Lovastatin biosynthesis depends on the carbon-nitrogen proportion: model development and controller design

Lovastatin biosynthesis depends on the relative concentrations of dissolved oxygen and the carbon and nitrogen resources. An elucidation of the underlying relationship would facilitate the derivation of a controller for the improvement of lovastatin yield in bioprocesses. To achieve this goal, batch submerged cultivation experiments of lovastatin production by Aspergillus flavipus BICC 5174, using both lactose and glucose as carbon sources, were performed in a 7 liter bioreactor and the data used to determine how the relative concentrations of lactose, glucose, glutamine and oxygen affected lovastatin yield. A model was developed based on these results and its prediction was validated using an independent set of batch data obtained from a 15-liter bioreactor using five statistical measures, including the Willmott index of agreement. A nonlinear controller was designed considering that dissolved oxygen and lactose concentrations could be measured online, and using the lactose feed rate and airflow rate as process inputs. Simulation experiments were performed to demonstrate that a practical implementation of the nonlinear controller would result in satisfactory outcomes. This is the first model that correlates lovastatin biosynthesis to carbon-nitrogen proportion and possesses a structure suitable for implementing a strategy for controlling lovastatin production.

Tailoring Plasmonic Metamaterials for DNA 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 that use specific conformation modulation of a guanine- and thymine- rich DNA, while the optical readout is enabled by the tunable alphabetical metamaterials, which serve as a substrate for surface enhanced Raman spectroscopy (MetaSERS). By computational and experimental investigations, we present a comprehensive solution to tailor the plasmonic responses of MetaSERS with respect to the metamaterial geometry, excitation energy, and polarization. Our tunable 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.

The effects of global climate change on the cycling and processes of persistent organic pollutants (POPs) in the North Sea

The fate and cycling of two selected legacy persistent organic pollutants (POPs), PCB 153 and gamma-HCH, in the North Sea in the 21st century have been modelled with combined hydrodynamic and fate and transport ocean models
(HAMSOM and FANTOM, respectively). To investigate the impact of climate variability on POPs in the North Sea in the 21st century, future scenario model runs for three 10-year periods to the year 2100 using plausible levels of both in
situ concentrations and atmospheric, river and open boundary inputs are performed. This slice mode under a moderate scenario (A1B) is sufficient to provide a basis for further analysis. For the HAMSOM and atmospheric forcing, results of the IPCC A1B (SRES) 21st century scenario are utilized, where surface forcing is provided by the REMO downscaling of the ECHAM5 global atmospheric model, and open boundary conditions are provided by the MPIOM global ocean model.
Dry gas deposition and volatilization of gamma-HCH increase in the future relative to the present by up to 20% (in the spring and summer months for deposition and in summer for volatilization). In the water column, total mass of
gamma-HCH and PCB 153 remain fairly steady in all three runs. In sediment,
gamma-HCH increases in the future runs, relative to the present, while PCB 153 in sediment decreases exponentially in all three runs, but even faster in the future, due to the increased number of storms, increased duration of gale wind conditions and increased water and air temperatures, all of which are the result of climate change. Annual net sinks exceed sources at the ends of all periods.
Overall, the model results indicate that the climate change scenarios considered here generally have a negligible influence on the simulated fate and transport of the two POPs in the North Sea, although the increased number and magnitude of storms in the 21st century will result in POP resuspension and ensuing revolatilization events. Trends in emissions from primary and secondary sources will remain the key driver of levels of these contaminants over time.

Modelling the fate of persistent organic pollutants (POPs) in the North Sea system

The environmental fate of selected persistent organic pollutants (POPs) in the North Sea system is modelled with a high resolution Fate and Transport Ocean Model (FANTOM) that uses hydrodynamic model output from the Hamburg Shelf Ocean Model (HAMSOM). Large amounts of POPs enter the North Sea from the surrounding highly populated, industrialised and agricultural countries. Major pathways to the North Sea are atmospheric deposition and river inputs, with additional contributions coming from bottom sediments and adjacent seas. The model domain covers the entire North Sea region, extending northward as far as the Shetland Islands, and includes adjacent basins such as the Skagerrak, Kattegat, and the westernmost part of the Baltic Sea. Model resolution (for both models) is 1.5’ latitude x 2.5’ longitude (approximately 3 km horizontal resolution) with 30 vertical levels. The POP model also has 20 sediment layers. Important model processes controlling the fate of POPs in the North Sea system are discussed. Results focus on Lindane gamma- HCH or gamma-hexachlorocyclohexane) and PCB 153.

(Re)-Introducing Themes of Religion and Spirituality to Professional Social Work Training in the Land of ‘Saints and Scholars’.

This chapter begins by alluding to Ireland’s historical reputation as the land of “Saints and Scholars” and then briefly charts its demise from this position. A parallel process in relation to religiously motivated provision of health and social care is outlined. The inclusion of themes of religion and spirituality within the current professional social work codes in the USA and Britain and the framework for social work training in Northern Ireland is noted. In this context the lack of any substantive inclusion of themes of religion and/or spirituality within the Bachelor of Social Work (BSW) degree at Queens University Belfast will be situated. A series of intersecting reasons for this lack of inclusion are proposed in terms of the experience of living through the recent troubled history of Northern Ireland and a variety of biases in academic thought.
A rationale for the re-introduction of inputs on religion and spirituality is articulated in terms of the widespread resurgence of these themes within health and social care and psychotherapy literature and the new emphasis on practicing in culturally sensitive ways in Britain. The first steps to re-introduce these themes under the higher context marker of “culturally competent practice” are described and an analysis of data from the students’ feedback presented along with illustrative quotations. The dissonance between the initial misgivings of staff and the overwhelmingly positive responses of students are highlighted. The chapter concludes with a discussion of lessons learned through the process with an emphasis on how the inclusion of these themes can result in better practice for service users, including those impacted by “the Troubles” in Northern Ireland.

Spatial and Temporal Changes in Soil Organic Carbon Assessment using an Integrated Geostatistical and Compositional Data Analysis Approach

The Irish and UK governments, along with other countries, have made a commitment to limit the concentrations of greenhouse gases in the atmosphere by reducing emissions from the burning of fossil fuels. This can be achieved (in part) through increasing the sequestration of CO2 from the atmosphere including monitoring the amount stored in vegetation and soils. A large proportion of soil carbon is held within peat due to the relatively high carbon density of peat and organic-rich soils. This is particularly important for a country such as Ireland, where some 16% of the land surface is covered by peat. For Northern Ireland, it has been estimated that the total amount of carbon stored in vegetation is 4.4Mt compared to 386Mt stored within peat and soils. As a result it has become increasingly important to measure and monitor changes in stores of carbon in soils. The conservation and restoration of peat covered areas, although ongoing for many years, has become increasingly important. This is summed up in current EU policy outlined by the European Commission (2012) which seeks to assess the relative contributions of the different inputs and outputs of organic carbon and organic matter to and from soil. Results are presented from the EU-funded Tellus Border Soil Carbon Project (2011 to 2013) which aimed to improve current estimates of carbon in soil and peat across Northern Ireland and the bordering counties of the Republic of Ireland.
Historical reports and previous surveys provide baseline data. To monitor change in peat depth and soil organic carbon, these historical data are integrated with more recently acquired airborne geophysical (radiometric) data and ground-based geochemical data generated by two surveys, the Tellus Project (2004-2007: covering Northern Ireland) and the EU-funded Tellus Border project (2011-2013) covering the six bordering counties of the Republic of Ireland, Donegal, Sligo, Leitrim, Cavan, Monaghan and Louth. The concept being applied is that saturated organic-rich soil and peat attenuate gamma-radiation from underlying soils and rocks. This research uses the degree of spatial correlation (coregionalization) between peat depth, soil organic carbon (SOC) and the attenuation of the radiometric signal to update a limited sampling regime of ground-based measurements with remotely acquired data. To comply with the compositional nature of the SOC data (perturbations of loss on ignition [LOI] data), a compositional data analysis approach is investigated. Contemporaneous ground-based measurements allow corroboration for the updated mapped outputs. This provides a methodology that can be used to improve estimates of soil carbon with minimal impact to sensitive habitats (like peat bogs), but with maximum output of data and knowledge.

The impacts of replacing air bubbles with microspheres for the clarification of algae from low cell-density culture

Dissolved Air Flotation (DAF) is a well-known coagulation-flotation system applied at large scale for microalgae harvesting. Compared to conventional harvesting technologies DAF allows high cell recovery at lower energy demand. By replacing microbubbles with microspheres, the innovative Ballasted Dissolved Air Flotation (BDAF) technique has been reported to achieve the same algae cell removal efficiency, while saving up to 80% of the energy required for the conventional DAF unit. Using three different algae cultures (Scenedesmus obliquus, Chlorella vulgaris and Arthrospira maxima), the present work investigated the practical, economic and environmental advantages of the BDAF system compared to the DAF system. 99% cells separation was achieved with both systems, nevertheless, the BDAF technology allowed up to 95% coagulant reduction depending on the algae species and the pH conditions adopted. In terms of floc structure and strength, the inclusion of microspheres in the algae floc generated a looser aggregate, showing a more compact structure within single cell alga, than large and filamentous cells. Overall, BDAF appeared to be a more reliable and sustainable harvesting system than DAF, as it allowed equal cells recovery reducing energy inputs, coagulant demand and carbon emissions. © 2014 Elsevier Ltd.

Linking watershed terrain and hydrology to soil chemical properties, microbial communities and impacts on soil organic C in a humid mid-latitude forested watershed

Understanding the response of humid mid-latitude forests to changes in precipitation, temperature, nutrient cycling, and disturbance is critical to improving our predictive understanding of changes in the surface-subsurface energy balance due to climate change. Mechanistic understanding of the effects of long-term and transient moisture conditions are needed to quantify
linkages between changing redox conditions, microbial activity, and soil mineral and nutrient interactions on C cycling and greenhouse gas releases. To illuminate relationships between the soil chemistry, microbial communities and organic C we established transects across hydraulic and topographic gradients in a small watershed with transient moisture conditions. Valley bottoms tend to be more frequently saturated than ridge tops and side slopes which generally are only saturated when shallow storm flow zones are active. Fifty shallow (~36”) soil cores were collected during timeframes representative of low CO2, soil winter conditions and high CO2, soil summer conditions. Cores were subdivided into 240 samples based on pedology and analyses of the geochemical (moisture content, metals, pH, Fe species, N, C, CEC, AEC) and microbial (16S rRNA gene
amplification with Illumina MiSeq sequencing) characteristics were conducted and correlated to watershed terrain and hydrology. To associate microbial metabolic activity with greenhouse gas emissions we installed 17 soil gas probes, collected gas samples for 16 months and analyzed them for CO2 and other fixed and greenhouse gasses. Parallel to the experimental efforts our data is being used to support hydrobiogeochemical process modeling by coupling the Community Land Model (CLM) with a subsurface process model (PFLOTRAN) to simulate processes and interactions from the molecular to watershed scales. Including above ground processes (biogeophysics, hydrology, and vegetation dynamics), CLM provides mechanistic water, energy, and organic matter inputs to the surface/subsurface models, in which coupled biogeochemical reaction
networks are used to improve the representation of below-ground processes. Preliminary results suggest that inclusion of above ground processes from CLM greatly improves the prediction of moisture response and water cycle at the watershed scale.

Low-Power Process-Variation Tolerant Arithmetic Units Using Input-Based Elastic Clocking

In this paper we propose a design methodology for low-power high-performance, process-variation tolerant architecture for arithmetic units. The novelty of our approach lies in the fact that possible delay failures due to process variations and/or voltage scaling are predicted in advance and addressed by employing an elastic clocking technique. The prediction mechanism exploits the dependence of delay of arithmetic units upon input data patterns and identifies specific inputs that activate the critical path. Under iso-yield conditions, the proposed design operates at a lower scaled down Vdd without any performance degradation, while it ensures a superlative yield under a design style employing nominal supply and transistor threshold voltage. Simulation results show power savings of upto 29%, energy per computation savings of upto 25.5% and yield enhancement of upto 11.1% compared to the conventional adders and multipliers implemented in the 70nm BPTM technology. We incorporated the proposed modules in the execution unit of a five stage DLX pipeline to measure performance using SPEC2000 benchmarks [9]. Maximum area and throughput penalty obtained were 10% and 3% respectively.

MSC-clustering and forward stepwise regression for virtual metrology in highly correlated input spaces

Increasingly semiconductor manufacturers are exploring opportunities for virtual metrology (VM) enabled process monitoring and control as a means of reducing non-value added metrology and achieving ever more demanding wafer fabrication tolerances. However, developing robust, reliable and interpretable VM models can be very challenging due to the highly correlated input space often associated with the underpinning data sets. A particularly pertinent example is etch rate prediction of plasma etch processes from multichannel optical emission spectroscopy data. This paper proposes a novel input-clustering based forward stepwise regression methodology for VM model building in such highly correlated input spaces. Max Separation Clustering (MSC) is employed as a pre-processing step to identify a reduced srt of well-conditioned, representative variables that can then be used as inputs to state-of-the-art model building techniques such as Forward Selection Regression (FSR), Ridge regression, LASSO and Forward Selection Ridge Regression (FCRR). The methodology is validated on a benchmark semiconductor plasma etch dataset and the results obtained are compared with those achieved when the state-of-art approaches are applied directly to the data without the MSC pre-processing step. Significant performance improvements are observed when MSC is combined with FSR (13%) and FSRR (8.5%), but not with Ridge Regression (-1%) or LASSO (-32%). The optimal VM results are obtained using the MSC-FSR and MSC-FSRR generated models. © 2012 IEEE.

Factors affecting the successful implementation and sustainability of the Liverpool Care Pathway for dying patients – a realist evaluation

Objectives: The Liverpool Care Pathway for the dying patient (LCP) was designed to improve end-of-life care in generalist health care settings. Controversy has led to its withdrawal in some jurisdictions. The main objective of this research was to identify the influences that facilitated or hindered successful LCP implementation.

Method: An organisational case study using realist evaluation in one health and social care trust in Northern Ireland. Two rounds of semi-structured interviews were conducted with two policy makers and twenty two participants with experience and/or involvement in management of the LCP during 2011 and 2012.

Results: Key resource inputs included facilitation with a view to maintaining LCP ‘visibility’, reducing anxiety among nurses and increasing their confidence regarding the delivery of end-of-life care; and nurse and medical education designed to increase professional self-efficacy and reduce misuse and misunderstanding of the LCP. Key enabling contexts were consistent senior management support; ongoing education and training tailored to the needs of each professional group; and an organisational cultural change in the hospital setting that encompassed end-of-life care.

Conclusion: There is a need to appreciate the organizationally complex nature of intervening to improve end-of-life care. Successful implementation of evidence-based interventions for end-of-life care requires commitment to planning, training and ongoing review that takes account of different perspectives, institutional hierarchies and relationships and the educational needs of professional disciplines. There is a need also to recognise that medical consultants require particular support in their role as gatekeepers and as a lead communication channel with patients and their relatives.

Integrating petrography, mineralogy and hydrochemistry to constrain the influence and distribution of groundwater contributions to baseflow in poorly productive aquifers: Insights from Gortinlieve catchment, Co. Donegal, NW Ireland

Identifying groundwater contributions to baseflowforms an essential part of surfacewater body characterisation. The Gortinlieve catchment (5 km2) comprises a headwater stream network of the Carrigans River, itself a tributary of the River Foyle, NW Ireland. The bedrock comprises poorly productive metasediments that are characterised by fracture porosity. We present the findings of a multi-disciplinary study that integrates new hydrochemical and mineralogical investigations with existing hydraulic, geophysical and structural data to identify the scales of groundwater flow and the nature of groundwater/bedrock interaction (chemical denudation). At the catchment scale, the development of deep weathering profiles is controlled by NE-SW regional scale fracture zones associated with mountain building during the Grampian orogeny. In-situ chemical denudation of mineral phases is controlled by micro- to meso-scale fractures related to Alpine compression during Palaeocene to Oligocene times. The alteration of primary muscovite, chlorite (clinochlore) and albite along the surfaces of these small-scale fractures has resulted in the precipitation of illite, montmorillonite and illite/montmorillonite clay admixtures. The interconnected but discontinuous nature of these small-scale structures highlights the role of larger scale faults and fissures in the supply and transportation of weathering solutions to/from the sites of mineral weathering. The dissolution of primarily mineral phases releases the major ions Mg, Ca and HCO3 that are shown to subsequently formthe chemical makeup of groundwaters. Borehole groundwater and stream baseflow hydrochemical data are used to constrain the depths of groundwater flow pathways influencing the chemistry of surface waters throughout the stream profile. The results show that it is predominantly the lower part of the catchment, which receives inputs from catchment/regional scale groundwater flow, that is found to contribute to the maintenance of annual baseflow levels. This study identifies the importance
of deep groundwater in maintaining annual baseflow levels in poorly productive bedrock systems.

Kernel-based local order estimation of nonlinear nonparametric systems

We consider the local order estimation of nonlinear autoregressive systems with exogenous inputs (NARX), which may have different local dimensions at different points. By minimizing the kernel-based local information criterion introduced in this paper, the strongly consistent estimates for the local orders of the NARX system at points of interest are obtained. The modification of the criterion and a simple procedure of searching the minimum of the criterion, are also discussed. The theoretical results derived here are tested by simulation examples.

Using Brain Data for Sentiment Analysis

We present the results of exploratory experiments using lexical valence extracted from brain using electroencephalography (EEG) for sentiment analysis. We selected 78 English words (36 for training and 42 for testing), presented as stimuli to 3 English native speakers. EEG signals were recorded from the subjects while they performed a mental imaging task for each word stimulus. Wavelet decomposition was employed to extract EEG features from the time-frequency domain. The extracted features were used as inputs to a sparse multinomial logistic regression (SMLR) classifier for valence classification, after univariate ANOVA feature selection. After mapping EEG signals to sentiment valences, we exploited the lexical polarity extracted from brain data for the prediction of the valence of 12 sentences taken from the SemEval-2007 shared task, and compared it against existing lexical resources.

ELM-induced transient tungsten melting in the JET divertor

The original goals of the JET ITER-like wall included the study of the impact of an all W divertor on plasma operation (Coenen et al 2013 Nucl. Fusion 53 073043) and fuel retention (Brezinsek et al 2013 Nucl. Fusion 53 083023). ITER has recently decided to install a full-tungsten (W) divertor from the start of operations. One of the key inputs required in support of this decision was the study of the possibility of W melting and melt splashing during transients. Damage of this type can lead to modifications of surface topology which could lead to higher disruption frequency or compromise subsequent plasma operation. Although every effort will be made to avoid leading edges, ITER plasma stored energies are sufficient that transients can drive shallow melting on the top surfaces of components. JET is able to produce ELMs large enough to allow access to transient melting in a regime of relevance to ITER.

Transient W melt experiments were performed in JET using a dedicated divertor module and a sequence of I-P = 3.0 MA/B-T = 2.9 T H-mode pulses with an input power of P-IN = 23 MW, a stored energy of similar to 6 MJ and regular type I ELMs at Delta W-ELM = 0.3 MJ and f(ELM) similar to 30 Hz. By moving the outer strike point onto a dedicated leading edge in the W divertor the base temperature was raised within similar to 1 s to a level allowing transient, ELM-driven melting during the subsequent 0.5 s. Such ELMs (delta W similar to 300 kJ per ELM) are comparable to mitigated ELMs expected in ITER (Pitts et al 2011 J. Nucl. Mater. 415 (Suppl.) S957-64).

Although significant material losses in terms of ejections into the plasma were not observed, there is indirect evidence that some small droplets (similar to 80 mu m) were released. Almost 1 mm (similar to 6 mm(3)) of W was moved by similar to 150 ELMs within 7 subsequent discharges. The impact on the main plasma parameters was minor and no disruptions occurred. The W-melt gradually moved along the leading edge towards the high-field side, driven by j x B forces. The evaporation rate determined from spectroscopy is 100 times less than expected from steady state melting and is thus consistent only with transient melting during the individual ELMs. Analysis of IR data and spectroscopy together with modelling using the MEMOS code Bazylev et al 2009 J. Nucl. Mater. 390-391 810-13 point to transient melting as the main process. 3D MEMOS simulations on the consequences of multiple ELMs on damage of tungsten castellated armour have been performed.

These experiments provide the first experimental evidence for the absence of significant melt splashing at transient events resembling mitigated ELMs on ITER and establish a key experimental benchmark for the MEMOS code.