Description and critical appraisal of principal components analysis (PCA) methodology applied to pulsed-field gel electrophoresis profiles of methicillin-resistant Staphylococcus aureus isolates

Principal components analysis (PCA) has been described for over 50 years; however, it is rarely applied to the analysis of epidemiological data. In this study PCA was critically appraised in its ability to reveal relationships between pulsed-field gel electrophoresis (PFGE) profiles of methicillin- resistant Staphylococcus aureus (MRSA) in comparison to the more commonly employed cluster analysis and representation by dendrograms. The PFGE type following SmaI chromosomal digest was determined for 44 multidrug-resistant hospital-acquired methicillin-resistant S. aureus (MR-HA-MRSA) isolates, two multidrug-resistant community-acquired MRSA (MR-CA-MRSA), 50 hospital-acquired MRSA (HA-MRSA) isolates (from the University Hospital Birmingham, NHS Trust, UK) and 34 community-acquired MRSA (CA-MRSA) isolates (from general practitioners in Birmingham, UK). Strain relatedness was determined using Dice band-matching with UPGMA clustering and PCA. The results indicated that PCA revealed relationships between MRSA strains, which were more strongly correlated with known epidemiology, most likely because, unlike cluster analysis, PCA does not have the constraint of generating a hierarchic classification. In addition, PCA provides the opportunity for further analysis to identify key polymorphic bands within complex genotypic profiles, which is not always possible with dendrograms. Here we provide a detailed description of a PCA method for the analysis of PFGE profiles to complement further the epidemiological study of infectious disease. © 2005 Elsevier B.V. All rights reserved.

Developing a scalable model of recombinant protein yield from Pichia pastoris:the influence of culture conditions, biomass and induction regime

Background The optimisation and scale-up of process conditions leading to high yields of recombinant proteins is an enduring bottleneck in the post-genomic sciences. Typical experiments rely on varying selected parameters through repeated rounds of trial-and-error optimisation. To rationalise this, several groups have recently adopted the 'design of experiments' (DoE) approach frequently used in industry. Studies have focused on parameters such as medium composition, nutrient feed rates and induction of expression in shake flasks or bioreactors, as well as oxygen transfer rates in micro-well plates. In this study we wanted to generate a predictive model that described small-scale screens and to test its scalability to bioreactors. Results Here we demonstrate how the use of a DoE approach in a multi-well mini-bioreactor permitted the rapid establishment of high yielding production phase conditions that could be transferred to a 7 L bioreactor. Using green fluorescent protein secreted from Pichia pastoris, we derived a predictive model of protein yield as a function of the three most commonly-varied process parameters: temperature, pH and the percentage of dissolved oxygen in the culture medium. Importantly, when yield was normalised to culture volume and density, the model was scalable from mL to L working volumes. By increasing pre-induction biomass accumulation, model-predicted yields were further improved. Yield improvement was most significant, however, on varying the fed-batch induction regime to minimise methanol accumulation so that the productivity of the culture increased throughout the whole induction period. These findings suggest the importance of matching the rate of protein production with the host metabolism. Conclusion We demonstrate how a rational, stepwise approach to recombinant protein production screens can reduce process development time.

An integrated scheduling problem of PCB components on sequential pick-and-place machines:mathematical models and heuristic solutions

This paper formulates several mathematical models for determining the optimal sequence of component placements and assignment of component types to feeders simultaneously or the integrated scheduling problem for a type of surface mount technology placement machines, called the sequential pick-andplace (PAP) machine. A PAP machine has multiple stationary feeders storing components, a stationary working table holding a printed circuit board (PCB), and a movable placement head to pick up components from feeders and place them to a board. The objective of integrated problem is to minimize the total distance traveled by the placement head. Two integer nonlinear programming models are formulated first. Then, each of them is equivalently converted into an integer linear type. The models for the integrated problem are verified by two commercial packages. In addition, a hybrid genetic algorithm previously developed by the authors is adopted to solve the models. The algorithm not only generates the optimal solutions quickly for small-sized problems, but also outperforms the genetic algorithms developed by other researchers in terms of total traveling distance.

The influence of formulation components on the aerosolisation properties of spray-dried powders

Dry powders suitable for inhalation containing β-estradiol, leucine as a dispersibility enhancer and lactose as a bulking agent were prepared by spray-drying from aqueous ethanol formulations. The influence of formulation components on the characteristics of the resultant spray-dried powders was examined through the use of a range of ethanol concentrations (10-50% v/v) in the solvent used to prepare the initial formulations. Additionally, the amount of leucine required to act as a dispersibility enhancer was investigated by varying the amount of leucine added to the formulation prior to spray-drying. Following spray-drying, resultant powders were characterised using scanning electron microscopy, laser diffraction and tapped density measurements, and the aerosolisation performance determined using Twin Stage Impinger and Andersen Cascade Impactor analysis. We demonstrate that selection of appropriate solvent systems and leucine concentration allows the preparation of spray-dried powders that display enhanced aerosolisation properties, and would be predicted to exhibit high deposition in the lower regions of the respiratory tract. © 2005 Elsevier B.V. All rights reserved.

Asynchrony and the grouping of vowel components:captor tones revisited

Asynchrony is an important grouping cue for separating sound mixtures. A harmonic incremented in level makes a reduced contribution to vowel timbre when it begins before the other components. This contribution can be partly restored by adding a captor tone in synchrony with, and one octave above, the leading portion of the incremented harmonic [Darwin and Sutherland, Q. J. Exp. Psychol. A 36, 193-208 (1984)]. The captor is too remote to evoke adaptation in peripheral channels tuned to the incremented harmonic, and so the restoration effect is usually attributed to the grouping of the leading portion with the captor. However, results are presented that contradict this interpretation. Captor efficacy does not depend on a common onset, or harmonic relations, with the leading component. Rather, captor efficacy is influenced by frequency separation, and extends to about 1.5 oct above the leading component. Below this cutoff, the captor effect is equivalent to attenuating the leading portion of the incremented harmonic by about 6 dB. These results indicate that high-level grouping does not govern the captor effect. Instead, it is proposed that the partial restoration of the contribution of an asynchronous component to vowel timbre depends on broadband inhibition within the central auditory system. © 2006 Acoustical Society of America.

The use of multivariate methods in the identification of subtypes of Alzheimer's disease: a comparison of principal components and cluster analysis

Two contrasting multivariate statistical methods, viz., principal components analysis (PCA) and cluster analysis were applied to the study of neuropathological variations between cases of Alzheimer's disease (AD). To compare the two methods, 78 cases of AD were analyzed, each characterised by measurements of 47 neuropathological variables. Both methods of analysis revealed significant variations between AD cases. These variations were related primarily to differences in the distribution and abundance of senile plaques (SP) and neurofibrillary tangles (NFT) in the brain. Cluster analysis classified the majority of AD cases into five groups which could represent subtypes of AD. However, PCA suggested that variation between cases was more continuous with no distinct subtypes. Hence, PCA may be a more appropriate method than cluster analysis in the study of neuropathological variations between AD cases.

16,000 km, 10 Gbits-1 soliton transmission over standard fibre by reduction of interactions through optimum amplifier positioning

We show that by optimizing the amplifier position in a two-stage dispersion map, the (dispersion-managed) soliton-soliton interaction can be reduced, enabling transmission of 10-Gbits-1 solitons over standard fiber over 16,000 km

10Gbit/s dispersion managed soliton transmission over 16,500km in standard fibre by reduction of soliton interactions

We show experimentally and numerically that in high-speed strongly dispersion-managed standard fiber soliton systems nonlinear interactions limit the propagation distance. We present results that show that the effect of these interactions can be significantly reduced by appropriate location of the amplifier within the dispersion map. Using this technique, we have been able to extend the propagation distance of 10-Gbit/s 231–1pseudorandom binary sequence soliton data to 16, 500km over standard fiber by use of dispersion compensation. To our knowledge this distance is the farthest transmission over standard fiber without active control ever reported, and it was achieved with the amplifier placed after the dispersion-compensating fiber in a recirculating loop.

Bioreaction and separation in preparative batch chromatographic columns : the hydrology of lactose to yield glucose,galactose and oligosaccharides

The initial aim of this project was to improve the performance of a chromatographic bioreactor-separator (CBRS). In such a system, a dilute enzyme solution is pumped continuously through a preparative chromatographic column, while pulses of substrate are periodically injected on to the column. Enzymic reaction and separation are therefore performed in a single unit operation. The chromatographic columns used were jacketed glass columns ranging from 1 to 2 metres long with an internal diameter of 1.5 cm. Linking these columns allowed 1, 2, 3 and 4 metre long CBRS systems to be constructed. The hydrolysis of lactose in the presence of β~galactosidase was the reaction of study. From previous work at Aston University, there appeared to be no difficulties in achieving complete lactose hydrolysis in a CBRS. There did, however, appear to be scope for improving the separative performance, so this was adopted as an initial goal. Reducing the particle size of the stationary phase was identified as a way of achieving this improvement. A cation exchange resin was selected which had an average particle size of around half that previously used when studying this reaction. A CBRS system was developed which overcame the operational problems (such as high pressure drop development) associated with use of such a particle size. A significant improvement in separative power was achieved. This was shown by an increase in the number of theoretical plates (N) from about 500 to about 3000 for a 2 metre long CBRS, coupled with higher resolution. A simple experiment with the 1 metre column showed that combined bioreaction and separation was achievable in this system. Having improved the separative performance of the system, the factors affecting enzymic reaction in a CBRS were investigated; including pulse volume and the degree of mixing between enzyme and substrate. The progress of reaction in a CBRS was then studied. This information was related to the interaction of reaction and separation over the reaction zone. The effect of injecting a pulse over a length of time as in CBRS operation was simulated by fed batch experiments. These experiments were performed in parallel with normal batch experiments where the substrate is mixed almost instantly with the enzyme. The batch experiments enabled samples to be taken every minute and revealed that reaction is very rapid. The hydrodynamic characteristics of the two injector configurations used in CBRS construction were studied using Magnetic Resonance Imaging, combined with hydrodynamic calculations. During the optimisation studies, galactooligosaccharides (GOS) were detected as intermediates in the hydrolysis process. GOS are valuable products with potential and existing applications in food manufacture (as nutraceuticals), medicine and drug targeting. The focus of the research was therefore turned to GOS production. A means of controlling reaction to arrest break down of GOS was required. Raising temperature was identified as a possible means of achieving this within a CBRS. Studies were undertaken to optimise the yield of oligosaccharides, culminating in the design, construction and evaluation of a Dithermal Chromatographic Bioreactor-separator.

Development of a sediment yield model for South East Ghana in the regions around Lake Volta

Soil erosion is one of the most pressing issues facing developing countries. The need for soil erosion assessment is paramount as a successful and productive agricultural base is necessary for economic growth and stability. In Ghana, a country with an expanding population and high potential for economic growth, agriculture is an important resource; however, most of the crop production is restricted to low technology shifting cultivation agriculture. The high intensity seasonal rainfall coincides with the early growing period of many of the crops meaning that plots are very susceptible to erosion, especially on steep sided valleys in the region south of Lake Volta. This research investigated the processes of soil erosion by rainfall with the aim of producing a sediment yield model for a small semi-agricultural catchment in rural Ghana. Various types of modelling techniques were considered to discover those most applicable to the sub-tropical environment of Southern Ghana. Once an appropriate model had been developed and calibrated, the aim was to look at how to enable the scaling up of the model using sub-catchments to calculate sedimentation rates of Lake Volta. An experimental catchment was located in Ghana, south west of Lake Volta, where data on rainstorms and the associated streamflow, sediment loads and soil data (moisture content, classification and particle size distribution) was collected to calibrate the model. Additional data was obtained from the Soil Research Institute in Ghana to explore calibration of the Universal Soil Loss Equation (USLE, Wischmeier and Smith, 1978) for Ghanaian soils and environment. It was shown that the USLE could be successfully converted to provide meaningful soil loss estimates in the Ghanaian environment. However, due to experimental difficulties, the proposed theory and methodology of the sediment yield model could only be tested in principle. Future work may include validation of the model and subsequent scaling up to estimate sedimentation rates in Lake Volta.

A study in the reduction of efficiency of nitrogen oxide removal catalysts for automobiles

Automotive catalysts are the most effective short-term answer to air pollution from automobiles. Since strict control of exhaust emissions is, or will be,covered by legislation in most developed countries in the world, catalytic devices will be increasingly fitted to cars. There is consequently an urgent need for the development of catalysts that will not compete for scarce precious metal resources. A number of problems have already been identified in connection with base metal catalysts but quantitative investigations are lacking. The base metal reduction catalysts developed by Imperial Chemical Industries Limited, catalysts and Chemical Group, in collaboration with the Air Pollution Control Laboratory, B L Cars Limited for automotive emission control, are susceptible to de-activation by three major mechanisms. These are: physical loss of the wash-coat (a high surface area coating which supports the active species), aggregation of the active species and poisoning by fuel and engine oil additives. This thesis is especially concerned with the first two of these and attempts to indicate the relative magnitude .of their effect on the activity of. the catalysts. Aggregation of the active species or sintering, as it is loosely called, was studied by using impregnated granules to overcome effects due to the loss of the wash-coat. Samples were aged in a synthetic exhaust gas, free from poisons, and metal crystallite sizes were measured by scanning-electron microscopy. The increase in particle size was correlated with the loss in catalytic activity. In order to maintain a link with the real conditions of service a number of monolithic catalysts were tested in an engine-dynamometer and several previously tested endurance catalysts were examined. A mechanism is proposed for the break-up and subsequent 10s.5 of the wash-coat and suggestions for improved resistance to loss of the' coating and active species are proposed.