The Environmental Fate of polybrominated diphenyl ethers in western Taiwan and coastal waters: evaluation with a fugacity based model

The environmental fate of polybrominated diphenyl ethers (PBDEs), a group of flame retardants that are considered to be persistent organic pollutants (POPs), around the Zhuoshui River and Changhua County regions of Taiwan was assessed. An investigation into emissions, partitioning, and fate of selected PBDEs was conducted based on the equilibrium constant (EQC) fugacity model developed at Trent University, Canada. Emissions for congeners PBDE 47, PBDE 99, and PBDE 209 to air (4.9–92 × 10−3 kg/h), soil (0.91–17.4 × 10−3 kg/h), and water (0.21–4.04 × 10−3 kg/h), were estimated by modifying previous models on PBDE emission rates by considering both industrial and domestic rates. It was found that fugacity modeling can give a reasonable estimation of the behavior, partitioning, and concentrations of PBDE congeners in and around Taiwan. Results indicate that PBDE congeners have a high affinity for partitioning into sediments then soils. As congener number decreases, the PBDEs then partition more readily into air. As the degree of bromination increases, congeners more readily partition to sediments. Sediments may then act as a long-term source of PBDEs which can be released back into the water column due to resuspension during storm events.

A critical review of labelling techniques used to quantify rhizosphere carbon-flow

The rhizosphere is a major sink for photo-assimilated carbon and quantifying inputs into this sink is one of the main goals of rhizosphere biology as organic carbon lost from plant roots supports a higher microbial population in the rhizosphere compared to bulk soil. Two fundamentally different¹⁴CO₂ labelling strategies have been developed to estimate carbon fluxes through the rhizosphere - continuous feeding of shoots with labelled carbon dioxide and pulse-chase experiments. The biological interpretation that can be placed on the results of labelling experiments is greatly biased by the technique used. It is the purpose of this paper to assess the advantages, disadvantages and the biological interpretation of both continuous and pulse labelling and to consider how to partition carbon fluxes within the rhizosphere. © 1994 Kluwer Academic Publishers.

Prevalence of the prothrombin G20210A mutation in the Irish populations:use of a novel polymerase chain reaction approach

The prothrombin G20210A polymorphism is associated with a threefold-increased risk of venous thrombosis. There is considerable variation in the reported prevalence of this polymorphism within normal populations, ranging from 0 to 6.5%. The prevalence within the Irish population has not been determined. A restriction fragment length polymorphism (RFLP)-based assay is commonly used for the detection of the prothrombin 20210A allele. This assay does not include a control restriction digest fragment and, consequently, failure of the enzyme activity or lack of addition of enzyme to the sample cannot be distinguished from wild-type prothrombin. We developed a RFLP-based assay, which incorporates an invariant digest site, resulting in the generation of a control digest fragment. Furthermore, we developed a nested polymerase chain reaction (PCR) method for the amplification and digestion of poor-quality or low-concentration DNA. In the Irish population studied, five of 385 (1.29%) were heterozygous and one patient was homozygous for the prothrombin 20210A polymorphism. This is the first reported data on an Irish or Celtic population and suggests that the allele frequency is similar to Anglo-Saxon populations. The nested PCR method successfully amplified and digested 100/100 (100%) of the archived samples; none of these samples could be analyzed by the standard single-round PCR method. In conclusion, nested PCR should be considered in the analysis of archived samples. Single-round PCR is appropriate for recently collected samples; however, an invariant control digest site should be incorporated in RFLP-based assays to validate the integrity of the digestion enzyme and limit the risk of false-negative results.

Sorting out mix-ups. The provenance of tissue sections may be confirmed by PCR using microsatellite markers

Standard identification systems usually ensure that biopsy material is correctly associated with a given patient. Sometimes, as when a tumor is unexpectedly found, the provenance (proof of origin) of a tissue sample may be questioned; the tissue may have been mislabelled or contaminated with tissue from another patient. Techniques used to confirm tissue provenance include comparing either tissue markers of gender or ABO blood groups; however, these methods have weak confirmatory power. Recently, the use of DNA-based polymerase chain reaction (PCR) techniques has been reported. Paired, formalin-fixed, paraffin-embedded, 10 microns tissue sections were selected from 17 patients, 8 of whom had carcinoma, either by dividing a biopsy section, using sequential biopsies, or sequential biopsy and autopsy tissue. The resulting 36 samples were coded before analysis. In two additional cases, 1-mm fragments of tumor from one patient were included in the tissue block of benign tissue from another patient, the tumor fragments were identified on hematoxylin-and-eosin-stained sections, separately scraped off the glass slide, and analyzed. Tissue from two clinical cases, one of suspected mislabelling and one with a suspected carry-over of malignant tissue were also investigated. Short tandem repeat sequences (STR) or microsatellites, are 2-5 base pair repeats that vary in their repeat number between individuals. This variation (polymorphism) can be assessed using a PCR. A panel of markers of 3 STRs; ACPP, INT 2, and CYP 19 (on chromosomes 3, 11, and 15, respectively) were used. DNA was isolated from the samples after xylene deparaffinization and proteinase digestion, and was then amplified in a radioactive PCR using primers selected to give a product size ranging from 136-178 bases. Amplified products were electrophoresed on denaturing polyacrylamide gels, dried, and autoradiographed. DNA segments were successfully extracted from all samples but one, which was fixed in Bouin's fluid. By comparing allele sizes from the panel, all tissue pairs (other than the Bouin's pair) were successfully matched, the 1-mm tumor fragments were correctly assigned, and the two clinical problems were solved. STRs are highly informative and robust markers, well suited to PCR of small portions of tissue sections, and are an effective method to confirm the provenance of benign and malignant biopsy and autopsy material.

Rapid-bTB: a novel lateral flow test able to differentiate Mycobacterium bovis from Mycobacterium tuberculosis in sputum

Background: A novel lateral flow, immunochromatographic assay (LFD) specific for Mycobacterium bovis, the cause of bovine tuberculosis and zoonotic TB, was recently developed at Queen’s University Belfast. The LFD detects whole M. bovis cells, in contrast to other commercially available LFD tests (BD MGITTM TBc ID, SD Bioline TB Ag MPT 64, Capilia TB-Neo kit) which detect MPT64 antigen secreted during growth. The new LFD test has been evaluated in the veterinary context, and its specificity for M. bovis in the broadest sense (i.e. subsp. bovis, subsp. caprae and BCG) and sensitivity to detect M. bovis in positive MGIT™ liquid cultures was demonstrated comprehensively.
Methods: Preliminary work was carried out by researchers at Queen’s University Belfast to optimise sputum sample preparation, estimate the limit of detection (LOD) of the LFD with M. bovis-spiked sputum samples, and check LFD specificity by testing a broad range of non-tuberculous Mycobacterium spp. (NTM) and other bacterial genera commonly encountered in sputum samples (Haemophilus, Klebsiella, Pseudomonas, Staphylococcus). In the Cameroon laboratory direct detection of M. bovis in human sputa was attempted, and 50 positive sputum MGIT™ cultures and 33 cultures of various Mycobacterium spp. originally isolated from human sputa were tested.
Results: Sputum sample preparation consisted of digestion with 1% NALC for 30 min, centrifugation at 3000g for 20 min, PBS wash, centrifugation again, and pellet resuspended in KPL blocking buffer before 100 µl was applied to the LFD. The LOD of the LFD applied to M. bovis-spiked sputum was estimated to be 104 CFU/ml. A small number of confirmed Ziehl-Neelsen ‘3+’ M. bovis positive sputum samples were tested directly but no positive LFD results were obtained. All of the sputum MGIT™ cultures and mycobacterial cultures (including M. tuberculosis, M. africanum, M. bovis, M. intracellulare, M. scrofulaceum, M. fortuitum, M. peregrinum, M. interjectum) tested LFD negative when read after 15 min except for the M. bovis cultures, thereby confirming specificity of LFD for M. bovis in the clinical microbiology context.
Conclusions: Results indicate that the ‘Rapid-bTB’ LFD is a very specific test, able to differentiate M. bovis from M. tuberculosis, M. africanum, and a range of NTM isolated from human sputa in MGITTM liquid cultures. However, the LFD lacks sufficient sensitivity to be applied earlier in the diagnostic process to directly test human sputa.

Query Suggestions for Textual Problem Solution Repositories

Textual problem-solution repositories are available today in
various forms, most commonly as problem-solution pairs from community
question answering systems. Modern search engines that operate on
the web can suggest possible completions in real-time for users as they
type in queries. We study the problem of generating intelligent query
suggestions for users of customized search systems that enable querying
over problem-solution repositories. Due to the small scale and specialized
nature of such systems, we often do not have the luxury of depending on
query logs for finding query suggestions. We propose a retrieval model
for generating query suggestions for search on a set of problem solution
pairs. We harness the problem solution partition inherent in such
repositories to improve upon traditional query suggestion mechanisms
designed for systems that search over general textual corpora. We evaluate
our technique over real problem-solution datasets and illustrate that
our technique provides large and statistically significant

Knowledge Management Techniques to Augment Textual CBR (PhD Thesis)

The past decade had witnessed an unprecedented growth in the amount of available digital content, and its volume is expected to continue to grow the next few years. Unstructured text data generated from web and enterprise sources form a large fraction of such content. Many of these contain large volumes of reusable data such as solutions to frequently occurring problems, and general know-how that may be reused in appropriate contexts. In this work, we address issues around leveraging unstructured text data from sources as diverse as the web and the enterprise within the Case-based Reasoning framework. Case-based Reasoning (CBR) provides a framework and methodology for systematic reuse of historical knowledge that is available in the form of problemsolution
pairs, in solving new problems. Here, we consider possibilities of enhancing Textual CBR systems under three main themes: procurement, maintenance and retrieval. We adapt and build upon the stateof-the-art techniques from data mining and natural language processing in addressing various challenges therein. Under procurement, we investigate the problem of extracting cases (i.e., problem-solution pairs) from data sources such as incident/experience
reports. We develop case-base maintenance methods specifically tuned to text targeted towards retaining solutions such that the utility of the filtered case base in solving new problems is maximized. Further, we address the problem of query suggestions for textual case-bases and show that exploiting the problem-solution partition can enhance retrieval effectiveness by prioritizing more useful query suggestions. Additionally, we illustrate interpretable clustering as a tool to drill-down to domain specific text collections (since CBR systems are usually very domain specific) and develop techniques for improved similarity assessment in social media sources such as microblogs. Through extensive empirical evaluations, we illustrate the improvements that we are able to
achieve over the state-of-the-art methods for the respective tasks.

Independent Ireland

Although many Irish nationalists at the turn of the twentieth century expected Ireland to achieve self-government within their own lifetime, few could have anticipated its form or consequences: the promised land that they envisioned was to be achieved through political means rather than insurrection and partition. But while the violence of the revolutionary decade created the political structures that shape present-day Ireland, the social and economic changes of the final decades of the twentieth century, by rupturing cultural patterns that predated independence, arguably brought about a more profound dislocation. Within Southern Ireland, the focus of this essay, the long era between these periods of upheaval was initially characterised by the pursuit of national sovereignty and self-sufficiency. In contrast, the decades after the Second World War saw the gradual abandonment of that vision in favour of a more pragmatic policy of economic liberalisation. The resulting ‘modernisation’ saw many traditional aspects of Irish society replaced by individualistic values more typical of contemporary European society.

Industrial scale microwave processing of tomato juice using a novel continuous microwave system

This study evaluated the effect of an industrial scale continuous flow microwave volumetric heating system in comparison to conventional commercial scale pasteurisation for the processing of tomato juice in terms of physicochemical properties, microbial characteristics and antioxidant capacity. The effect against oxidative stress in Caco-2 cells, after in vitro digestion was also investigated. Physicochemical and colour characteristics of juices were very similar between technologies and during storage. Both conventional and microwave pasteurisation inactivated microorganisms and kept them in low levels throughout storage. ABTS⁺ values, but not ORAC, were higher for the microwave pasteurised juice at day 0 however no significant differences between juices were observed during storage. Juice processed with the microwave system showed an increased cytoprotective effect against H₂O₂ induced oxidation in Caco-2 cells. Organoleptic analysis revealed that the two tomato juices were very similar. The continuous microwave volumetric heating system appears to be a viable alternative to conventional pasteurisation.

Substance P production by human dental pulp fibroblasts

The inflammatory response to pulpal injury or infection has major clinical significance. Neurogenic inflammation describes the local release of neuropeptides, notably substance P (SP), from afferent neurones, and may play a role in the pathogenesis of pulpal disease. The fibroblast is the most numerous cell type in the dental pulp and recent work has suggested that it is involved in the inflammatory response. Objectives: The aims of the study were to determine whether pulp fibroblasts could produce SP, and to investigate the expression of the SP receptor, NK-1, by these cells. Methods: Primary pulp fibroblast cell populations were isolated by enzymatic digestion from non-carious teeth extracted for orthodontic reasons. Whole pulp tissue was obtained from freshly extracted sound (n=35) and carious (n=39) teeth. Expression of SP and NK-1 mRNA was determined by RT-PCR. The effects of interleukin-1β (IL-1β) and transforming growth factor-β1 (TGF-β1) on SP and NK-1 expression were also determined. The presence of NK-1 on fibroblast cell membranes was established by western blotting. The effects of the cytokines on each parameter were analysed by ANOVA. Radioimmunoassay (RIA) was carried out to quantify SP expression by pulp fibroblasts and in whole pulp tissue. Results: SP was expressed by pulpal fibroblasts both at the mRNA level and the protein level. In addition, NK-1 was detected in fibroblast cultures at the mRNA level and appeared as a double band on western blots of membrane extracts. IL-1β and TGF-β1 significantly stimulated the expression of SP and NK-1. SP levels were significantly greater (p<0.05) in carious compared to sound teeth. Conclusion: Pulp fibroblasts are capable of synthesising and secreting SP, as well as expressing the SP receptor, NK-1. These findings suggest that pulp fibroblasts play a role in neurogenic inflammation in pulpal disease. (Supported by the European Society of Endodontology.)

Heterogeneous error-resilient scheme for spectral analysis in ultra-low power wearable electrocardiogram devices

Wearable devices performing advanced bio-signal analysis algorithms are aimed to foster a revolution in healthcare provision of chronic cardiac diseases. In this context, energy efficiency is of paramount importance, as long-term monitoring must be ensured while relying on a tiny power source. Operating at a scaled supply voltage, just above the threshold voltage, effectively helps in saving substantial energy, but it makes circuits, and especially memories, more prone to errors, threatening the correct execution of algorithms. The use of error detection and correction codes may help to protect the entire memory content, however it incurs in large area and energy overheads which may not be compatible with the tight energy budgets of wearable systems. To cope with this challenge, in this paper we propose to limit the overhead of traditional schemes by selectively detecting and correcting errors only in data highly impacting the end-to-end quality of service of ultra-low power wearable electrocardiogram (ECG) devices. This partition adopts the protection of either significant words or significant bits of each data element, according to the application characteristics (statistical properties of the data in the application buffers), and its impact in determining the output. The proposed heterogeneous error protection scheme in real ECG signals allows substantial energy savings (11% in wearable devices) compared to state-of-the-art approaches, like ECC, in which the whole memory is protected against errors. At the same time, it also results in negligible output quality degradation in the evaluated power spectrum analysis application of ECG signals.

Techno-Economic Feasibility of Selective CO2 Capture Processes from Biogas Streams using Ionic Liquids as Physical Absorbents

Biogas from anaerobic digestion of sewage sludge is a renewable resource with high energy content, which is formed mainly of CH4 (40-75 vol.%) and CO2 (15-60 vol.%) Other components such as water (H2O, 5-10 vol.%) and trace amounts of hydrogen sulfide and siloxanes can also be present. A CH4-rich stream can be produced by removing the CO2 and other impurities so that the upgraded bio-methane can be injected into the natural gas grid or used as a vehicle fuel. The main objective of this paper is to develop a new modeling methodology to assess the technical and economic performance of biogas upgrading processes using ionic liquids which physically absorb CO2. Three different ionic liquids, namely the 1-ethyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, 1-hexyl-3-methylimidazoliumbis[(trifluoromethyl)sulfonyl]imide and trihexyl(tetradecyl)phosphonium bis[(trifluoromethyl)sulfonyl]imide, are considered for CO2 capture in a pressure-swing regenerative absorption process. The simulation software Aspen Plus and Aspen Process Economic Analyzer is used to account for mass and energy balances as well as equipment cost. In all cases, the biogas upgrading plant consists of a multistage compressor for biogas compression, a packed absorption column for CO2 absorption, a flash evaporator for solvent regeneration, a centrifugal pump for solvent recirculation, a pre-absorber solvent cooler and a gas turbine for electricity recovery. The evaluated processes are compared in terms of energy efficiency, capital investment and bio-methane production costs. The overall plant efficiency ranges from 71-86 % whereas the bio-methane production cost ranges from £6.26-7.76 per GJ (LHV). A sensitivity analysis is also performed to determine how several technical and economic parameters affect the bio-methane production costs. The results of this study show that the simulation methodology developed can predict plant efficiencies and production costs of large scale CO2 capture processes using ionic liquids without having to rely on gas solubility experimental data.

Size Matters: The Effect of the Size of Ethnic Groups on Development

The share of ethnic groups is one of the most important features of African politics. It affects civil wars, representation in government positions, distributive and allocative policies. In this paper we use the partition of ethnic groups as a natural experiment in order to estimate the effect of the share of these ethnic groups on development. We show that larger groups have an advantage in terms of development and that the partition in itself does not matter for development. This result is explained by the fact that the partition matters only when the resulting groups are relatively small, since their lack of political representation may weaken support for institutions, may bias policies and the provision of ethnic/regional public goods.

Contaminated soil exposure assessment in Portugal and in the EU

Este estudo baseou-se na análise dos mecanismos de transferência de elementos potencialmente tóxicos (PTE’s) entre o solo, a solução do solo e as plantas como forma de realizar uma avaliação mais eficaz do risco em áreas agrícolas. Foram aplicados conceitos recentemente desenvolvidos para a avaliação da reactividade biogeoquímica de contaminantes no solo e da sua partição sólido:solução recorrendo-se a modelos empíricos (tipo Freundlich). Estes modelos permitiram analisar a transferência de PTE’s ao longo da cadeia alimentar e avaliar o impacto da contaminação do solo na qualidade da alimentação animal (forragens) e Humana (vegetais e carne) em Portugal. Os modelos empíricos de transferência solo-planta de PTE’s foram utilizadas para obter limites críticos para estes elementos em solos agrícolas em Portugal, a partir dos seus limites legais nos alimentos para animais e teores máximos nos géneros alimentícios. Simultaneamente, modelos de exposição Humana a contaminantes do solo, desenvolvidos noutros países da UE foram analisados e foi proposto um modelo de exposição para Portugal. Este trabalho é uma contribuição para o desenvolvimento de critérios de qualidade de solos para áreas agrícolas em Portugal, tendo em vista a protecção da saúde animal e Humana. Contribuiu também para o desenvolvimento de uma estratégia de harmonização de políticas de protecção do solo (nomeadamente no que diz respeito aos problemas de contaminação) na União Europeia.