Probabilistic principal component analysis

Principal component analysis (PCA) is a ubiquitous technique for data analysis and processing, but one which is not based upon a probability model. In this paper we demonstrate how the principal axes of a set of observed data vectors may be determined through maximum-likelihood estimation of parameters in a latent variable model closely related to factor analysis. We consider the properties of the associated likelihood function, giving an EM algorithm for estimating the principal subspace iteratively, and discuss the advantages conveyed by the definition of a probability density function for PCA.

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.

Macro determinants of FDI inflows to Japan:an analysis of source country characteristics

This paper examines the source country determinants of FDI into Japan. The paper highlights certain methodological and theoretical weaknesses in the previous literature and offers some explanations for hitherto ambiguous results. Specifically, the paper highlights the importance of panel data analysis, and the identification of fixed effects in the analysis rather than simply pooling the data. Indeed, we argue that many of the results reported elsewhere are a feature of this mis-specification. To this end, pooled, fixed effects and random effects estimates are compared. The results suggest that FDI into Japan is inversely related to trade flows, such that trade and FDI are substitutes. Moreover, the results also suggest that FDI increases with home country political and economic stability. The paper also shows that previously reported results, regarding the importance of exchange rates, relative borrowing costs and labour costs in explaining FDI flows, are sensitive to the econometric specification and estimation approach. The paper also discusses the importance of these results within a policy context. In recent years Japan has sought to attract FDI, though many firms still complain of barriers to inward investment penetration in Japan. The results show that cultural and geographic distance are only of marginal importance in explaining FDI, and that the results are consistent with the market-seeking explanation of FDI. As such, the attitude to risk in the source country is strongly related to the size of FDI flows to Japan. © 2007 The Authors Journal compilation © 2007 Blackwell Publishing Ltd.

The application of analysis of variance (ANOVA) to different experimental designs in optometry

Analysis of variance (ANOVA) is the most efficient method available for the analysis of experimental data. Analysis of variance is a method of considerable complexity and subtlety, with many different variations, each of which applies in a particular experimental context. Hence, it is possible to apply the wrong type of ANOVA to data and, therefore, to draw an erroneous conclusion from an experiment. This article reviews the types of ANOVA most likely to arise in clinical experiments in optometry including the one-way ANOVA ('fixed' and 'random effect' models), two-way ANOVA in randomised blocks, three-way ANOVA, and factorial experimental designs (including the varieties known as 'split-plot' and 'repeated measures'). For each ANOVA, the appropriate experimental design is described, a statistical model is formulated, and the advantages and limitations of each type of design discussed. In addition, the problems of non-conformity to the statistical model and determination of the number of replications are considered. © 2002 The College of Optometrists.

Spatially clustered associations in health GIS

Overlaying maps using a desktop GIS is often the first step of a multivariate spatial analysis. The potential of this operation has increased considerably as data sources and Web services to manipulate them are becoming widely available via the Internet. Standards from the OGC enable such geospatial mashups to be seamless and user driven, involving discovery of thematic data. The user is naturally inclined to look for spatial clusters and correlation of outcomes. Using classical cluster detection scan methods to identify multivariate associations can be problematic in this context, because of a lack of control on or knowledge about background populations. For public health and epidemiological mapping, this limiting factor can be critical but often the focus is on spatial identification of risk factors associated with health or clinical status. Spatial entropy index HSu for the ScankOO analysis of the hypothetical dataset using a vicinity which is fixed by the number of points without distinction between their labels. (The size of the labels is proportional to the inverse of the index) In this article we point out that this association itself can ensure some control on underlying populations, and develop an exploratory scan statistic framework for multivariate associations. Inference using statistical map methodologies can be used to test the clustered associations. The approach is illustrated with a hypothetical data example and an epidemiological study on community MRSA. Scenarios of potential use for online mashups are introduced but full implementation is left for further research.

Development and evaluation of an ion induced x-ray emission system for the analysis of light and medium weight elements

The present work describes the development of a proton induced X-ray emission (PIXE) analysis system, especially designed and builtfor routine quantitative multi-elemental analysis of a large number of samples. The historical and general developments of the analytical technique and the physical processes involved are discussed. The philosophy, design, constructional details and evaluation of a versatile vacuum chamber, an automatic multi-sample changer, an on-demand beam pulsing system and ion beam current monitoring facility are described.The system calibration using thin standard foils of Si, P, S,Cl, K, Ca, Ti, V, Fe, Cu, Ga, Ge, Rb, Y and Mo was undertaken at proton beam energies of 1 to 3 MeV in steps of 0.5 MeV energy and compared with theoretical calculations. An independent calibration check using bovine liver Standard Reference Material was performed.  The minimum detectable limits have been experimentally determined at detector positions of 90° and 135° with respect to the incident beam for the above range of proton energies as a function of atomic number Z. The system has detection limits of typically 10- 7 to 10- 9 g for elements 14data analysis and calculations of areal density of thin foils using Rutherford backscattering data.  Amniotic fluid samples supplied by South Sefton Health Authority were successfully analysed for their low base line elemental concentrations. In conclusion the findings of this work are discussed with suggestions for further work .

Negotiating face in feedback conferences:a linguistic ethnographic analysis

This article examines the negotiation of face in post observation feedback conferences on an initial teacher training programme. The conferences were held in groups with one trainer and up to four trainees and followed a set of generic norms. These norms include the right to offer advice and to criticise, speech acts which are often considered to be face threatening in more normal contexts. However, as the data analysis shows, participants also interact in ways that challenge the generic norms, some of which might be considered more conventionally face attacking. The article argues that face should be analysed at the level of interaction (Haugh and Bargiela-Chiappini, 2010) and that situated and contextual detail is relevant to its analysis. It suggests that linguistic ethnography, which 'marries' (Wetherell, 2007) linguistics and ethnography, provides a useful theoretical framework for doing so. To this end the study draws on real-life talk-in-interaction (from transcribed recordings), the participants' perspectives (from focus groups and interviews) and situated detail (from fieldnotes) to produce a contextualised and nuanced analysis. © 2011 Elsevier B.V.

A regional analysis of contraction rate in written Standard American English

The goal of this study is to determine if various measures of contraction rate are regionally patterned in written Standard American English. In order to answer this question, this study employs a corpus-based approach to data collection and a statistical approach to data analysis. Based on a spatial autocorrelation analysis of the values of eleven measures of contraction across a 25 million word corpus of letters to the editor representing the language of 200 cities from across the contiguous United States, two primary regional patterns were identified: easterners tend to produce relatively few standard contractions (not contraction, verb contraction) compared to westerners, and northeasterners tend to produce relatively few non-standard contractions (to contraction, non-standard not contraction) compared to southeasterners. These findings demonstrate that regional linguistic variation exists in written Standard American English and that regional linguistic variation is more common than is generally assumed.

Statistical analysis in microbiology:statnotes

This book is aimed primarily at microbiologists who are undertaking research and who require a basic knowledge of statistics to analyse their experimental data. Computer software employing a wide range of data analysis methods is widely available to experimental scientists. The availability of this software, however, makes it essential that investigators understand the basic principles of statistics. Statistical analysis of data can be complex with many different methods of approach, each of which applies in a particular experimental circumstance. Hence, it is possible to apply an incorrect statistical method to data and to draw the wrong conclusions from an experiment. The purpose of this book, which has its origin in a series of articles published in the Society for Applied Microbiology journal ‘The Microbiologist’, is an attempt to present the basic logic of statistics as clearly as possible and therefore, to dispel some of the myths that often surround the subject. The 28 ‘Statnotes’ deal with various topics that are likely to be encountered, including the nature of variables, the comparison of means of two or more groups, non-parametric statistics, analysis of variance, correlating variables, and more complex methods such as multiple linear regression and principal components analysis. In each case, the relevant statistical method is illustrated with examples drawn from experiments in microbiological research. The text incorporates a glossary of the most commonly used statistical terms and there are two appendices designed to aid the investigator in the selection of the most appropriate test.

The geochemistry of the sedimentary rocks of the Harlech Dome, North Wales

Bedrock geochemical analysis, coupled with detailed data analysis, was carried out on some 260 samples taken from two areas of 'the Harlech Dome, near Dolgellau, North Wales. This was done to determine if rocks from mineralised and non-mineralised areas could be distinguished, and to determine mineralisation types and wall rock alterations. The Northern Area, near Talsarnau, has no recorded mineralisation, while the Southern Area, near Bontddu, has been exploited for gold. The rocks sampled, in both areas, were from the Cambrian Gamlan Flags, Clogau Shales, Vigra Flags, later vein materials, and igneous intrusions. All samples were analysed, using a new rapid, atomic absorption spectrophotometric technique, for Si, AI, Fe, Cu, Ni, Zn, Pb, Sr, Hg, and Ba. In addition 60 samples were analysed by X-ray fluorescence for Mn, Ti, Ca, K, Na, P, Cr, Ce, La, S, Y , Rh, and Th. Total CO2 was determined, on selected samples, using a combustion technique. Elemental distributions, for each rock type, in each area, were· plotted, and means, standard deviations, and enrichment indices were calculated. Multivariate statistical analysis on the results distinguished a Cu-type mineralisation in the Northern area, and both Cu and Pb/Zn types in the Southern Area. It also showed the Northern Area to be less strongly mineralised than the Southern one in which both mineralisation types are associated with wall rock alteration. Elemental associations and trends due to sedimentary processes were distinguished from those related to mineralisation. Hg is related to mineralisation, and plots of factor scores, on the sampling grid, produced clusters of mineralisation related factors in areas of known mineralisation. A double Fourier Trend Analysis program, with a wavelength search routine, was developed and used to recognise sedimentary trends for Sr. Y., Rb, and Th. These trends were interpreted to represent areas of low pH and reducing conditions. They also indicate that the supply of sediment remained constant over Gamlan, Clogau, and Vigra times. The trend surface of Hg showed no association with rock type. It is shown that analysis of a small number of samples, for a carefully selected number of elements, with detailed data analysis, can provide more useful information than analysis of a large number of samples for many elements. The mineralisation is suggested to have been the result of water solutions leaching ore metals from the sedimentary rocks and redepositing them in veins.

A tale of two analyses: the use of archived qualitative data

This article provides a unique contribution to the debates about archived qualitative data by drawing on two uses of the same data - British Migrants in Spain: the Extent and Nature of Social Integration, 2003-2005 - by Jones (2009) and Oliver and O'Reilly (2010), both of which utilise Bourdieu's concepts analytically and produce broadly similar findings. We argue that whilst the insights and experiences of those researchers directly involved in data collection are important resources for developing contextual knowledge used in data analysis, other kinds of critical distance can also facilitate credible data use. We therefore challenge the assumption that the idiosyncratic relationship between context, reflexivity and interpretation limits the future use of data. Moreover, regardless of the complex genealogy of the data itself, given the number of contingencies shaping the qualitative research process and thus the potential for partial or inaccurate interpretation, contextual familiarity need not be privileged over other aspects of qualitative praxis such as sustained theoretical insight, sociological imagination and methodological rigour. © Sociological Research Online, 1996-2012.

Efficacy and safety of second-generation antipsychotic long-acting injections (SGA LAIs) in maintenance treatment of bipolar disorder:protocol for a systematic review and meta-analysis

INTRODUCTION: Bipolar disorder requires long-term treatment but non-adherence is a common problem. Antipsychotic long-acting injections (LAIs) have been suggested to improve adherence but none are licensed in the UK for bipolar. However, the use of second-generation antipsychotics (SGA) LAIs in bipolar is not uncommon albeit there is a lack of systematic review in this area. This study aims to systematically review safety and efficacy of SGA LAIs in the maintenance treatment of bipolar disorder. METHODS AND ANALYSIS: The protocol is based on Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) and will include only randomised controlled trials comparing SGA LAIs in bipolar. PubMed, EMBASE, CINAHL, Cochrane Library (CENTRAL), PsychINFO, LiLACS, http://www.clinicaltrials.gov will be searched, with no language restriction, from 2000 to January 2016 as first SGA LAIs came to the market after 2000. Manufacturers of SGA LAIs will also be contacted. Primary efficacy outcome is relapse rate or delayed time to relapse or reduction in hospitalisation and primary safety outcomes are drop-out rates, all-cause discontinuation and discontinuation due to adverse events. Qualitative reporting of evidence will be based on 21 items listed on standards for reporting qualitative research (SRQR) focusing on study quality (assessed using the Jadad score, allocation concealment and data analysis), risk of bias and effect size. Publication bias will be assessed using funnel plots. If sufficient data are available meta-analysis will be performed with primary effect size as relative risk presented with 95% CI. Sensitivity analysis, conditional on number of studies and sample size, will be carried out on manic versus depressive symptoms and monotherapy versus adjunctive therapy.

Approximation of Experimental Data by Bezier Curves

Very often the experimental data are the realization of the process, fully determined by some unknown function, being distorted by hindrances. Treatment and experimental data analysis are substantially facilitated, if these data to represent as analytical expression. The experimental data processing algorithm and the example of using this algorithm for spectrographic analysis of oncologic preparations of blood is represented in this article.

Oxidiative lipidomics coming of age:advances in analysis of oxidized phospholipids in physiology and pathology

Significance: Oxidized phospholipids are now well-recognized as markers of biological oxidative stress and bioactive molecules with both pro-inflammatory and anti-inflammatory effects. While analytical methods continue to be developed for studies of generic lipid oxidation, mass spectrometry (MS) has underpinned the advances in knowledge of specific oxidized phospholipids by allowing their identification and characterization, and is responsible for the expansion of oxidative lipidomics. Recent Advances: Studies of oxidized phospholipids in biological samples, both from animal models and clinical samples, have been facilitated by the recent improvements in MS, especially targeted routines that depend on the fragmentation pattern of the parent molecular ion and improved resolution and mass accuracy. MS can be used to identify selectively individual compounds or groups of compounds with common features, which greatly improves the sensitivity and specificity of detection. Application of these methods have enabled important advances in understanding the mechanisms of inflammatory diseases such as atherosclerosis, steatohepatitis, leprosy and cystic fibrosis, and offer potential for developing biomarkers of molecular aspects of the diseases. Critical Issues and Future Directions: The future in this field will depend on development of improved MS technologies, such as ion mobility, novel enrichment methods and databases and software for data analysis, owing to the very large amount of data generated in these experiments. Imaging of oxidized phospholipids in tissue MS is an additional exciting direction emerging that can be expected to advance understanding of physiology and disease.

Analyzing the Data in OLAP Data Cubes

* Supported partially by the Bulgarian National Science Fund under Grant MM-1405/2004