Successful development and testing of a Method for Aggregating The Reporting of Interventions in Complex Studies (MATRICS)

Objectives: To develop a tool for the accurate reporting and aggregation of findings from each of the multiple methods used in a complex evaluation in an unbiased way. Study Design and Setting: We developed a Method for Aggregating The Reporting of Interventions in Complex Studies (MATRICS) within a gastroenterology study [Evaluating New Innovations in (the delivery and organisation of) Gastrointestinal (GI) endoscopy services by the NHS Modernisation Agency (ENIGMA)]. We subsequently tested it on a different gastroenterology trial [Multi-Institutional Nurse Endoscopy Trial (MINuET)]. We created three layers to define the effects, methods, and findings from ENIGMA. We assigned numbers to each effect in layer 1 and letters to each method in layer 2. We used an alphanumeric code based on layers 1 and 2 to every finding in layer 3 to link the aims, methods, and findings. We illustrated analogous findings by assigning more than one alphanumeric code to a finding. We also showed that more than one effect or method could report the same finding. We presented contradictory findings by listing them in adjacent rows of the MATRICS. Results: MATRICS was useful for the effective synthesis and presentation of findings of the multiple methods from ENIGMA. We subsequently successfully tested it by applying it to the MINuET trial. Conclusion: MATRICS is effective for synthesizing the findings of complex, multiple-method studies.

Data analysis methods in optometry Part 7: multiple linear regression

Multiple regression analysis is a complex statistical method with many potential uses. It has also become one of the most abused of all statistical procedures since anyone with a data base and suitable software can carry it out. An investigator should always have a clear hypothesis in mind before carrying out such a procedure and knowledge of the limitations of each aspect of the analysis. In addition, multiple regression is probably best used in an exploratory context, identifying variables that might profitably be examined by more detailed studies. Where there are many variables potentially influencing Y, they are likely to be intercorrelated and to account for relatively small amounts of the variance. Any analysis in which R squared is less than 50% should be suspect as probably not indicating the presence of significant variables. A further problem relates to sample size. It is often stated that the number of subjects or patients must be at least 5-10 times the number of variables included in the study.5 This advice should be taken only as a rough guide but it does indicate that the variables included should be selected with great care as inclusion of an obviously unimportant variable may have a significant impact on the sample size required.

Automated assessment of visual fields and their inter-relation to evoked potentials in visual disorders

The Octopus Automated Perimeter was validated in a comparative study and found to offer many advantages in the assessment of the visual field. The visual evoked potential was investigated in an extensive study using a variety of stimulus parameters to simulate hemianopia and central visual field defects. The scalp topography was recorded topographically and a technique to compute the source derivation of the scalp potential was developed. This enabled clarification of the expected scalp distribution to half field stimulation using different electrode montages. The visual evoked potential following full field stimulation was found to be asymmetrical around the midline with a bias over the left occiput particularly when the foveal polar projections of the occipital cortex were preferentially stimulated. The half field response reflected the distribution asymmetry. Masking of the central 3° resulted in a response which was approximately symmetrical around the midline but there was no evidence of the PNP-complex. A method for visual field quantification was developed based on the neural representation of visual space (Drasdo and Peaston 1982) in an attempt to relate visual field depravation with the resultant visual evoked potentials. There was no form of simple, diffuse summation between the scalp potential and the cortical generators. It was, however, possible to quantify the degree of scalp potential attenuation for M-scaled full field stimuli. The results obtained from patients exhibiting pre-chiasmal lesions suggested that the PNP-complex is not scotomatous in nature but confirmed that it is most likely to be related to specific diseases (Harding and Crews 1982). There was a strong correlation between the percentage information loss of the visual field and the diagnostic value of the visual evoked potential in patients exhibiting chiasmal lesions.

Causality and synchronisation in complex systems with applications to neuroscience

This thesis presents an investigation, of synchronisation and causality, motivated by problems in computational neuroscience. The thesis addresses both theoretical and practical signal processing issues regarding the estimation of interdependence from a set of multivariate data generated by a complex underlying dynamical system. This topic is driven by a series of problems in neuroscience, which represents the principal background motive behind the material in this work. The underlying system is the human brain and the generative process of the data is based on modern electromagnetic neuroimaging methods . In this thesis, the underlying functional of the brain mechanisms are derived from the recent mathematical formalism of dynamical systems in complex networks. This is justified principally on the grounds of the complex hierarchical and multiscale nature of the brain and it offers new methods of analysis to model its emergent phenomena. A fundamental approach to study the neural activity is to investigate the connectivity pattern developed by the brain’s complex network. Three types of connectivity are important to study: 1) anatomical connectivity refering to the physical links forming the topology of the brain network; 2) effective connectivity concerning with the way the neural elements communicate with each other using the brain’s anatomical structure, through phenomena of synchronisation and information transfer; 3) functional connectivity, presenting an epistemic concept which alludes to the interdependence between data measured from the brain network. The main contribution of this thesis is to present, apply and discuss novel algorithms of functional connectivities, which are designed to extract different specific aspects of interaction between the underlying generators of the data. Firstly, a univariate statistic is developed to allow for indirect assessment of synchronisation in the local network from a single time series. This approach is useful in inferring the coupling as in a local cortical area as observed by a single measurement electrode. Secondly, different existing methods of phase synchronisation are considered from the perspective of experimental data analysis and inference of coupling from observed data. These methods are designed to address the estimation of medium to long range connectivity and their differences are particularly relevant in the context of volume conduction, that is known to produce spurious detections of connectivity. Finally, an asymmetric temporal metric is introduced in order to detect the direction of the coupling between different regions of the brain. The method developed in this thesis is based on a machine learning extensions of the well known concept of Granger causality. The thesis discussion is developed alongside examples of synthetic and experimental real data. The synthetic data are simulations of complex dynamical systems with the intention to mimic the behaviour of simple cortical neural assemblies. They are helpful to test the techniques developed in this thesis. The real datasets are provided to illustrate the problem of brain connectivity in the case of important neurological disorders such as Epilepsy and Parkinson’s disease. The methods of functional connectivity in this thesis are applied to intracranial EEG recordings in order to extract features, which characterize underlying spatiotemporal dynamics before during and after an epileptic seizure and predict seizure location and onset prior to conventional electrographic signs. The methodology is also applied to a MEG dataset containing healthy, Parkinson’s and dementia subjects with the scope of distinguishing patterns of pathological from physiological connectivity.

Complex temporal patterns in molecular dynamics:a direct measure of the phase-space exploration by the trajectory at macroscopic time scales

Computer simulated trajectories of bulk water molecules form complex spatiotemporal structures at the picosecond time scale. This intrinsic complexity, which underlies the formation of molecular structures at longer time scales, has been quantified using a measure of statistical complexity. The method estimates the information contained in the molecular trajectory by detecting and quantifying temporal patterns present in the simulated data (velocity time series). Two types of temporal patterns are found. The first, defined by the short-time correlations corresponding to the velocity autocorrelation decay times (â‰0.1â€ps), remains asymptotically stable for time intervals longer than several tens of nanoseconds. The second is caused by previously unknown longer-time correlations (found at longer than the nanoseconds time scales) leading to a value of statistical complexity that slowly increases with time. A direct measure based on the notion of statistical complexity that describes how the trajectory explores the phase space and independent from the particular molecular signal used as the observed time series is introduced. © 2008 The American Physical Society.

Non-rigid object tracking in complex scenes

A recently proposed colour based tracking algorithm has been established to track objects in real circumstances [Zivkovic, Z., Krose, B. 2004. An EM-like algorithm for color-histogram-based object tracking. In: Proc, IEEE Conf. on Computer Vision and Pattern Recognition, pp. 798-803]. To improve the performance of this technique in complex scenes, in this paper we propose a new algorithm for optimally adapting the ellipse outlining the objects of interest. This paper presents a Lagrangian based method to integrate a regularising component into the covariance matrix to be computed. Technically, we intend to reduce the residuals between the estimated probability distribution and the expected one. We argue that, by doing this, the shape of the ellipse can be properly adapted in the tracking stage. Experimental results show that the proposed method has favourable performance in shape adaption and object localisation.

Statnote 13: a more complex analysis of variance incorporating a 'repeated measures' factor

Experiments combining different groups or factors and which use ANOVA are a powerful method of investigation in applied microbiology. ANOVA enables not only the effect of individual factors to be estimated but also their interactions; information which cannot be obtained readily when factors are investigated separately. In addition, combining different treatments or factors in a single experiment is more efficient and often reduces the sample size required to estimate treatment effects adequately. Because of the treatment combinations used in a factorial experiment, the degrees of freedom (DF) of the error term in the ANOVA is a more important indicator of the ‘power’ of the experiment than the number of replicates. A good method is to ensure, where possible, that sufficient replication is present to achieve 15 DF for the error term of the ANOVA testing effects of particular interest. Finally, it is important to always consider the design of the experiment because this determines the appropriate ANOVA to use. Hence, it is necessary to be able to identify the different forms of ANOVA appropriate to different experimental designs and to recognise when a design is a split-plot or incorporates a repeated measure. If there is any doubt about which ANOVA to use in a specific circumstance, the researcher should seek advice from a statistician with experience of research in applied microbiology.

A simple, sensitive and selective quantum-dot-based western blot method for the simultaneous detection of multiple targets from cell lysates

Quantum dots (Qdots) are fluorescent nanoparticles that have great potential as detection agents in biological applications. Their optical properties, including photostability and narrow, symmetrical emission bands with large Stokes shifts, and the potential for multiplexing of many different colours, give them significant advantages over traditionally used fluorescent dyes. Here, we report the straightforward generation of stable, covalent quantum dot-protein A/G bioconjugates that will be able to bind to almost any IgG antibody, and therefore can be used in many applications. An additional advantage is that the requirement for a secondary antibody is removed, simplifying experimental design. To demonstrate their use, we show their application in multiplexed western blotting. The sensitivity of Qdot conjugates is found to be superior to fluorescent dyes, and comparable to, or potentially better than, enhanced chemiluminescence. We show a true biological validation using a four-colour multiplexed western blot against a complex cell lysate background, and have significantly improved previously reported non-specific binding of the Qdots to cellular proteins.

Living cationic polymerization

The kinetics of the polymerization of styrene iniated by 1-chloro-1-phenyltehane/tin (IV) chloride in the presence of tetrabutylammonium chloride have been studied. Dilatometry studies at 25 °C were conducted and the orders of reaction were established. Molecular weight studies were conducted for these experiments using size exclusion chromatography. These studies indicated that transfer/termination reactions were present. The observed kinetics may be explained by a polymerization mechanism involving a single propagating species which is present in low concentrations. Reactions at 0 °C and -15 °C have shown that a "living" polymerization could be obtained at low temperatures. A method was derived to study the kinetics of a "living" polymerization by following the increase in degree of polymerization with time. Polymerizations of styrene were conducted using 1,4-bis(bromomethyl)benzene as a difunctional co-catalyst. These reactions produced polymers with broad or bimodal molecular weight distributions. These observations may be explained by the rate of initiation being slower than the rate of propagation or the presence of transfer/termination reactions. Reactions were conducted using a co-catalyst using a co-catalyst produced by the addition of 1,1-diphenylethane to 1,4-bis(bromomethyl)benzene. Size exclusion chromatography studies showed that the polymers produced had a narrower molecular weight distribution than those produced by polymerizations initiated by 1,4-bis(bromomethyl)benzene alone. However the polydispersity was still observed to increase with reaction time. This may also be explained by slow initiation compared to the rate of propagation. Polymerizations initiated by both bifunctional initiators were examined using the method of studying reaction kinetics by following the change in number average degree of polymerization. The results indicated that a straight line relationship could also be obtained with a non-living polymerization.

Studies in the anionic polymerization of methyl methacrylate

A study has been made of the anionic polymerization of methyl methacrylate using butyllithium and polystyryl lithium as initiators and using aluminium triisobutyl as a cocatalyst. The aspects of the polymerization that were examined were the effect of changing the order of addition of reagents, the temperature at which polymerization takes place and the polarity of the solvent. Trends were assessed in terms of molecular weight, molecular weight distribution and tacticity. In addition, a second monomer addition test was carried out to verify that the polymerization was truly a living one, and a kinetic study was attempted. Studies to investigate the effect of changing the order of addition of reagents showed that polymer with similar polydispersities and tacticities are produced whether the pre-mixing (mixing initiator and cocatalyst before addition of monomer) or the post-mixing (mixing monomer and cocatalyst before addition of initiator) method were used. However, polymerizations using the post-mixing mixing method demonstrated lower initiator efficiencies, possibly indicating a different initiating species. Investigations into the effect of changing the polymerization temperature show the molecular weight distribution to narrow as the temperature decreases, although a small amount of low molecular weight tailing was also observed at low temperature. A clear relationship between tacticity and temperature was observed with syndiotacticity increasing with decreasing temperature. Changes in solvent polarity were achieved by using mixtures of the standard solvent, toluene, with varying amounts of cyclohexane, tetrahydrofuran or dichloromethane. Experiments at low solvent polarity (using toluene/cyclohexane mixtures) showed problems with initiator solubility but produced polymer with lower polydispersity and higher syndiotacticity than in toluene alone. Experiments using toluene/THF mixtures yielded no polymer, thought to be owing to a side reaction between THF and aluminium triisobutyl. Increased solvent polarity, achieved using toluene/dichloromethane mixtures produced polymer with higher polydispersity and at lower yields than the conventional system, but also with higher syndiotacticity. Second monomer addition reactions demonstrated that the polymerization was 'living' since an increase in molecular weight was observed with no increase in polydispersity. Kinetic studies demonstrated the high speed of the polymerization but yielded no useful data.

Living cationic polymerization of isobutene

The polymerization of isobutene initiated by 1-chloro-1-phenylethane has been investigated, and molecular weight studies conducted using size exclusion chromatography. Polymerizations carried out in a 40/60 (v/v) mixture of dichloromethaneIcyclohexane, using titanium (IV) chloride as a catalyst in the presence of pyridine at -30 °C were found to be controlled and living. The number average molecular weights of the polymers increased linearly with monomer conversion, and the molecular weight distributions were between 1.15 and 1.20. Efficiencies of initiation were between 80 and 100%, and evidence was found to suggest that backbiting to the initiator had occurred, resulting in the formation of cyclic oligomers during the early stages of polymerization. The kinetics of polymerization can be explained in terms of active species in. equilibrium with dormant species. The effects of temperature. and dielectric constant on this equilibrium were studied and a model based upon the Fuoss equation was developed. Pyridine was found to behave as proton trap in the system, and when it was used in excess the rate of polymerization was retarded. By assuming that the catalyst and pyridine formed a one to one complex, it was possible to show that the reaction was second order with respect to the catalyst. The synthesis of low molecular weight polyisobutenes was studied. When the concentration of initiator was increased relative to that of the isobutene, such that the theoretical degree of polymerization was 20 or less, the rate of initiation was slow compared to propagation. The efficiency of initiation in these polymerizations was typically between 30 and 40 %. Optimal conditions of temperature. and.catalyst concentration were established, leading to a 60 % efficiency of initiation. A one-pot synthesis of phenol end-capped polyisobutene was attempted by adding phenol at the end of a living polymerization. Evidence to substantiate the existence of capped polymer chains in the resultant product was inconclusive. Block copolymerizations of oxetane and isobutene were conducted using 1-chloro-1phenylethane/TiCl4, but no copolymer or oxetane homopolymer could be isolated.

Living cationic polymerization of styrene monomers

This thesis describes an experimental investigation of synthesis of polystyrene under various polymerization conditions such as solvent polarity, temperature, initial concentrations of initiator, catalyst, monomer and added salts or co-catalyst, which was achieved using the living cationic polymerization technology in conjunction with gel permeation chromatography (GPC) and NMR spectroscopy. Polymerizations of styrene were conducted using 1-phenyl ethylchloride (1-PEC) as an initiator and tin tetrachloride (SnCI4) as a catalyst in the presence of tetra-n-Butylammonium chloride (nBu4NCI). Effects of solvent polarity varied by mixing dichloromethane (DCM) and less polar cyclohexane (C.hex), temperature, initial concentrations of SnC14, 1-PEC and nBu4NCI on the polymerizations were examined, and the conditions under which a living polymerization can be obtained were optimised as: [styrene]o ~ 0.75 - 2 M; [1-PEC]o ~ 0.005 - 0.05 M; [SnCI4Jo ~ 0.05 - 0.4 M; [nBu4NCIJo ~ 0.001 - 0.1 M; DCM/C.hex ~ 50/0 - 20/30 v/v; T ~ 0 to -45°C. Kinetic studies of styrene polymerization using the Omnifit sampling method showed that the number average molecular weight (Mn) of the polymers obtained increased in direct proportion to monomer conversion and agreed well with the theoretical Mn expected from the concentration ratios of monomer to initiator. The linearities of both the 1n([MJoI[M]) vs. time plot and the Mn vs. monomer conversion plot, and the narrow molecular weight distribution (MWD) measured using GPC demonstrated the livingness of the polymerizations, indicating the absence of irreversible termination and transfer within the lifetimes of the polymerizations. The proposed 'two species' propagation mechanism was found to apply for the styrene polymerization with 1-PEC/SnCI4 in the presence of nBu4NCl. The further kinetic experiments showed that living styrene polymerizations were achieved using the 1-PEC/SnCI4 initiating system in mixtures of DCM/C.hex 30/20 v/v at -15°C in the presence of various bromide salts, tetra-n-butylammonium bromide, tetra-n-pentylammonium bromide, tetra-n-heptylammonium bromide, and tetra-n-octylammonium bromide, respectively. The types of the bromide salts were found to have no significant effect on monomer conversion, Mn, polydispersity and initiation efficiency. Living polymerizations of styrene were also achieved using titanium tetrachloride (TiCI4) as a catalyst and 1-PEC as an initiator in the presence of a small amount of 2,6-di-tert-butylpyridine or pyridine instead of nBu4NCl. GPC analysis showed that the polymers obtained had narrow polydispersities (P.D. < 1.3), and the linearities of both the In([MJo/[MJ) vs. time plot and the Mn vs. monomer conversion plot demonstrated that the polymerizations are living, when the ratio of DCM and C.hex was less than 40 : 10 and the reaction temperature was not lower than -15°C. The reaction orders relative to TiCl4 and 1-PEC were estimated from the investigations into the rate of polymerization to be 2.56 and 1.0 respectively. lH and 13C NMR analysis of the resultant polystyrene would suggest the end-functionality of the product polymers is chlorine for all living polymerizations.

The polymerization of lactic acid anhydrosulphite by anionic initiators

This thesis is primarily concerned with the synthesis and polymerization of 5-methyl-1;3, 2-dioxathiolan-4-one-2-oxide (lactic acid anhydrosulphite (LAAS)) using anionic initiators under various conditions. Poly(lactic acid) is a biodegradable polymer which finds many uses in biomedical applications such as drug-delivery and wound-support systems. For such applications it is desirable to produce polymers having predictable molecular weight distributions and crystallinity, The use of anionic initiators offers a potential route to the creation of living polymers. The synthesis of LAAS was achieved by means of an established route though the procedure was modified to some extent and a new method of purification of the monomer using copper oxides was introduced, Chromatographic purification methods were also examined but found to be ineffective. An unusual impurity was discovered in some syntheses and this was identified by means of 1H and 13C NMR, elemental analysis and GC-MS. Since poly-α-esters having hydroxyl-bearing substituents might be expected to have high equilibrium water contents and hence low surface tension characteristics which might aid bio-compatibility, synthesis of gluconic acid anhydrosulphite was also attempted and the product characterised by 1H and 13C NMR. The kinetics of the decomposition of lactic acid anhydrosulphite by lithium tert-butoxide in nitrobenzene has been examined by means of gas evolution measurements. The kinetics of the reaction with potassium tert-butoxide (and also sec-butyl lithium) in tetrahydrofuran has been studied using calorimetric techniques. LAAS was block co-polymerized with styrene and also with 1,3-butadiene in tetrahydrofuran (in the latter case a statistical co-polymer was also produced).

The ring opening polymerization of ring strained cyclic ethers

The kinetics and mechanisms of the ring-opening polymerization of oxetane were studied using cationic and coordinated anionic catalysts. The cationic initiators used were BF30Et2!/ethanol, BF30Et2!/ethanediol and BF30Et2/propantriol. Kinetic determinations with the BF30Et2/diol system indicated that a 1: 1 BF3:0H ratio gave the maximum rate of polymerization and this ratio was employed to detenmne the overall rates of polymerization. An overall second-order dependence was obtained when the system involved ethanediol or propantriol as co-catalyst and a 3/2-order dependence with ethanol, in each case the monomer gave a first-order relationship. This suggested that two mechanisms accounted for the cationic polymerization. These mechanisms were investigated and further evidence for these was obtained from the study of the complex formation of BF30Et2 and the co-catalysts by 1H NMR. Molecular weight studies (using size-exclusion chromatography) indicated that the hydroxyl ion acted as a chain transfer reagent when the [OH] > [BF3]. A linear relationship was observed when the number average molecular weight was plotted against [oxetane] at constant [BF3:0H], and similarly a linear dependency was observed on the BF3:0H 1:1 adduct at constant oxetane concentration. Copolymerization of oxetane and THF was carried out using BF30Et2/ethanol system. The reactivity ratios were calculated as rOXT = 1.2 ± 0.30 and rTHF = 0.14 ± 0.03. These copolymers were random copolymers with no evidence of oligomer formation. The coordinated anionic catalyst, porphinato-aluminium chloride [(TPP)AICl], was used to produce a living polymerization of oxetane. An overall third-order kinetics was obtained, with a second-order with respect to the [(TPP)AICl] and a first-order with respect to the [oxetane] and a mechanism was postulated using these results. The stereochemistry of [(TPP)AlCl] catalyst was investigated using cyclohexene and cyclopentene oxide monomers, using extensive 1H NMR, 2-D COSY and decoupling NMR techniques it was concluded that [(TPP)AlCl] gave rise to stereoregular polymers.

Managing uncertainty in complex stochastic models: design and emulation of a Rabies model

In this paper we present a novel method for emulating a stochastic, or random output, computer model and show its application to a complex rabies model. The method is evaluated both in terms of accuracy and computational efficiency on synthetic data and the rabies model. We address the issue of experimental design and provide empirical evidence on the effectiveness of utilizing replicate model evaluations compared to a space-filling design. We employ the Mahalanobis error measure to validate the heteroscedastic Gaussian process based emulator predictions for both the mean and (co)variance. The emulator allows efficient screening to identify important model inputs and better understanding of the complex behaviour of the rabies model.