Novel monoclonal antibody and peptide binders for Mycobacterium avium subsp. paratuberculosis and their application for magnetic separation

The generation of novel Mycobacterium avium subsp. paratuberculosis (MAP)-specific monoclonal antibodies and phage-display derived peptide binders, along with their application for the magnetic separation (MS) of MAP cells, is described. Our aim was to achieve even greater MAP capture capability than is possible with peptide-mediated magnetic separation (PMS) using a 50:50 mix of biotinylated-aMp3 and biotinylated-aMptD peptide-coated beads. Gamma-irradiated whole MAP cells and ethanol extracted antigens (EEA) from these cells were used to elicit an immune response and as phage-display biopanning targets. A range of novel binders was obtained and coated onto paramagnetic beads, both individually and in various combinations, for MS evaluation. IS900 PCR was employed after MS to provide quick results. Capture sensitivity was assessed using a range of MAP concentrations after which the most promising beads were tested for their specificity for MAP, by performing MS followed by culture using 10 other Mycobacterium species. Magnetic beads coated with the biotinylated EEA402 peptide demonstrated a greater level of MAP capture than the current PMS method, even when low numbers of MAP (<10 cfu/ml) were present; however these beads also captured a range of other mycobacteria and so lacked capture specificity. Magnetic beads coated with monoclonal antibodies 6G11 and 15D10 (used as a 50:50 mix or as dually coated beads) also demonstrated improved MAP capture relative to the current PMS method, but with little cross-reactivity to other Mycobacterium spp. Therefore, two new MS protocols are suggested, the application of which would be dependent upon the required endpoint. Biotinylated EEA402-coated beads could potentially be used with a MAP-specific PCR to ensure detection specificity, while beads coated with 6G11 and 15D10 monoclonal antibodies could be used with culture or the phage amplification assay.

Tailoring Plasmonic Metamaterials for Ultrasenstive Detection of Mercury Trace Contaminants via Molecular Logic Gates

Structural and functional information encoded in DNA combined with unique properties of nanomaterials could be of use for the construction of novel biocomputational circuits and intelligent biomedical nanodevices. However, at present their practical applications are still limited by either low reproducibility of fabrication, modest sensitivity, or complicated handling procedures. Here, we demonstrate the construction of label-free and switchable molecular logic gates (AND, INHIBIT, and OR) that use specific conformation modulation of a guanine- and thymine-rich DNA, while the optical readout is enabled by the tunable metamaterials which serve as a substrate for surface enhanced Raman spectroscopy (MetaSERS). Our MetaSERS-based DNA logic is simple to operate, highly reproducible, and can be stimulated by ultra-low concentration of the external inputs, enabling an extremely sensitive detection of mercury ions down to 2×10-4 ppb, which is four orders of magnitude lower than the exposure limit allowed by United States Environmental Protection Agency

Deep separation of benzene from cyclohexane by liquid extraction using ionic liquids as the solvent

Separation of benzene and cyclohexane is one of the most important and difficult processes in the petrochemical industry, especially for low benzene concentration. In this work, three ionic liquids (ILs), [Bmim][BF ₄], [Bpy][BF ₄], and [Bmim][SCN], were investigated as the solvent in the extraction of benzene from cyclohexane. The corresponding ternary liquid-liquid equilibria (LLE) were experimentally determined at T = 298.15 K and atmospheric pressure. The LLE data were correlated with the nonrandom two-liquid model, and the parameters were fitted. The separation capabilities of the ILs were evaluated in terms of the benzene distribution coefficient and solvent selectivity. The effect of the IL structure on the separation was explained based on a well-founded physical model, COSMO-RS. Finally, the extraction processes were defined, and the operation parameters were analyzed. It shows that the ILs studied are suitable solvents for the extractive separation of benzene and cyclohexane, and their separation efficiency can be generally ranked as [Bmim][BF ₄] > [Bpy][BF ₄] > [Bmim][SCN]. The extraction process for a feed with 15 mol % benzene was optimized. High product purity (cyclohexane 0.997) and high recovery efficiency (cyclohexane 96.9% and benzene 98.1%) can be reached. © 2012 American Chemical Society.

Energy versus data integrity trade-offs in embedded high-density logic compatible dynamic memories

Current variation aware design methodologies, tuned for worst-case scenarios, are becoming increasingly pessimistic from the perspective of power and performance. A good example of such pessimism is setting the refresh rate of DRAMs according to the worst-case access statistics, thereby resulting in very frequent refresh cycles, which are responsible for the majority of the standby power consumption of these memories. However, such a high refresh rate may not be required, either due to extremely low probability of the actual occurrence of such a worst-case, or due to the inherent error resilient nature of many applications that can tolerate a certain number of potential failures. In this paper, we exploit and quantify the possibilities that exist in dynamic memory design by shifting to the so-called approximate computing paradigm in order to save power and enhance yield at no cost. The statistical characteristics of the retention time in dynamic memories were revealed by studying a fabricated 2kb CMOS compatible embedded DRAM (eDRAM) memory array based on gain-cells. Measurements show that up to 73% of the retention power can be saved by altering the refresh time and setting it such that a small number of failures is allowed. We show that these savings can be further increased by utilizing known circuit techniques, such as body biasing, which can help, not only in extending, but also in preferably shaping the retention time distribution. Our approach is one of the first attempts to access the data integrity and energy tradeoffs achieved in eDRAMs for utilizing them in error resilient applications and can prove helpful in the anticipated shift to approximate computing.

Extent and mechanism of phase separation during the extrusion of calcium phosphate pastes

The aim of this study was to increase understanding of the mechanism and dominant drivers influencing phase separation during ram extrusion of calcium phosphate (CaP) paste for orthopaedic applications. The liquid content of extrudate was determined, and the flow of liquid and powder phases within the syringe barrel during extrusion were observed, subject to various extrusion parameters. Increasing the initial liquid-to-powder mass ratio, LPR, (0.4-0.45), plunger rate (5-20 mm/min), and tapering the barrel exit (45°-90°) significantly reduced the extent of phase separation. Phase separation values ranged from (6.22 ± 0.69 to 18.94 ± 0.69 %). However altering needle geometry had no significant effect on phase separation. From powder tracing and liquid content determination, static zones of powder and a non-uniform liquid distribution was observed within the barrel. Measurements of extrudate and paste LPR within the barrel indicated that extrudate LPR remained constant during extrusion, while LPR of paste within the barrel decreased steadily. These observations indicate the mechanism of phase separation was located within the syringe barrel. Therefore phase separation can be attributed to either; (1) the liquid being forced downstream by an increase in pore pressure as a result of powder consolidation due to the pressure exerted by the plunger or (2) the liquid being drawn from paste within the barrel, due to suction, driven by dilation of the solids matrix at the barrel exit. Differentiating between these two mechanisms is difficult; however results obtained suggest that suction is the dominant phase separation mechanism occurring during extrusion of CaP paste.

Porous organic cages for sulfur hexafluoride separation

A series of porous organic cages is examined for the selective adsorption of sulphur hexafluoride (SF6) over nitrogen. Despite lacking any metal sites, a porous cage, CC3, shows the highest SF6/N2 selectivity reported for any material at ambient temperature and pressure, which translates to real separations in a gas breakthrough column. The SF6 uptake of these materials is considerably higher than would be expected from the static pore structures. The location of SF6 within these materials is elucidated by x-ray crystallography, and it is shown that cooperative diffusion and structural rearrangements in these molecular crystals can rationalize their superior SF6/N2 selectivity.

Separation Science and Technology - Theory

I have completed 80% of a teaching text book (text and graphics) on Separation Science and Technology - Theory. The book's content is what I've learned over many years of practice and teaching with an emphasis on clarifying and explaining the nuances within the theories associated with various practical approaches to chemical and biochemical separations.

The book is divided into self-contained Chapters with many worked examples and practice questions. It very much aligns with my teaching on CHM3005D, CHM2010, CHM2007 and is ideal for PMY8105 and the new proposed MSci in Analytical Chemistry Programme. The book brings together diverse material in single space and will be a valuable pedagogical resource for the teaching of this key discipline within QUB and elsewhere.

Laterality as an indicator of emotional stress in ewes and lambs during a separation test

We assessed motor laterality in sheep to explore species-specific brain hemi-field dominance and how this could be affected by genetic or developmental factors. Further, we investigated whether directionality and strength of laterality could be linked to emotional stress in ewes and their lambs during partial separation. Forty-three ewes and their singleton lambs were scored on the (left/right) direction of turn in a y-maze to rejoin a conspecific (laterality test). Further, their behavioural response (i.e. time spent near the fence, vocalisations, and activity level) during forced separation by an open-mesh fence was assessed (separation test). Individual laterality was recorded for 44.2 % ewes (significant right bias) and 81.4 % lambs (equally biased to the left and the right). There was no significant association in side bias between dams and offspring. The Chi-squared test revealed a significant population bias for both groups (p < 0.05). Evolutionary adaptive strategies or stimuli-related visual laterality may provide explanation for this decision-making process. Absolute strength of laterality (irrespective of side) was high (Kolmogorov–Smirnov test, dams: D = 0.2; p < 0.001; lambs: D = 0.36, p < 0.0001). The Wilcoxon test showed that lateralised lambs and dams spent significantly more time near each other during separation than non-lateralised animals (p < 0.05), and that lateralised dams were also more active than non-lateralised ones. Arguably, the lateralised animals showed a greater attraction to their pair because they were more disturbed and thus required greater reassurance. The data show that measures of laterality offer a potential novel non-invasive indicator of separation stress.

Logic Brightens My Day: Evidence for Implicit Sensitivity to Logical Validity.

A key assumption of dual process theory is that reasoning is an explicit, effortful, deliberative process. The present study offers evidence for an implicit, possibly intuitive component of reasoning. Participants were shown sentences embedded in logically valid or invalid arguments. Participants were not asked to reason but instead rated the sentences for liking (Experiment 1) and physical brightness (Experiments 2-3). Sentences that followed logically from preceding sentences were judged to be more likable and brighter. Two other factors thought to be linked to implicit processing-sentence believability and facial expression-had similar effects on liking and brightness ratings. The authors conclude that sensitivity to logical structure was implicit, occurring potentially automatically and outside of awareness. They discuss the results within a fluency misattribution framework and make reference to the literature on discourse comprehension. 

The Exclusive Brethren ‘Doctrine of Separation’: An Anthropology of Theology

Why do the Exclusive Brethren attend church ten times a week? Why do they shun excommunicated members, including immediate family? Why do they refuse to eat with outsiders? Why will they employ outsiders in their businesses, but never be employed by them? Why do they reject modern media as “pipelines of filth”? Why do they refuse to vote, while simultaneously campaigning for Conservative Party candidates? Why do they only live in detached houses, and build churches entirely without windows? How, in other words, do the Exclusive Brethren try to live good lives? And what can we learn anthropologically from these models of ‘the good’, and from the objections they provoke? Drawing inspiration from Keane’s (2014) suggestion that ‘we shouldn’t decide in advance what ethics will look like’, this paper seeks to critically contribute to new scholarship within the anthropology of morality and detachment by constructing, in a very literal sense, an anthropology of theology via an analysis of the Exclusive Brethren ‘doctrine of separation’.

Logic Programming and Artificial Neural Networks in Pharmacological Screening of Schinus Essential Oils

Some plants of genus Schinus have been used in the folk medicine as topical antiseptic, digestive, purgative, diuretic, analgesic or antidepressant, and also for respiratory and urinary infections. Chemical composition of essential oils of S. molle and S. terebinthifolius had been evaluated and presented high variability according with the part of the plant studied and with the geographic and climatic regions. The pharmacological properties, namely antimicrobial, anti-tumoural and anti-inflammatory activities are conditioned by chemical composition of essential oils. Taking into account the difficulty to infer the pharmacological properties of Schinus essential oils without hard experimental approach, this work will focus on the development of a decision support system, in terms of its knowledge representation and reasoning procedures, under a formal framework based on Logic Programming, complemented with an approach to computing centered on Artificial Neural Networks and the respective Degree-of-Confidence that one has on such an occurrence.

Avaliação do desempenho docente e o professor titular: um estudo de caso numa perspetiva organizacional

A avaliação do desempenho docente tem vindo a adquirir uma centralidade crescente nos contextos educativos. Para além de razões mais abrangentes que têm a ver com a importância gradual que a avaliação adquire nas políticas educativas, considera-se que a avaliação do desempenho docente contribui para a melhoria da qualidade do trabalho docente, das aprendizagens e dos resultados escolares dos alunos. As alterações do Estatuto da Carreira Docente introduziram, a partir de 2007, a par com um novo e mais exigente sistema de avaliação, a divisão da carreira em duas categorias – professor e professor titular. Os professores titulares passaram a desempenhar funções de avaliação e coordenação dos seus colegas. Estas mudanças trouxeram alterações significativas na carreira, na profissão e no trabalho docente. O propósito deste estudo foi pesquisar, do ponto de vista da análise organizacional, o modo como foi percecionado pelos docentes o processo de avaliação do desempenho (relativo ao ciclo 2007-2009), centrando-nos, em particular, no papel desempenhado pelos professores titulares num modelo de avaliação por pares e num quadro legal de verticalização da carreira docente. Desenvolvemos este estudo num agrupamento de escolas da zona centro do território continental português seguindo uma metodologia de estudo de caso. Como principais conclusões, e tendo em conta as lógicas organizacionais de que partimos, ressalta-se: i) ao nível da lógica burocrática, a burocratização e morosidade do concurso dos professores titulares, a complexidade dos procedimentos conducentes à implementação do sistema de avaliação e o formalismo na construção dos respetivos instrumentos; ii) dentro da lógica conflitual, as tensões decorrentes da discordância com a divisão da carreira entre professor e professor titular, a atribuição aos professores titulares da função avaliativa, não tendo estes sido reconhecidos pelos seus pares com legitimidade para os avaliar, e a existência de conflitos entre os diversos intervenientes; iii) na lógica artificial, o facto de este sistema de avaliação não ter implicado alterações significativas nas práticas, tendo em conta a exígua adesão dos professores à avaliação da componente cientifico-pedagógica, a ritualização de processos e o restringir-se ao cumprimento dos requisitos mínimos.

MUSA: A Scalable Multi-Touch and Multi-Perspective Variability Management Tool

Variability management is one of the main activities in the Software Product Line Engineering process. Common and varied features of related products are modelled along with the dependencies and relationships among them. With the increase in size and complexity of product lines and the more holistic systems approach to the design process, managing the ever- growing variability models has become a challenge. In this paper, we present MUSA, a tool for managing variability and features in large-scale models. MUSA adopts the Separation of Concerns design principle by providing multiple perspectives to the model, each conveying different set of information. The demonstration is conducted using a real-life model (comprising of 1000+ features) particularly showing the Structural View, which is displayed using a mind-mapping visualisation technique (hyperbolic trees), and the Dependency View, which is displayed graphically using logic gates.

On Investor Preferences and Mutual Fund Separation

We extend Cass and Stiglitz’s analysis of preference-based mutual fund separation. We show that high degrees of fund separation can be constructed by adding inverse marginal utility functions exhibiting lower degrees of separation. However, this method does not allow us to find all utility functions satisfying fund separation. In general, we do not know how to write the primal utility functions in these models in closed form, but we can do so in the special case of SAHARA utility defined by Chen et al. and for a new class of GOBI preferences introduced here. We show that there is money separation (in which the riskless asset can be one of the funds) if and only if there is a fund (which may not be the riskless asset) with a constant allocation as wealth changes.