Latest developments in the microarray analysis of human brain mRNA

Microarrays are used to monitor the expression of thousands of gene transcripts. This technique requires high-quality RNA, which can be extracted from a variety sources, including autopsy brain tissue. Most nucleic acids and proteins are reasonably stable post mortem. However, their abundance and integrity can exhibit marked intraand inter-subject variability, so care must be taken when comparisons between case-groups are made. We will review issues associated with the sampling of RNA from autopsy brain tissue in relation to various ante- and post-mortem factors.

Use of fundus imaging in quantification of age-related macular change

This review will discuss the use of manual grading scales, digital photography, and automated image analysis in the quantification of fundus changes caused by age-related macular disease. Digital imaging permits processing of images for enhancement, comparison, and feature quantification, and these techniques have been investigated for automated drusen analysis. The accuracy of automated analysis systems has been enhanced by the incorporation of interactive elements, such that the user is able to adjust the sensitivity of the system, or manually add and remove pixels. These methods capitalize on both computer and human image feature recognition and the advantage of computer-based methodologies for quantification. The histogram-based adaptive local thresholding system is able to extract useful information from the image without being affected by the presence of other structures. More recent developments involve compensation for fundus background reflectance, which has most recently been combined with the Otsu method of global thresholding. This method is reported to provide results comparable with manual stereo viewing. Developments in this area are likely to encourage wider use of automated techniques. This will make the grading of photographs easier and cheaper for clinicians and researchers. © 2007 Elsevier Inc. All rights reserved.

Reducing patient mortality in hospitals:the role of human resource management

Developing effective health care organizations is increasingly complex as a result of demographic changes, globalization, and developments in medicine. This study examines the potential contribution of organizational behavior theory and research by investigating the relationship between systems of human resource management (HRM) practices and effectiveness of patient care in hospitals. Relatively little research has been conducted to explore these issues in health care settings. In a sample of 52 hospitals in England, we examine the relationship between the HRM system and health care outcome. Specifically, we study the association between high performance HRM policies and practices and standardized patient mortality rates. The research reveals that, after controlling for prior mortality and other potentially confounding factors such as the ratio of doctors to patients, greater use of a complementary set of HRM practices has a statistically and practically significant relationship with patient mortality. The findings suggest that managers and policy makers should focus sharply on improving the functioning of relevant HR management systems in health care organizations as one important means by which to improve patient care. Copyright © 2006 John Wiley & Sons, Ltd.

Measuring the degree of spatial correlation between histological features in thin sections of brain tissue

Histological features visible in thin sections of brain tissue, such as neuronal perikarya, blood vessels, or pathological lesions may exhibit a degree of spatial association or correlation. In neurodegenerative disorders such as AD, Pick's disease, and CJD, information on whether different types of pathological lesion are spatially correlated may be useful in elucidating disease pathogenesis. In the present article the statistical methods available for studying spatial association in histological sections are reviewed. These include tests of interspecific association between two or more histological features using χ2 contingency tables, measurement of 'complete' and 'absolute' association, and more complex methods that use grids of contiguous samples. In addition, the use of correlation matrices and stepwise multiple regression methods are described. The advantages and limitations of each method are reviewed and possible future developments discussed.

Apoptosis of neurons and oligodendrocytes in the spinal cord of spinal hyperostotic mouse (twy/twy):possible pathomechanism of human cervical compressive myelopathy

Cervical compressive myelopathy is the most serious complication of cervical spondylosis or ossification of the posterior longitudinal ligament (OPLL) and the most frequent cause of spinal cord dysfunction. There is little information on the exact pathophysiological mechanism responsible for the progressive loss of neural tissue in the spinal cord of such patients. In this study, we used the spinal hyperostotic mouse (twy/twy) as a suitable model of human spondylosis, and OPLL to investigate the cellular and molecular changes in the spinal cord. Mutant twy/twy mouse developed ossification of the ligamentum flavum at C2-C3 and exhibited progressive paralysis.

The use of expert systems for decision making in organizations

The research described in this thesis investigates three issues related to the use of expert systems for decision making in organizations. These are the effectiveness of ESs when used in different roles, to replace a human decision maker or to advise a human decision maker, the users' behaviourand opinions towards using an expertadvisory system and, the possibility of organization-wide deployment of expert systems and the role of an ES in different organizational levels. The research was based on the development of expert systems within a business game environment, a simulation of a manufacturing company. This was chosen to give more control over the `experiments' than would be possible in a real organization. An expert system (EXGAME) was developed based on a structure derived from Anthony's three levels of decision making to manage the simulated company in the business game itself with little user intervention. On the basis of EXGAME, an expert advisory system (ADGAME) was built to help game players to make better decisions in managing the game company. EXGAME and ADGAME are thus two expert systems in the same domain performing different roles; it was found that ADGAME had, in places, to be different from EXGAME, not simply an extension of it. EXGAME was tested several times against human rivals and was evaluated by measuring its performance. ADGAME was also tested by different users and was assessed by measuring the users' performance and analysing their opinions towards it as a helpful decision making aid. The results showed that an expert system was able to replace a human at the operational level, but had difficulty at the strategic level. It also showed the success of the organization-wide deployment of expert systems in this simulated company.

Evaluation of DNA enzymes targeted against the RNA component of human telomerase

Glioblastoma Multiforme (GBM) is a highly malignant form of brain cancer for which there is currently no effective cure. Consequently, developing new therapies and elucidating effective targets is crucial for this fatal disease. In recent years, DNA enzymes, deoxyribonucleic acid molecules with enzymatic activity, have emerged. In the same manner as ribozymes, DNA enzymes are able to effect cleavage of RNA in a sequence-specific manner, and operate with catalytic efficiency. In this study, two DNA enzymes were designed to target the template region of human telomerase RNA (hTR), utilising the 10-23 and 8-17 catalytic motifs elucidated by Santoro and Joyce (1997). Telomerase is an RNA-dependent DNA polymerase, which stabilises telomere lengths by adding hexameric repeats (TTAGGG in humans) to chromosome termini, thus preventing the telomere shortening that usually occurs during mitotic cell division. Telomerase activity, whilst absent in normal somatic tissues, is present in almost 90% of all tumours. Thus, there is speculation that telomerase may be the much sought universal target for therapeutic intervention in cancer. In vitro cleavage assays showed both DNA enzymes to be catalytically competent. Unmodified phosphodiester (PO) backbone DNA enzymes were rapidly degraded in the presence of serum, with a half-life of 10 minutes. The common approach of introducing phosphorothioate (PS) linkages was used in an effort to overcome this instability. As a result of concurrent activity and stability studies on the DNA enzymes with various numbers of PS linkages, the DNA enzymes with a PO core and PS arms were chosen for use in further cell work. The cleavage activity of both was shown to be specific and affected by temperature, pH, MgCI2 concentration and enzyme concentration. Both DNA enzyme motifs reduced telomerase activity in cell lysates, as assessed by the telomerase repeat amplification protocol (TRAP) with an IC50 of 100nM. DNA enzymes being polyanionic molecules do not readily cross biological barriers. Cellular association of naked DNA enzyme was inefficient at less than 2%. Cellular delivery of the DNA enzymes was effectively improved using commercial cationic lipid formulations. However, the lipid-mediated delivery of DNA enzymes to U87-MG cells over a 4-hour period did not significantly inhibit cell proliferation compared to controls. This is possibly due to an expected lag period between the inhibition of telomere maintenance and cell death. Therefore, biodegradable polymer microspheres were investigated as a potential delivery option for prolonged and sustained delivery. In vitro release profiles showed that after an initial burst, sustained release of DNA enzymes was observed over 35 days. Finally, the efficacy and specificity of the DNA enzymes were demonstrated in a luciferase based reporter assay. Specific inhibition of luciferase expression was displayed at 10nM. Thus DNA enzymes have potential against endogenous cellular targets.

An optical study of human ocular dimensions

Many workers have studied the ocular components which occur in eyes exhibiting differing amounts of central refractive error but few have ever considered the additional information that could be derived from a study of peripheral refraction. Before now, peripheral refraction has either been measured in real eyes or has otherwise been modelled in schematic eyes of varying levels of sophistication. Several differences occur between measured and modelled results which, if accounted for, could give rise to more information regarding the nature of the optical and retinal surfaces and their asymmetries. Measurements of ocular components and peripheral refraction, however, have never been made in the same sample of eyes. In this study, ocular component and peripheral refractive measurements were made in a sample of young near-emmetropic, myopic and hyperopic eyes. The data for each refractive group was averaged. A computer program was written to construct spherical surfaced schematic eyes from this data. More sophisticated eye models were developed making use of linear algebraic ray tracing program. This method allowed rays to be traced through toroidal aspheric surfaces which were translated or rotated with respect to each other. For simplicity, the gradient index optical nature of the crystalline lens was neglected. Various alterations were made in these eye models to reproduce the measured peripheral refractive patterns. Excellent agreement was found between the modelled and measured peripheral refractive values over the central 70o of the visual field. This implied that the additional biometric features incorporated in each eye model were representative of those which were present in the measured eyes. As some of these features are not otherwise obtainable using in vivo techniques, it is proposed that the variation of refraction in the periphery offers a very useful optical method for studying human ocular component dimensions.

A smart sensing platform for the discrimination of human movement

This thesis documents the design, implementation and testing of a smart sensing platform that is able to discriminate between differences or small changes in a persons walking. The distributive tactile sensing method is used to monitor the deflection of the platform surface using just a small number of sensors and, through the use of neural networks, infer the characteristics of the object in contact with the surface. The thesis first describes the development of a mathematical model which uses a novel method to track the position of a moving load as it passes over the smart sensing surface. Experimental methods are then described for using the platform to track the position of swinging pendulum in three dimensions. It is demonstrated that the method can be extended to that of real-time measurement of balance and sway of a person during quiet standing. Current classification methods are then investigated for use in the classification of different gait patterns, in particular to identify individuals by their unique gait pattern. Based on these observations, a novel algorithm is developed that is able to discriminate between abnormal and affected gait. This algorithm, using the distributive tactile sensing method, was found to have greater accuracy than other methods investigated and was designed to be able to cope with any type of gait variation. The system developed in this thesis has applications in the area of medical diagnostics, either as an initial screening tool for detecting walking disorders or to be able to automatically detect changes in gait over time. The system could also be used as a discrete biometric identification method, for example identifying office workers as they pass over the surface.

Use of narrow mass-window, high-resolution extracted product ion chromatograms for the sensitive and selective identification of protein modifications

Protein modifications, including oxidative modifications, glycosylations, and oxidized lipid-protein adducts, are becoming increasingly important as biomarkers and in understanding disease etiology. There has been a great deal of interest in mapping these on Apo B100 from low density lipoprotein (LDL). We have used extracted ion chromatograms of product ions generated using a very narrow mass window from high-resolution tandem mass spectrometric data collected on a rapid scanning quadrupole time-of-flight (QTOF) instrument, to selectively and sensitively detect modified peptides and identify the site and nature of a number of protein modifications in parallel. We have demonstrated the utility of this method by characterizing for the first time oxidized phospholipid adducts to LDL and human serum albumin and for the detection of glycosylation and kynurenin formation from the oxidation of tryptophan residues in LDL. © 2013 American Chemical Society.

A comparison of five lipid extraction solvent systems for lipidomic studies of human LDL

Lipidome profile of fluids and tissues is a growing field as the role of lipids as signaling molecules is increasingly understood, relying on an effective and representative extraction of the lipids present. A number of solvent systems suitable for lipid extraction are commonly in use, though no comprehensive investigation of their effectiveness across multiple lipid classes has been carried out. To address this, human LDL from normolipidemic volunteers was used to evaluate five different solvent extraction protocols [Folch, Bligh and Dyer, acidified Bligh and Dyer, methanol (MeOH)-tert-butyl methyl ether (TBME), and hexane-isopropanol] and the extracted lipids were analyzed by LC-MS in a high-resolution instrument equipped with polarity switching. Overall, more than 350 different lipid species from 19 lipid subclasses were identified. Solvent composition had a small effect on the extraction of predominant lipid classes (triacylglycerides, cholesterol esters, and phosphatidylcholines). In contrast, extraction of less abundant lipids (phosphatidylinositols, lyso-lipids, ceramides, and cholesterol sulfates) was greatly influenced by the solvent system used. Overall, the Folch method was most effective for the extraction of a broad range of lipid classes in LDL, although the hexane-isopropanol method was best for apolar lipids and the MeOH-TBME method was suitable for lactosyl ceramides. Copyright © 2013 by the American Society for Biochemistry and Molecular Biology, Inc.

On the use of software models during software execution

Increasingly software systems are required to survive variations in their execution environment without or with only little human intervention. Such systems are called "eternal software systems". In contrast to the traditional view of development and execution as separate cycles, these modern software systems should not present such a separation. Research in MDE has been primarily concerned with the use of models during the first cycle or development (i.e. during the design, implementation, and deployment) and has shown excellent results. In this paper the author argues that an eternal software system must have a first-class representation of itself available to enable change. These runtime representations (or runtime models) will depend on the kind of dynamic changes that we want to make available during execution or on the kind of analysis we want the system to support. Hence, different models can be conceived. Self-representation inevitably implies the use of reflection. In this paper the author briefly summarizes research that supports the use of runtime models, and points out different issues and research questions. © 2009 IEEE.

Human intervertebral disc cells promote nerve growth over substrata of human intervertebral disc aggrecan

Study Design. Coculture assays of the migration and interaction of human intervertebral disc cells and chick sensory nerves on alternate substrata of collagen and aggrecan. Objective. To examine the effects of aggrecan on disc cell migration, how disc cells and sensory nerves interact, and whether disc cells affect previously reported inhibitory effects of aggrecan on sensory nerve growth. Summary of Background Data. Human intervertebral disc aggrecan is inhibitory to sensory nerve growth in vitro, suggesting that a loss of aggrecan from the disc may have a role in the increased innervation seen in disc degeneration. Endothelial cells that appear to co-migrate with nerves into degenerated intervertebral disc express neurotrophic factors, but the effects of disc cells on nerve growth are not known. Methods. Human disc cells were seeded onto tissue culture plates that had been coated with type I collagen and human intervertebral disc aggrecan. Explants of chick dorsal root ganglions (DRGs) were subsequently added to the plates and sensory neurite outgrowth stimulated by the addition of nerve growth factor. Time-lapse video and fluorescence microscopy were used to examine the migration and interaction of the disc cells and sensory neurites, in the context of the different matrix substrata. The effects of disc cell conditioned medium on nerve growth were also examined. Results. Disc cells spread and migrated on collagen until they encountered the aggrecan substrata, where some cells, but not all, were repelled. In coculture, DRG neurites extended onto the collagen/disc cells until they encountered the aggrecan, where, like the disc cells, many were repelled. However, in the presence of disc cells, some neurites were able to cross onto this normally inhibitory substratum. The number of neurite crossings onto aggrecan correlated significantly with the number of disc cells present on the aggrecan. In control experiments using DRG alone, all extending neurites were repelled at the collagen/aggrecan border. Conditioned medium from disc cell cultures stimulated DRG neurite outgrowth on collagen but did not increase neurite crossing onto aggrecan substrata. Conclusions. Human disc cells migrate across aggrecan substrata that are repellent to sensory DRG neurites. Disc cells synthesize neurotrophic factors in vitro that promote neurite outgrowth. Furthermore, the presence of disc cells in coculture with DRG partially abrogates the inhibitory effects of aggrecan on nerve growth. These findings have important implications for the regulation of nerve growth into the intervertebral disc, but whether disc cells promote nerve growth in vivo remains to be determined.