CD14 and innate immune clearance of apoptotic cells

Rapid elimination of cells undergoing programmed cell death (apoptosis) is vital to maintain tissue homeostasis. The phagocytic removal of apoptotic cells (AC) is mediated by innate immune molecules, professional phagocytes and amateur phagocytes that recognise "eat me" signals on the surface of the AC. CD14, a pattern recognition receptor expressed on macrophages, is widely known for its ability to recognise the pathogen-associated molecular pattern lipopolysaccharide (LPS) and promote inflammation. CD14 also mediates the binding and removal of AC, a process that is considered to be anti-inflammatory therefore suggesting CD14 is capable of producing two distinct ligand-dependent responses. Our work seeks to define the molecular mechanisms underlying the involvement of CD14 in the non-inflammatory clearance of AC. Here we describe three different differentiation strategies used to generate macrophages from the monocytic cell line THP-1. Whilst CD14 expression was increased in each macrophage model we demonstrate significant differences in the various macrophage models' abilities to respond to LPS and clear AC. We show that CD14 expression correlates with CD14-dependent AC clearance and anti-inflammatory responses to AC. However LPS responsiveness correlates, as expected, with TLR4 but not CD14 expression. These observations suggest CD14-dependent AC clearance is not dependent on TLR4. Taken together our data support the notion that CD14 ligand-dependent responses to LPS and AC are derived from changes at the macrophage surface. The nature and composition of the CD14-co-receptor complex for LPS and AC binding and consequent responses is the subject of further study.

A study of cluster analysis techniques and their applications

This thesis seeks to describe the development of an inexpensive and efficient clustering technique for multivariate data analysis. The technique starts from a multivariate data matrix and ends with graphical representation of the data and pattern recognition discriminant function. The technique also results in distances frequency distribution that might be useful in detecting clustering in the data or for the estimation of parameters useful in the discrimination between the different populations in the data. The technique can also be used in feature selection. The technique is essentially for the discovery of data structure by revealing the component parts of the data. lhe thesis offers three distinct contributions for cluster analysis and pattern recognition techniques. The first contribution is the introduction of transformation function in the technique of nonlinear mapping. The second contribution is the us~ of distances frequency distribution instead of distances time-sequence in nonlinear mapping, The third contribution is the formulation of a new generalised and normalised error function together with its optimal step size formula for gradient method minimisation. The thesis consists of five chapters. The first chapter is the introduction. The second chapter describes multidimensional scaling as an origin of nonlinear mapping technique. The third chapter describes the first developing step in the technique of nonlinear mapping that is the introduction of "transformation function". The fourth chapter describes the second developing step of the nonlinear mapping technique. This is the use of distances frequency distribution instead of distances time-sequence. The chapter also includes the new generalised and normalised error function formulation. Finally, the fifth chapter, the conclusion, evaluates all developments and proposes a new program. for cluster analysis and pattern recognition by integrating all the new features.

Deep hole drilling with twist drills: aspects of the CNC process and its real time monitoring and adaptive control

Deep hole drilling is one of the most complicated metal cutting processes and one of the most difficult to perform on CNC machine-tools or machining centres under conditions of limited manpower or unmanned operation. This research work investigates aspects of the deep hole drilling process with small diameter twist drills and presents a prototype system for real time process monitoring and adaptive control; two main research objectives are fulfilled in particular : First objective is the experimental investigation of the mechanics of the deep hole drilling process, using twist drills without internal coolant supply, in the range of diarneters Ø 2.4 to Ø4.5 mm and working length up to 40 diameters. The definition of the problems associated with the low strength of these tools and the study of mechanisms of catastrophic failure which manifest themselves well before and along with the classic mechanism of tool wear. The relationships between drilling thrust and torque with the depth of penetration and the various machining conditions are also investigated and the experimental evidence suggests that the process is inherently unstable at depths beyond a few diameters. Second objective is the design and implementation of a system for intelligent CNC deep hole drilling, the main task of which is to ensure integrity of the process and the safety of the tool and the workpiece. This task is achieved by means of interfacing the CNC system of the machine tool to an external computer which performs the following functions: On-line monitoring of the drilling thrust and torque, adaptive control of feed rate, spindle speed and tool penetration (Z-axis), indirect monitoring of tool wear by pattern recognition of variations of the drilling thrust with cumulative cutting time and drilled depth, operation as a data base for tools and workpieces and finally issuing of alarms and diagnostic messages.

The Riesz transform and simultaneous representations of phase, energy and orientation in spatial vision

To represent the local orientation and energy of a 1-D image signal, many models of early visual processing employ bandpass quadrature filters, formed by combining the original signal with its Hilbert transform. However, representations capable of estimating an image signal's 2-D phase have been largely ignored. Here, we consider 2-D phase representations using a method based upon the Riesz transform. For spatial images there exist two Riesz transformed signals and one original signal from which orientation, phase and energy may be represented as a vector in 3-D signal space. We show that these image properties may be represented by a Singular Value Decomposition (SVD) of the higher-order derivatives of the original and the Riesz transformed signals. We further show that the expected responses of even and odd symmetric filters from the Riesz transform may be represented by a single signal autocorrelation function, which is beneficial in simplifying Bayesian computations for spatial orientation. Importantly, the Riesz transform allows one to weight linearly across orientation using both symmetric and asymmetric filters to account for some perceptual phase distortions observed in image signals - notably one's perception of edge structure within plaid patterns whose component gratings are either equal or unequal in contrast. Finally, exploiting the benefits that arise from the Riesz definition of local energy as a scalar quantity, we demonstrate the utility of Riesz signal representations in estimating the spatial orientation of second-order image signals. We conclude that the Riesz transform may be employed as a general tool for 2-D visual pattern recognition by its virtue of representing phase, orientation and energy as orthogonal signal quantities.

A smart sensing platform for the classification of ambulatory patterns

This paper describes an innovative sensing approach allowing capture, discrimination, and classification of transients automatically in gait. A walking platform is described, which offers an alternative design to that of standard force plates with advantages that include mechanical simplicity and less restriction on dimensions. The scope of the work is to investigate as an experiment the sensitivity of the distributive tactile sensing method with the potential to address flexibility on gait assessment, including patient targeting and the extension to a variety of ambulatory applications. Using infrared sensors to measure plate deflection, gait patterns are compared with stored templates using a pattern recognition algorithm. This information is input into a neural network to classify normal and affected walking events, with a classification accuracy of just under 90 per cent achieved. The system developed has potential applications in gait analysis and rehabilitation, whereby it can be used as a tool for early diagnosis of walking disorders or to determine changes between pre- and post-operative gait.

Resource-aware configuration in smart camera networks

A recent trend in smart camera networks is that they are able to modify the functionality during runtime to better reflect changes in the observed scenes and in the specified monitoring tasks. In this paper we focus on different configuration methods for such networks. A configuration is given by three components: (i) a description of the camera nodes, (ii) a specification of the area of interest by means of observation points and the associated monitoring activities, and (iii) a description of the analysis tasks. We introduce centralized, distributed and proprioceptive configuration methods and compare their properties and performance. © 2012 IEEE.

Large scale multi-view stereopsis evaluation

The seminal multiple view stereo benchmark evaluations from Middlebury and by Strecha et al. have played a major role in propelling the development of multi-view stereopsis methodology. Although seminal, these benchmark datasets are limited in scope with few reference scenes. Here, we try to take these works a step further by proposing a new multi-view stereo dataset, which is an order of magnitude larger in number of scenes and with a significant increase in diversity. Specifically, we propose a dataset containing 80 scenes of large variability. Each scene consists of 49 or 64 accurate camera positions and reference structured light scans, all acquired by a 6-axis industrial robot. To apply this dataset we propose an extension of the evaluation protocol from the Middlebury evaluation, reflecting the more complex geometry of some of our scenes. The proposed dataset is used to evaluate the state of the art multiview stereo algorithms of Tola et al., Campbell et al. and Furukawa et al. Hereby we demonstrate the usability of the dataset as well as gain insight into the workings and challenges of multi-view stereopsis. Through these experiments we empirically validate some of the central hypotheses of multi-view stereopsis, as well as determining and reaffirming some of the central challenges.

Individual identification via electrocardiogram analysis

Background: During last decade the use of ECG recordings in biometric recognition studies has increased. ECG characteristics made it suitable for subject identification: it is unique, present in all living individuals, and hard to forge. However, in spite of the great number of approaches found in literature, no agreement exists on the most appropriate methodology. This study aimed at providing a survey of the techniques used so far in ECG-based human identification. Specifically, a pattern recognition perspective is here proposed providing a unifying framework to appreciate previous studies and, hopefully, guide future research. Methods: We searched for papers on the subject from the earliest available date using relevant electronic databases (Medline, IEEEXplore, Scopus, and Web of Knowledge). The following terms were used in different combinations: electrocardiogram, ECG, human identification, biometric, authentication and individual variability. The electronic sources were last searched on 1st March 2015. In our selection we included published research on peer-reviewed journals, books chapters and conferences proceedings. The search was performed for English language documents. Results: 100 pertinent papers were found. Number of subjects involved in the journal studies ranges from 10 to 502, age from 16 to 86, male and female subjects are generally present. Number of analysed leads varies as well as the recording conditions. Identification performance differs widely as well as verification rate. Many studies refer to publicly available databases (Physionet ECG databases repository) while others rely on proprietary recordings making difficult them to compare. As a measure of overall accuracy we computed a weighted average of the identification rate and equal error rate in authentication scenarios. Identification rate resulted equal to 94.95 % while the equal error rate equal to 0.92 %. Conclusions: Biometric recognition is a mature field of research. Nevertheless, the use of physiological signals features, such as the ECG traits, needs further improvements. ECG features have the potential to be used in daily activities such as access control and patient handling as well as in wearable electronics applications. However, some barriers still limit its growth. Further analysis should be addressed on the use of single lead recordings and the study of features which are not dependent on the recording sites (e.g. fingers, hand palms). Moreover, it is expected that new techniques will be developed using fiducials and non-fiducial based features in order to catch the best of both approaches. ECG recognition in pathological subjects is also worth of additional investigations.

The immune system as drug target

The immune system is perhaps the largest yet most diffuse and distributed somatic system in vertebrates. It plays vital roles in fighting infection and in the homeostatic control of chronic disease. As such, the immune system in both pathological and healthy states is a prime target for therapeutic interventions by drugs-both small-molecule and biologic. Comprising both the innate and adaptive immune systems, human immunity is awash with potential unexploited molecular targets. Key examples include the pattern recognition receptors of the innate immune system and the major histocompatibility complex of the adaptive immune system. Moreover, the immune system is also the source of many current and, hopefully, future drugs, of which the prime example is the monoclonal antibody, the most exciting and profitable type of present-day drug moiety. This brief review explores the identity and synergies of the hierarchy of drug targets represented by the human immune system, with particular emphasis on the emerging paradigm of systems pharmacology. © the authors, publisher and licensee Libertas Academica Limited.

Unfolding kernel embeddings of graphs:enhancing class separation through manifold learning

In this paper, we investigate the use of manifold learning techniques to enhance the separation properties of standard graph kernels. The idea stems from the observation that when we perform multidimensional scaling on the distance matrices extracted from the kernels, the resulting data tends to be clustered along a curve that wraps around the embedding space, a behavior that suggests that long range distances are not estimated accurately, resulting in an increased curvature of the embedding space. Hence, we propose to use a number of manifold learning techniques to compute a low-dimensional embedding of the graphs in an attempt to unfold the embedding manifold, and increase the class separation. We perform an extensive experimental evaluation on a number of standard graph datasets using the shortest-path (Borgwardt and Kriegel, 2005), graphlet (Shervashidze et al., 2009), random walk (Kashima et al., 2003) and Weisfeiler-Lehman (Shervashidze et al., 2011) kernels. We observe the most significant improvement in the case of the graphlet kernel, which fits with the observation that neglecting the locational information of the substructures leads to a stronger curvature of the embedding manifold. On the other hand, the Weisfeiler-Lehman kernel partially mitigates the locality problem by using the node labels information, and thus does not clearly benefit from the manifold learning. Interestingly, our experiments also show that the unfolding of the space seems to reduce the performance gap between the examined kernels.

A quantum Jensen-Shannon graph kernel for unattributed graphs

In this paper, we use the quantum Jensen-Shannon divergence as a means of measuring the information theoretic dissimilarity of graphs and thus develop a novel graph kernel. In quantum mechanics, the quantum Jensen-Shannon divergence can be used to measure the dissimilarity of quantum systems specified in terms of their density matrices. We commence by computing the density matrix associated with a continuous-time quantum walk over each graph being compared. In particular, we adopt the closed form solution of the density matrix introduced in Rossi et al. (2013) [27,28] to reduce the computational complexity and to avoid the cumbersome task of simulating the quantum walk evolution explicitly. Next, we compare the mixed states represented by the density matrices using the quantum Jensen-Shannon divergence. With the quantum states for a pair of graphs described by their density matrices to hand, the quantum graph kernel between the pair of graphs is defined using the quantum Jensen-Shannon divergence between the graph density matrices. We evaluate the performance of our kernel on several standard graph datasets from both bioinformatics and computer vision. The experimental results demonstrate the effectiveness of the proposed quantum graph kernel.

A quantum Jensen-Shannon graph kernel using discrete-time quantum walks

In this paper, we develop a new graph kernel by using the quantum Jensen-Shannon divergence and the discrete-time quantum walk. To this end, we commence by performing a discrete-time quantum walk to compute a density matrix over each graph being compared. For a pair of graphs, we compare the mixed quantum states represented by their density matrices using the quantum Jensen-Shannon divergence. With the density matrices for a pair of graphs to hand, the quantum graph kernel between the pair of graphs is defined by exponentiating the negative quantum Jensen-Shannon divergence between the graph density matrices. We evaluate the performance of our kernel on several standard graph datasets, and demonstrate the effectiveness of the new kernel.

A quantum Jensen-Shannon graph kernel using the continuous-time quantum walk

In this paper, we use the quantum Jensen-Shannon divergence as a means to establish the similarity between a pair of graphs and to develop a novel graph kernel. In quantum theory, the quantum Jensen-Shannon divergence is defined as a distance measure between quantum states. In order to compute the quantum Jensen-Shannon divergence between a pair of graphs, we first need to associate a density operator with each of them. Hence, we decide to simulate the evolution of a continuous-time quantum walk on each graph and we propose a way to associate a suitable quantum state with it. With the density operator of this quantum state to hand, the graph kernel is defined as a function of the quantum Jensen-Shannon divergence between the graph density operators. We evaluate the performance of our kernel on several standard graph datasets from bioinformatics. We use the Principle Component Analysis (PCA) on the kernel matrix to embed the graphs into a feature space for classification. The experimental results demonstrate the effectiveness of the proposed approach. © 2013 Springer-Verlag.

A continuous-time quantum walk kernel for unattributed graphs

Kernel methods provide a way to apply a wide range of learning techniques to complex and structured data by shifting the representational problem from one of finding an embedding of the data to that of defining a positive semidefinite kernel. In this paper, we propose a novel kernel on unattributed graphs where the structure is characterized through the evolution of a continuous-time quantum walk. More precisely, given a pair of graphs, we create a derived structure whose degree of symmetry is maximum when the original graphs are isomorphic. With this new graph to hand, we compute the density operators of the quantum systems representing the evolutions of two suitably defined quantum walks. Finally, we define the kernel between the two original graphs as the quantum Jensen-Shannon divergence between these two density operators. The experimental evaluation shows the effectiveness of the proposed approach. © 2013 Springer-Verlag.

Attributed graph similarity from the quantum Jensen-Shannon divergence

One of the most fundamental problem that we face in the graph domain is that of establishing the similarity, or alternatively the distance, between graphs. In this paper, we address the problem of measuring the similarity between attributed graphs. In particular, we propose a novel way to measure the similarity through the evolution of a continuous-time quantum walk. Given a pair of graphs, we create a derived structure whose degree of symmetry is maximum when the original graphs are isomorphic, and where a subset of the edges is labeled with the similarity between the respective nodes. With this compositional structure to hand, we compute the density operators of the quantum systems representing the evolution of two suitably defined quantum walks. We define the similarity between the two original graphs as the quantum Jensen-Shannon divergence between these two density operators, and then we show how to build a novel kernel on attributed graphs based on the proposed similarity measure. We perform an extensive experimental evaluation both on synthetic and real-world data, which shows the effectiveness the proposed approach. © 2013 Springer-Verlag.