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.

Characterisation of Aeromonas strains and species by pulsed field gel electrophoresis and principal components analysis

Aeromonas genomes were investigated by restriction digesting chromosomal DNA with the endonuclease XbaI, separation of restriction fragments by pulsed field gel electrophoresis (PFGE) and principal components analysis (PCA) of resulting separation patterns. A. salmonicida salmonicida were unique amongst the isolates investigated. Separation profiles of these isolates were similar and all characterised by a distinct absence of bands in the 250kb region. Principal components analysis represented these strains as a clearly defined homogeneous group separated by insignificant Euclidian distances. However, A. salmonicida achromogenes isolates in common with those of A. hydrophila and A. sobria were shown by principal components analysis to be more heterogeneous in nature. Fragments from these isolates were more uniform in size distribution but as demonstrated by the Euclidian distances attained through PCA potentially characteristic of each strain. Furthermore passaging of Aeromonas isolates through an appropriate host did not greatly modify fragment separation profiles, indicative of the genomic stability of test aeromonads and the potential of restriction digesting/PFGE/PCA in Aeromonas typing.

Analysis of plasmid profiles of Aeromonas salmonicida isolates by pulsed field gel electrophoresis

Plasmid constitutions of Aeromonas salmonicida isolates were characterised by flat-bed and pulsed field gel electrophoresis. Resolution of plasmids by pulsed field gel electrophoresis was greater and more consistent than that achieved by flat-bed gel electrophoresis. The number of plasmids separated by pulsed field gel electrophoresis varied between A. salmonicida isolates, with five being the most common number present in the isolates used in this study. Plasmid profiles were diverse and the reproducibility of the distances migrated facilitated the use of principal components analysis for the characterisation of the isolates. Isolates were grouped according to the number of plasmids supported. Further principal components analysis of groups of isolates supporting five and seven plasmids showed a spatial separation of plasmids based upon distance migrated. Principal components analysis of plasmid profiles and antimicrobial minimum inhibitory concentrations could not be correlated suggesting that resistance to antimicrobial agents is not associated with either one plasmid or a particular plasmid constitution.

Low-loss waveguides in borosilicate glass fabricated by high-repetition-Rate femtosecond chirp-pulsed oscillator

We describe fabrication and characterisation of smooth low-loss waveguides in BK7 optical glass bymeans of direct femtosecond inscription with chirp-pulse oscillator, operating at 800 nm and 11 MHz repetition rate.

A study of the dynamic behaviour of a pulsed column solvent extraction plant

A study has been made of the dynamic behaviour of a nuclear fuel reprocessing plant utilising pulsed solvent extraction columns. A flowsheet is presented and the choice of an extraction device is discussed. The plant is described by a series of modules each module representing an item of equipment. Each module consists of a series of differential equations describing the dynamic behaviour of the equipment. The model is written in PMSP, a language developed for dynamic simulation models. The differential equations are solved to predict plant behaviour with time. The dynamic response of the plant to a range of disturbances has been assessed. The interactions between pulsed columns have been demonstrated and illustrated. The importance of auxillary items of equipment to plant performance is demonstrated. Control of the reprocessing plant is considered and the effect of control parameters on performance assessed.

The hydrodynamic behaviour and mass transfer characteristics of single droplets in a pulsed sieve plate column

The literature relating to the performance of pulsed sieve plate liquid-liquid extraction columns and the relevant hydrodynamic phenomenon have been surveyed. Hydrodynamic behaviour and mass transfer characteristics of droplets in turbulent and non-turbulent conditions have also been reviewed. Hydrodynamic behaviour, i.e. terminal and characteristic velocity of droplets, droplet size and droplet breakup processes, and mass transfer characteristics of single droplets (d≤0.6 cm) were investigated under pulsed (mixer-settler & transitional regimes) and non-pulsed conditions in a 5.0 cm diameter, 100 cm high, pulsed sieve plate column with three different sieve plate types and variable plate spacing. The system used was toluene (displaced) - acetone - distilled water. Existing photographic techniques for following and recording the droplet behaviour, and for observing the parameters of the pulse and the pulse shape were further developed and improved. A unique illumination technique was developed by which a moving droplet could be photographed using cine or video photography with good contrast without using any dye. Droplet size from a given nozzle and droplet velocity for a given droplet diameter are reduced under pulsing condition, and it was noted that this effect is enhanced in the presence of sieve plate. The droplet breakup processes are well explained by reference to an impact-breakup mechanism. New correlations to predict droplet diameter based on this mechanism are given below.vskip 1.0cm or in dimensionless groups as follows:- (We)crit= 3.12 - 1.79 (Eo)crit A correlation based on the isotropic turbulence theory was developed to calculate droplet diameter in the emulsion regime.vskip 1.0cm Experimental results show that in the mixer-settler and transitional regimes, pulsing parameters had little effect on the overall dispersed phase mass transfer coefficient during the droplet formation and unhindered travel periods.

Effect of pulsed current on the electrodeposition of chromium and copper

This research was concerned with the effects of pulsed current on the electrodeposition of chromium and copper. In the case of the latter metal, a novel application has been studied and a theory proposed for the ability to improve throwing power by the joint use of organic additives and pulsed reverse current. During the course of the research, several improvements were made to the pulse plating unit.Chromium. A study was made of the effect of square wave pulsed current on various physical properties of deposits from three hard chromium plating electrolytes. The effect of varying frequency at a duty cycle of 50% on the mean bulk internal stress, visual appearance, hardness, crack characteristics and surface topography of the electrodeposits was determined. X-ray diffraction techniques were used to study the phases present in the deposits. The effect of varying frequency on the cathodic efficiencies of the electrolytes was also determined. It was found that pulsed current reduced the internal stress of deposits from the sulphate catalysed electrolyte. It also reduced or eliminated cracking of deposits and reduced deposit brightness. Under certain conditions, pulsed current was found to induce the co-deposition of hydrides of chromium. Deposit hardness was found to be reduced by the use of pulsed current. Cathodic efficiencies of the high efficiency electrolytes were reduced by use of pulsed current although this effect was minimised at high frequencies. The sulphate catalysed electrolyte showed an increase in efficiency over the frequency range where hydrides were co-deposited.Copper. The polarisation behaviour of acid copper solutions containing polyethers, sulphopropyl sulphides and chloride ions was studied using both direct and pulse reverse current. The effect of these additives on the rest potentials of copper deposits immersed in the electrolyte was also studied. Hole Throwing Power on printed circuit boards was determined using a specially designed test cell. The effect of pulsed reverse current on the hole throwing power of commercially produced printed circuit boards was also studied. Polyethers were found to have an inhibiting effect on the deposition of copper whereas the sulphopropyl sulphides produced a stimulating (i.e. depolarising) effect. Studies of rest potentials made when both additives were present indicated that the sulphopropyl sulphide was preferentially adsorbed. The use of pulsed reverse current in solutions containing both polyether and sulphopropyl sulphide was found to cause desorption of the sulphopropyl sulphide at the cathode surface. Thus, at higher current densities, the inhibiting effect of the polyether produced an increase in the cathodic polarisation potential. At lower current densities, the depolarisation effect of the sulphopropyl sulphide could still occur. On printed circuit boards, this effect was found to produce an increase in the `hole throwing power' due to depolarisation of the holes relative to the surface of the boards. Typically, using direct current, hole/surface thickness ratios of 40% were obtained when plating 0.6 mm holes in a 3.2 mm thick board at a current density of 3 A/dm2 whereas using pulsed reverse current, ratios of 80% could be obtained at an equivalent rate of deposition. This was observed both in laboratory tests and on commercially plated boards.

The effect of heat treatment on mechanical properties of pulsed Nd:YAG welded thin Ti6Al4V

Pulsed Nd:YAG has been adopted successfully in welding process of thin (0.7 mm) Ti6Al4V. Laser welding of such thin sheet requires a small focal spot, good laser beam quality and fast travel speed, since too much heat generation can cause distortion for thin sheet weld. The microstructures of Ti6Al4V were complex and strongly affected the mechanical properties. These structures include: a´ martensite, metastable ß, Widmanstätten, bimodal, lamellar and equiaxed microstructure. Bimodal and Widmanstätten structures exhibit a good-balance between strength and ductility. The microstructure of pulsed Nd:YAG welded Ti6Al4V was primarily a´ martensite, which showed the lowest ductility but not significantly high strength. A heat treatment at 950 followed by furnace cooling can transform the microstructure in the weld from a´ martensite structure into Widmanstätten structure.

A novel all-fiber bipolar transversal filter with complementary outputs

A novel all-fiber bipolar delay line filter is realized in a single-line cascaded high birefringence fiber structure. Optically coherent operation is achieved with suppression of interference noise. Complementary filter outputs give simultaneous lowpass and highpass responses.

Gamma-shaped long-cavity normal-dispersion mode-locked Er-fiber laser for sub-nanosecond high-energy pulsed generation

We propose the design of a novel ?-shaped fiber laser resonator and apply it to build a long-cavity normaldispersion mode-locked Er-fiber laser which features enhanced functionalities for management and optimization of pulsed lasing regimes. We report the generation of sub-nanosecond pulses with the energy of ~0.5 µJ at a kilohertz-scale repetition rate in an all-fiber system based on the new laser design. A combination of special design solutions in the laser, such as polarization instability compensation in the ultra-long arm of the resonator, intra-cavity spectral selection of radiation with a broadband fiber Bragg grating, and polarization selection by means of a tilted refractive index grating, ensures low amplified spontaneous emission (ASE) noise and high stability of the laser system output parameters.

Knowledge-based development in leading regions across the globe:an exploratory analysis of the co-evolution of resources, capabilities, and outputs

It is widely observed that the global geography of innovation is rapidly evolving. This paper presents evidence concerning the contemporary evolution of the globe's most productive regions. The paper uncovers the underlying structure and co-evolution of knowledge-based resources, capabilities and outputs across these regions. The analysis identifies two key trends by which the economic evolution and growth patterns of these regions are differentiated-namely, knowledge-based growth and labour market growth. The knowledge-based growth factor represents the underlying commonality found between the growth of economic output, earnings and a range of knowledge-based resources. The labour market growth factor represents the capability of regions to draw on their human capital. Overall, spectacular knowledge-based growth of leading Chinese regions is evident, highlighting a continued shift of knowledge-based resources to Asia. It is concluded that regional growth in knowledge production investment and the capacity to draw on regional human capital reserves are neither necessarily traded-off nor complementary to each other. © 2012 Urban Studies Journal Limited.

An overview of Total Factor Productivity estimations adjusted for pollutant outputs:an application to sugarcane farming

The conventional Total Factor Productivity (TFP) measurement does not incorporate the effects of undesirable outputs, which are harmful to the environment. Using sugarcane farming in Kenya, this paper illustrates the differences between the conventional Malmquist index measures where the environment variable is not adjusted and environment-adjusted measures using both hyperbolic and directional distance functions. The mean TFP change estimates for the conventional Malmquist index, adjusted hyperbolic index and Luenberger indicator were 3.13%, 0.11% and 2.21%, respectively. The conventional non-adjusted measure lies between the two adjusted measures of hyperbolic index and Luenberger indicator. © 2012 Inderscience Enterprises Ltd.

An integer-valued data envelopment analysis model with bounded outputs

Integer-valued data envelopment analysis (DEA) with alternative returns to scale technology has been introduced and developed recently by Kuosmanen and Kazemi Matin. The proportionality assumption of their introduced "natural augmentability" axiom in constant and nondecreasing returns to scale technologies makes it possible to achieve feasible decision-making units (DMUs) of arbitrary large size. In many real world applications it is not possible to achieve such production plans since some of the input and output variables are bounded above. In this paper, we extend the axiomatic foundation of integer-valuedDEAmodels for including bounded output variables. Some model variants are achieved by introducing a new axiom of "boundedness" over the selected output variables. A mixed integer linear programming (MILP) formulation is also introduced for computing efficiency scores in the associated production set. © 2011 The Authors. International Transactions in Operational Research © 2011 International Federation of Operational Research Societies.

Gamma-shaped long-cavity normal-dispersion mode-locked Er-fiber laser for sub-nanosecond high-energy pulsed generation

We propose the design of a novel ?-shaped fiber laser resonator and apply it to build a long-cavity normaldispersion mode-locked Er-fiber laser which features enhanced functionalities for management and optimization of pulsed lasing regimes. We report the generation of sub-nanosecond pulses with the energy of ~0.5 µJ at a kilohertz-scale repetition rate in an all-fiber system based on the new laser design. A combination of special design solutions in the laser, such as polarization instability compensation in the ultra-long arm of the resonator, intra-cavity spectral selection of radiation with a broadband fiber Bragg grating, and polarization selection by means of a tilted refractive index grating, ensures low amplified spontaneous emission (ASE) noise and high stability of the laser system output parameters.

A novel all fiber microwave transversal filter with complementary outputs

A novel all-fiber bipolar delay line filter is realized in a single-line cascaded high birefringence fiber structure. Optically coherent operation is achieved with suppression of interference noise. Complementary filter outputs give simultaneous lowpass and highpass responses.