Source apportionment of PM2.5 in Cork Harbour, Ireland using a combination of single particle mass spectrometry and quantitative semi-continuous measurements

An aerosol time-of-flight mass spectrometer (ATOFMS) was deployed for the measurement of the size resolved chemical composition of single particles at a site in Cork Harbour, Ireland for three weeks in August 2008. The ATOFMS was co-located with a suite of semi-continuous instrumentation for the measurement of particle number, elemental carbon (EC), organic carbon (OC), sulfate and particulate matter smaller than 2.5 μm in diameter (PM2.5). The temporality of the ambient ATOFMS particle classes was subsequently used in conjunction with the semi-continuous measurements to apportion PM2.5 mass using positive matrix factorisation. The synergy of the single particle classification procedure and positive matrix factorisation allowed for the identification of six factors, corresponding to vehicular traffic, marine, long-range transport, various combustion, domestic solid fuel combustion and shipping traffic with estimated contributions to the measured PM2.5 mass of 23%, 14%, 13%, 11%, 5% and 1.5% respectively. Shipping traffic was found to contribute 18% of the measured particle number (20–600 nm mobility diameter), and thus may have important implications for human health considering the size and composition of ship exhaust particles. The positive matrix factorisation procedure enabled a more refined interpretation of the single particle results by providing source contributions to PM2.5 mass, while the single particle data enabled the identification of additional factors not possible with typical semi-continuous measurements, including local shipping traffic.

Investigation of factors driving the costs of operating the 2020 Irish power system with large-scale wind generation

The main goal of this work is to determine the true cost incurred by the Republic of Ireland and Northern Ireland in order to meet their EU renewable electricity targets. The primary all-island of Ireland policy goal is that 40% of electricity will come from renewable sources in 2020. From this it is expected that wind generation on the Irish electricity system will be in the region of 32-37% of total generation. This leads to issues resulting from wind energy being a non-synchronous, unpredictable and variable source of energy use on a scale never seen before for a single synchronous system. If changes are not made to traditional operational practices, the efficient running of the electricity system will be directly affected by these issues in the coming years. Using models of the electricity system for the all-island grid of Ireland, the effects of high wind energy penetration expected to be present in 2020 are examined. These models were developed using a unit commitment, economic dispatch tool called PLEXOS which allows for a detailed representation of the electricity system to be achieved down to individual generator level. These models replicate the true running of the electricity system through use of day-ahead scheduling and semi-relaxed use of these schedules that reflects the Transmission System Operator's of real time decision making on dispatch. In addition, it carefully considers other non-wind priority dispatch generation technologies that have an effect on the overall system. In the models developed, three main issues associated with wind energy integration were selected to be examined in detail to determine the sensitivity of assumptions presented in other studies. These three issues include wind energy's non-synchronous nature, its variability and spatial correlation, and its unpredictability. This leads to an examination of the effects in three areas: the need for system operation constraints required for system security; different onshore to offshore ratios of installed wind energy; and the degrees of accuracy in wind energy forecasting. Each of these areas directly impact the way in which the electricity system is run as they address each of the three issues associated with wind energy stated above, respectively. It is shown that assumptions in these three areas have a large effect on the results in terms of total generation costs, wind curtailment and generator technology type dispatch. In particular accounting for these issues has resulted in wind curtailment being predicted in much larger quantities than had been previously reported. This would have a large effect on wind energy companies because it is already a very low profit margin industry. Results from this work have shown that the relaxation of system operation constraints is crucial to the economic running of the electricity system with large improvements shown in the reduction of wind curtailment and system generation costs. There are clear benefits in having a proportion of the wind installed offshore in Ireland which would help to reduce variability of wind energy generation on the system and therefore reduce wind curtailment. With envisaged future improvements in day-ahead wind forecasting from 8% to 4% mean absolute error, there are potential reductions in wind curtailment system costs and open cycle gas turbine usage. This work illustrates the consequences of assumptions in the areas of system operation constraints, onshore/offshore installed wind capacities and accuracy in wind forecasting to better inform the true costs associated with running Ireland's changing electricity system as it continues to decarbonise into the near future. This work also proposes to illustrate, through the use of Ireland as a case study, the effects that will become ever more prevalent in other synchronous systems as they pursue a path of increasing renewable energy generation.

Genome analysis and characterisation of the exopolysaccharide produced by Bifidobacterium longum subsp. longum 35624™

The Bifibobacterium longum subsp. longum 35624™ strain (formerly named Bifidobacterium longum subsp. infantis) is a well described probiotic with clinical efficacy in Irritable Bowel Syndrome clinical trials and induces immunoregulatory effects in mice and in humans. This paper presents (a) the genome sequence of the organism allowing the assignment to its correct subspeciation longum; (b) a comparative genome assessment with other B. longum strains and (c) the molecular structure of the 35624 exopolysaccharide (EPS624). Comparative genome analysis of the 35624 strain with other B. longum strains determined that the sub-speciation of the strain is longum and revealed the presence of a 35624-specific gene cluster, predicted to encode the biosynthetic machinery for EPS624. Following isolation and acid treatment of the EPS, its chemical structure was determined using gas and liquid chromatography for sugar constituent and linkage analysis, electrospray and matrix assisted laser desorption ionization mass spectrometry for sequencing and NMR. The EPS consists of a branched hexasaccharide repeating unit containing two galactose and two glucose moieties, galacturonic acid and the unusual sugar 6-deoxy-L-talose. These data demonstrate that the B. longum 35624 strain has specific genetic features, one of which leads to the generation of a characteristic exopolysaccharide.

Towards Next Generation Vertical Search Engines

As the Web evolves unexpectedly fast, information grows explosively. Useful resources become more and more difficult to find because of their dynamic and unstructured characteristics. A vertical search engine is designed and implemented towards a specific domain. Instead of processing the giant volume of miscellaneous information distributed in the Web, a vertical search engine targets at identifying relevant information in specific domains or topics and eventually provides users with up-to-date information, highly focused insights and actionable knowledge representation. As the mobile device gets more popular, the nature of the search is changing. So, acquiring information on a mobile device poses unique requirements on traditional search engines, which will potentially change every feature they used to have. To summarize, users are strongly expecting search engines that can satisfy their individual information needs, adapt their current situation, and present highly personalized search results. In my research, the next generation vertical search engine means to utilize and enrich existing domain information to close the loop of vertical search engine's system that mutually facilitate knowledge discovering, actionable information extraction, and user interests modeling and recommendation. I investigate three problems in which domain taxonomy plays an important role, including taxonomy generation using a vertical search engine, actionable information extraction based on domain taxonomy, and the use of ensemble taxonomy to catch user's interests. As the fundamental theory, ultra-metric, dendrogram, and hierarchical clustering are intensively discussed. Methods on taxonomy generation using my research on hierarchical clustering are developed. The related vertical search engine techniques are practically used in Disaster Management Domain. Especially, three disaster information management systems are developed and represented as real use cases of my research work.

Reduced resilience of a globally distributed coccolithophore to ocean acidification: Confirmed up to 2000 generations

Ocean acidification (OA), induced by rapid anthropogenic CO2 rise and its dissolution in seawater, is known to have consequences for marine organisms. However, knowledge on the evolutionary responses of phytoplankton to OA has been poorly studied. Here we examined the coccolithophore Gephyrocapsa oceanica, while growing it for 2000 generations under ambient and elevated CO2 levels. While OA stimulated growth in the earlier selection period (from generations 700 to 1550), it reduced it in the later selection period up to 2000 generations. Similarly, stimulated production of particulate organic carbon and nitrogen reduced with increasing selection period and decreased under OA up to 2000 generations. The specific adaptation of growth to OA disappeared in generations 1700 to 2000 when compared with that at 1000 generations. Both phenotypic plasticity and fitness decreased within selection time, suggesting that the species' resilience to OA decreased after 2000 generations under high CO2 selection.

Dissolution of a spatially variable DNAPL (dense non aqueous phase liquid) source

Dissolution of non-aqueous phase liquids (NAPLs) or gases into groundwater is a key process, both for contamination problems originating from organic liquid sources, and for dissolution trapping in geological storage of CO2. Dissolution in natural systems typically will involve both high and low NAPL saturations and a wide range of pore water flow velocities within the same source zone for dissolution to groundwater. To correctly predict dissolution in such complex systems and as the NAPL saturations change over time, models must be capable of predicting dissolution under a range of saturations and flow conditions. To provide data to test and validate such models, an experiment was conducted in a two-dimensional sand tank, where the dissolution of a spatially variable, 5x5 cm**2 DNAPL tetrachloroethene source was carefully measured using x-ray attenuation techniques at a resolution of 0.2x0.2 cm**2. By continuously measuring the NAPL saturations, the temporal evolution of DNAPL mass loss by dissolution to groundwater could be measured at each pixel. Next, a general dissolution and solute transport code was written and several published rate-limited (RL) dissolution models and a local equilibrium (LE) approach were tested against the experimental data. It was found that none of the models could adequately predict the observed dissolution pattern, particularly in the zones of higher NAPL saturation. Combining these models with a model for NAPL pool dissolution produced qualitatively better agreement with experimental data, but the total matching error was not significantly improved. A sensitivity study of commonly used fitting parameters further showed that several combinations of these parameters could produce equally good fits to the experimental observations. The results indicate that common empirical model formulations for RL dissolution may be inadequate in complex, variable saturation NAPL source zones, and that further model developments and testing is desirable.

Supporting the Model-Driven Development of Real-time Embedded Systems with Run-Time Monitoring and Animation via Highly Customizable Code Generation

This paper presents a vision that allows the combined use of model-driven engineering, run-time monitoring, and animation for the development and analysis of components in real-time embedded systems. Key building block in the tool environment supporting this vision is a highly-customizable code generation process. Customization is performed via a configuration specification which describes the ways in which input is provided to the component, the ways in which run-time execution information can be observed, and how these observations drive animation tools. The environment is envisioned to be suitable for different activities ranging from quality assurance to supporting certification, teaching, and outreach and will be built exclusively with open source tools to increase impact. A preliminary prototype implementation is described.

Upper-Pleistocene terrace deposits in Mediterranean climate: geomorphological and source-rock control on mineral and geochemical signatures (Betic Cordillera, SE Spain)

Mineral and chemical composition of alluvial Upper-Pleistocene deposits from the Alto Guadalquivir Basin (SE Spain) were studied as a tool to identify sedimentary and geomorphological processes controlling its formation. Sediments located upstream, in the north-eastern sector of the basin, are rich in dolomite, illite, MgO and KB2BO. Downstream, sediments at the sequence base are enriched in calcite, smectite and CaO, whereas the upper sediments have similar features to those from upstream. Elevated rare-earth elements (REE) values can be related to low carbonate content in the sediments and the increase of silicate material produced and concentrated during soil formation processes in the neighbouring source areas. Two mineralogical and geochemical signatures related to different sediment source areas were identified. Basal levels were deposited during a predominantly erosive initial stage, and are mainly composed of calcite and smectite materials enriched in REE coming from Neogene marls and limestones. Then the deposition of the upper levels of the alluvial sequences, made of dolomite and illitic materials depleted in REE coming from the surrounding Sierra de Cazorla area took place during a less erosive later stage of the fluvial system. Such modification was responsible of the change in the mineralogical and geochemical composition of the alluvial sediments.

Source Provenance of Pre-Historic Granitic Grindstones: The Case Study of the Cogotas I Archaeological Site of Arroyo Mucientes/San Lázaro (Castronuño, Valladolid) and a Proposal on the General Methodological Flow Process

The occurrence of hand grindstones at the Cogotas I archaeological sites is considered to be a common feature. Given that a distant-provenance raw material is frequently involved, determination of its source is a basic factor in the search for a better understanding of resource management and for any Political Economy approach. To progress in these directions an overall study should be planned, using selected grindstones with a view to covering diverse sub-zones of the Cogotas I dispersal area, especially because of its considerable distance from the granite basement source. Such a study may today includes diverse analytical procedures combining successive geographic, petrographic, mineralogical and geochemical criteria. To check the plausibility of the proposed methodology, a preliminary test has been carried out on two granite grindstones, obtained at the archaeological excavation at the Castronuño (Valladolid) Cogotian site, which is fifty km away from an inferred source area that was presumably located at Peñausende (Zamora). The result obtained validates the proposed operational process, yielding a generalizable knowledge to other similar situations.

Resistance is futile: the borg, the hive, and corporate hegemony

The Borg, a collective of humanoid cyborgs linked together in a hive-mind and modeled on the earthly superorganisms of ant colonies and beehives, has been the most feared alien race in the Star Trek universe. The formidable success of the Borg in assimilating their foes corresponds to the astounding success of superorganisms in our own biosphere. Yet the Borg also serves as a metaphor for another collective of biological entities known as the corporation. In the Anthropocene epoch, corporations have become the most powerful force on the planet; their influence on the social world and the environment exceeds any government and may determine the continued sustainability of human life. Corporations have been described as people and as machines, but neither metaphor accurately describes their essence or contributes to an understanding that might resist their power. This paper reframes our understanding of the corporation by examining the metaphors that are used to describe it, and by suggesting an entirely new metaphor viewing the Borg and the corporation through the lens of sociobiology. I will argue that the corporation is a new form of superorganism that has become the dominant species on the planet and that the immense, intractable power of a globalized, corporate hive-mind has become the principal obstacle to addressing the planetary emergency of climate change. Reframing our metaphoric understanding of corporations as biological entities in the planetary biosphere may enable us to imagine ways to resist their increasing dominance and create a sustainable future. 

Inter-Laboratory Evaluation of a Next-Generation Sequencing Panel for Acute Myeloid Leukemia

INTRODUCTION: Acute myeloid leukemia (AML) is a heterogeneous clonal disorder often associated with dismal overall survival. The clinical diversity of AML is reflected in the range of recurrent somatic mutations in several genes, many of which have a prognostic and therapeutic value. Targeted next-generation sequencing (NGS) of these genes has the potential for translation into clinical practice. In order to assess this potential, an inter-laboratory evaluation of a commercially available AML gene panel across three diagnostic centres in the UK and Ireland was performed.

METHODS: DNA from six AML patient samples was distributed to each centre and processed using a standardised workflow, including a common sequencing platform, sequencing chips and bioinformatics pipeline. A duplicate sample in each centre was run to assess inter- and intra-laboratory performance.

RESULTS: An average sample read depth of 2725X (range 629-5600) was achieved using six samples per chip, with some variability observed in the depth of coverage generated for individual samples and between centres. A total of 16 somatic mutations were detected in the six AML samples, with a mean of 2.7 mutations per sample (range 1-4) representing nine genes on the panel. 15/16 mutations were identified by all three centres. Allelic frequencies of the mutations ranged from 5.6 to 53.3 % (median 44.4 %), with a high level of concordance of these frequencies between centres, for mutations detected.

CONCLUSION: In this inter-laboratory comparison, a high concordance, reproducibility and robustness was demonstrated using a commercially available NGS AML gene panel and platform.

Damping Torque Analysis of Power Systems with DFIGs for Wind Power Generation

A grid-connected DFIG for wind power generation can affect power system small-signal angular stability in two ways: by changing the system load flow condition and dynamically interacting with synchronous generators (SGs). This paper presents the application of conventional method of damping torque analysis (DTA) to examine the effect of DFIG’s dynamic interactions with SGs on the small-signal angular stability. It shows that the effect is due to the dynamic variation of power exchange between the DFIG and power system and can be estimated approximately by the DTA. Consequently, if the DFIG is modelled as a constant power source when the effect of zero dynamic interactions is assumed, the impact of change of load flow brought about by the DFIG can be determined. Thus the total effect of DFIG can be estimated from the result of DTA added on that of constant power source model. Applications of the DTA method proposed in the paper are discussed. An example of multi-machine power systems with grid-connected DFIGs are presented to demonstrate and validate the DTA method proposed and conclusions obtained in the paper.

Optimized operations of Distributed Renewable Energy Sources in Smart Grid

The renewable energy sources (RES) will play a vital role in the future power needs in view of the increasing demand of electrical energy and depletion of fossil fuel with its environmental impact. The main constraints of renewable energy (RE) generation are high capital investment, fluctuation in generation and requirement of vast land area. Distributed RE generation on roof top of buildings will overcome these issues to some extent. Any system will be feasible only if it is economically viable and reliable. Economic viability depends on the availability of RE and requirement of energy in specific locations. This work is directed to examine the economic viability of the system at desired location and demand.

MEG-measured visually induced gamma-band oscillations in chronic schizophrenia: Evidence for impaired generation of rhythmic activity in ventral stream regions

Background: Gamma-band oscillations are prominently impaired in schizophrenia, but the nature of the deficit and relationship to perceptual processes is unclear. Methods: 16 patients with chronic schizophrenia (ScZ) and 16 age-matched healthy controls completed a visual paradigm while magnetoencephalographic (MEG) data was recorded. Participants had to detect randomly occurring stimulus acceleration while viewing a concentric moving grating. MEG data were analyzed for spectral power (1-100 Hz) at sensorand source-level to examine the brain regions involved in aberrant rhythmic activity, and for contribution of differences in baseline activity towards the generation of low- and highfrequency power. Results: Our data show reduced gamma-band power at sensor level in schizophrenia patients during stimulus processing while alpha-band and baseline spectrum were intact. Differences in oscillatory activity correlated with reduced behavioral detection rates in the schizophrenia group and higher scores on the “Cognitive Factor” of the Positive and Negative Syndrome Scale. Source reconstruction revealed that extra-striate (fusiform/lingual gyrus), but not striate (cuneus), visual cortices contributed towards the reduced activity observed at sensorlevel in ScZ patients. Importantly, differences in stimulus-related activity were not due to differences in baseline activity. Conclusions: Our findings highlight that MEG-measured high-frequency oscillations during visual processing can be robustly identified in ScZ. Our data further suggest impairments that involve dysfunctions in ventral stream processing and a failure to increase gamma-band activity in a task-context. Implications of these findings are discussed in the context of current theories of cortical-subcortical circuit dysfunctions and perceptual processing in ScZ.

Continuous acquisition of MHC:peptide complexes by recipient cells contributes to the generation of anti-graft CD8+T cell immunity

Understanding the evolution of the direct and indirect pathways of allorecognition following tissue transplantation is essential in the design of tolerance-promoting protocols. On the basis that donor bone marrow-derived antigen presenting cells are eliminated within days of transplantation, it has been argued that the indirect response represents the major threat to long term transplant survival, and is consequently the key target for regulation. However, the detection of MHC transfer between cells, and particularly the capture of MHC:peptide complexes by dendritic cells, led us to propose a third, semi-direct, pathway of MHC allorecognition. Persistence of this pathway would lead to sustained activation of direct pathway T cells, arguably persisting for the life of the transplant. In this study, we focused on the contribution of acquired MHC class I, on recipient DCs, during the life span of a skin graft. We observed that MHC class I acquisition by recipient DCs occurs for at least one month following transplantation and may be the main source of alloantigen that drives CD8+ cytotoxic T cell responses. In addition, acquired MHC class I-peptide complexes stimulate T cell responses in vivo further emphasizing the need to regulate both pathways to induce indefinite survival of the graft.