies with domatia morphology and (3) how ant colony size varies with domatia size and species. We found that Crematogaster sp. occupy the largest thorns, followed by C. intrudens, with T. subtile in the smallest thorns. Thorn age, as well as nest entrance hole size correlated closely with ant species occupant. These differing occupancy patterns may help to explain the unusual coexistence of three ant species on individual myrmecophytic trees. In all three common ant species, colony size, as measured by total number of ants, increased with domatia size. Additionally, domatia volume and species identity interact to predict ant numbers, suggesting differing responses between species to increased availability of nesting space. The proportion of total ants in nests that were immatures varied with thorn volume and species, highlighting the importance of domatia morphology in influencing colony structure.

Integrated palaeoecology and archaeology: a powerful approach for understanding pre-Columbian Amazonia

The old paradigm that Amazonia's tropical ecosystems prevented cultural development beyond small-scale shifting agricultural economies, that had little environmental impact, no longer holds true for much of Amazonia. A diversity of archaeological evidence, including terra preta soils, raised fields, causeways, large habitation mounds, geometric earthworks, and megalithic monuments, all point to considerable cultural complexity and environmental impacts. However, uncertainty remains over the chronology of these cultures, their diet and economy, and the scale of environmental impact and land use associated with them. Here, we argue that a cross-disciplinary approach, closely coupling palaeoecology and archaeology, can potentially resolve these uncertainties. We show how, with careful site selection (pairing small and large lakes, close proximity to archaeological sites, transects of soil pits) and choice of techniques (e.g., pollen, phytoliths, starch grains, charcoal, stable isotopes), these two disciplines can be successfully integrated to provide a powerful tool for investigating the relationship between pre-Columbian cultures and their environment.

Investigation of the accuracy of historical irradiance products and interannual variability of solar irradiance using Met Office ground data

Met Office station data from 1980 to 2012 has been used to characterise the interannual variability of incident solar irradiance across the UK. The same data are used to evaluate four popular historical irradiance products to determine which are most suitable for use by the UK PV industry for site selection and system design. The study confirmed previous findings that interannual variability is typically 3–6% and weighted average probability of a particular percentage deviation from the mean at an average site in the UK was calculated. This weighted average showed that fewer than 2% of site-years could be expected to fall below 90% of the long-term site mean. The historical irradiance products were compared against Met Office station data from the input years of each product. This investigation has found that all products perform well. No products have a strong spatial trend. Meteonorm 7 is most conservative (MBE = −2.5%), CMSAF is most optimistic (MBE = +3.4%) and an average of all four products performs better than any one individual product (MBE = 0.3%)