Measuring the spatial arrangement patterns of pathological lesions in histological sections of brain tissue

The development of abnormal protein aggregates in the form of extracellular plaques and intracellular inclusions is a characteristic feature of many neurodegenerative diseases such as Alzheimer's disease (AD), Creutzfeldt-Jakob disease (CJD) and the fronto-temporal dementias (FTD). An important aspect of a pathological protein aggregate is its spatial topography in the tissue. Lesions may not be randomly distributed within a histological section but exhibit spatial pattern, a departure from randomness either towards regularity or clustering. Information on the spatial pattern of a lesion may be useful in elucidating its pathogenesis and in studying the relationships between different lesions. This article reviews the methods that have been used to study the spatial topography of lesions. These include simple tests of whether the distribution of a lesion departs significantly from random using randomized points or sample fields, and more complex methods that employ grids or transects of contiguous fields and which can detect the intensity of aggregation and the sizes, distribution and spacing of the clusters. The usefulness of these methods in elucidating the pathogenesis of protein aggregates in neurodegenerative disease is discussed.

Methods of studying the planar distribution of objects in histological sections of brain tissue

This article reviews the statistical methods that have been used to study the planar distribution, and especially clustering, of objects in histological sections of brain tissue. The objective of these studies is usually quantitative description, comparison between patients or correlation between histological features. Objects of interest such as neurones, glial cells, blood vessels or pathological features such as protein deposits appear as sectional profiles in a two-dimensional section. These objects may not be randomly distributed within the section but exhibit a spatial pattern, a departure from randomness either towards regularity or clustering. The methods described include simple tests of whether the planar distribution of a histological feature departs significantly from randomness using randomized points, lines or sample fields and more complex methods that employ grids or transects of contiguous fields, and which can detect the intensity of aggregation and the sizes, distribution and spacing of clusters. The usefulness of these methods in understanding the pathogenesis of neurodegenerative diseases such as Alzheimer's disease and Creutzfeldt-Jakob disease is discussed. © 2006 The Royal Microscopical Society.

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.

Burning questions, but no burning answers: collocation and idiomaticity

The attention of linguists has increasingly shifted from grammar to lexis. Collocation has emerged as a key feature of lexis. Research using large language corpora has not only helped to identify the significant collocates of individual words but also to confirm the importance of collocation in the language system. John Sinclair has suggested that language operates on two principles: open choice and idiom. If so, then collocation would appear to be the minimal level of idiomaticity. One problem with collocation is that words that habitually co-occur form less distinct, often discontinuous, idiomatic units, whereas grammar generally works with more precisely delineated and contiguous structural units. This paper uses examples from corpus evidence to look at various aspects of collocation.

The SEF14 fimbrial antigen of Salmonella enterica serovar Enteritidis is encoded within a pathogenicity islet

The DNA sequence of the chromosomal gene cluster encoding the SEF14 fimbriae of Salmonella enterica serovar Enteritidis was determined. Five contiguous open reading frames, sefABCDE, were identified. The sefE gene shared significant homology with araC-like positive regulators. Serovar-associated virulence plasmid (SAP) genes orf7,8,9 and pefI were identified immediately adjacent to the sef operon. The pefI gene encoded a putative regulator of the Plasmid-encoded fimbrial antigen (PEF) expression. The entire sef--pef region, flanked by two IS-like elements, was inserted adjacent to leuX that encoded a transfer RNA molecule. The organisation of this region was suggestive of a classic pathogenicity islet. Southern hybridisation confirmed two copies of the SAP derived orf7,8,9 and pefI region in S. Enteritidis, one in the chromosome and one on the SAP. Of other group D Salmonella, only S. Blegdam and S. Moscow harboured both chromosomal and plasmid copies of pefI--orf9 region although polymorphism was evident.

Analysis of spatial patterns in histological sections of brain tissue using a method based on regression

A method of determining the spatial pattern of any histological feature in sections of brain tissue which can be measured quantitatively is described and compared with a previously described method. A measurement of a histological feature such as density, area, amount or load is obtained for a series of contiguous sample fields. The regression coefficient (β) is calculated from the measurements taken in pairs, first in pairs of adjacent samples and then in pairs of samples taken at increasing degrees of separation between them, i.e. separated by 2, 3, 4,..., n units. A plot of β versus the degree of separation between the pairs of sample fields reveals whether the histological feature is distributed randomly, uniformly or in clusters. If the feature is clustered, the analysis determines whether the clusters are randomly or regularly distributed, the mean size of the clusters and the spacing of the clusters. The method is simple to apply and interpret and is illustrated using simulated data and studies of the spatial patterns of blood vessels in the cerebral cortex of normal brain, the degree of vacuolation of the cortex in patients with Creutzfeldt-Jacob disease (CJD) and the characteristic lesions present in Alzheimer's disease (AD). Copyright (C) 2000 Elsevier Science B.V.

Analysis of spatial patterns in histological sections of brain tissue

A method is described which enables the spatial pattern of discrete objects in histological sections of brain tissue to be determined. The method can be applied to cell bodies, sections of blood vessels or the characteristic lesions which develop in the brain of patients with neurodegenerative disorders. The density of the histological feature under study is measured in a series of contiguous sample fields arranged in a grid or transect. Data from adjacent sample fields are added together to provide density data for larger field sizes. A plot of the variance/mean ratio (V/M) of the data versus field size reveals whether the objects are distributed randomly, uniformly or in clusters. If the objects are clustered, the analysis determines whether the clusters are randomly or regularly distributed and the mean size of the clusters. In addition, if two different histological features are clustered, the analysis can determine whether their clusters are in phase, out of phase or unrelated to each other. To illustrate the method, the spatial patterns of senile plaques and neurofibrillary tangles were studied in histological sections of brain tissue from patients with Alzheimer's disease.

Measuring the degree of spatial correlation between pathological lesions in Alzheimer's disease

The pathological lesions characteristic of Alzheimer's disease (AD), viz., senile plaques (SP) and neurofibrillary tangles (NFT) may not be randomly distributed with reference to each other but exhibit a degree of sptial association or correlation, information on the degree of association between SP and NFT or between the lesions and normal histological features, such as neuronal perikarya and blood vessels, may be valuable in elucidating the pathogenesis of AD. This article reviews the statistical methods available for studying the degree of spatial association in histological sections of AD tissue. These include tests of interspecific association between two or more histological features using chi-square contingency tables, measurement of 'complete' and 'absolute' association, and more complex methods that use grids of contiguous samples. In addition, analyses of association using correlation matrices and stepwise multiple regression methods are described. The advantages and limitations of each method are reviewed and possible future developments discussed.

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.

Business cycles, long waves, and company langevity in Birmingham area metal industries 1780-1980

This doctoral thesis originates from an observational incongruence between the perennial aims and aspirations of economic endeavour and actually recorded outcomes, which frequently seem contrary to those intended and of a recurrent, cyclical type. The research hypothesizes parallel movement between unstable business environments through time, as expressed by periodically fluctuating levels of economic activity, and the precipitation rates of industrial production companies. A major problem arose from the need to provide theoretical and empirical cohesion from the conflicting, partial and fragmented interpretations of several hundred historians and economists, without which the research question would remain unanswerable. An attempt to discover a master cycle, or superimposition theorem, failed, but was replaced by minute analysis of both the concept of cycles and their underlying data-bases. A novel technique of congregational analysis emerged, resulting in an integrated matrix of numerical history. Two centuries of industrial revolution history in England and Wales was then explored and recomposed for the first time in a single account of change, thereby providing a factual basis for the matrix. The accompanying history of the Birmingham area provided the context of research into the failure rates and longevities of firms in the city's staple metal industries. Sample specific results are obtained for company longevities in the Birmingham area. Some novel presentational forms are deployed for results of a postal questionnaire to surviving firms. Practical demonstration of the new index of national economic activity (INEA) in relation to company insolvencies leads to conclusions and suggestions for further applications of research into the tempo of change, substantial Appendices support the thesis and provide a compendium of information covering immediately contiguous domains.

Antitumour imidazotetrazines: probes for the major groove of DNA

The antitumour imidazotetrazinones are believed to act as prodrugs for the triazene series of alkylating agents, showing a marked pteference for the alkylation of the middle guanine residue in a run of three or more contiguous guanines. However, the. exact nature of the interactions of imidazotetrazinones within the micro~environment of DNA are; as yet unknown. In order to examine such interactions a three pronged approach involving molecular modelling, synthetic chemistry and biological analysis has been undertaken during the course of this project. . Molecular modelling studies have shown that for the 8-carboxamido substituted imidazotetrazinones antitumour activity is dependent upon the. presence of a free NH group which can be involved in the formation of both intramolecular and intermolecular hydrogen bonds, and the presence of a non-bulky substituent with a small negative potential . volume. Modelling studies involving the docking of .mitozolomide into the major groove of DNA in the region of a triguanine sequence has shown that a number of hydrogen bonding interactions are feasible. A series of 8-substituted carboxamide derivatives of mitozolomide have been synthesised via the 8-acid chloride and 8-carboxylic acid derivatives including a number of peptide analogues. The peptide derivatives were based upon the key structural features of the helix-turn-helix motif of DNA-binding proteins with a view to developing agents that are capable of binding to DNA with greater selectivity. An examination of the importance of intramolecular hydrogen bonding in influencing the antitumour activity:of :the imidazotetrazinones has led to the synthesis of the novel pyrimido[4',5' :4,3]pyrazolo[5,1-d]-1,2,3,5-tetrazine ring system. In general, in vitro cytotoxicity assays showed that the new derivatives were less active against the TLX5 lymphoma cell line. than the parent compound mitozolomide despite an increased potential for hydrogen bonding interactions. Due to the high reactivity of the: tetrazinone ring system it is difficult to study the interactions between the imidazotetrazinones and DNA. Consequently a number of structural analogues that are stable under physiological conditions have been. prepared based upon the 1,2,3 triazin-4(3H)-one ring system fused with both benzene and pyrazole rings. Although the 3-methylbenzotriazinones failed to antagonise the cytotoxic activity of temozolomide encouraging results with a 3-methylpyrazolotriazinone may suggest the existence of an imidazotetrazinone receptor site within DNA. The potential of guanine rich sequences to promote the alkylating selectivity of imidazotetrazinones by acting as a catalyst for ring cleavage and thereby generation of the alkylating agent was examined. Experiments involving the monitoring: of the rate of breakdown of mitozolomide incubated in the presence of synthetic oIigonucleotides did not reveal any catalytic effect resulting from the DNA. However, it was noted that the breakdown of mitozolomide was dependent upon the type of buffer used in the incubations and this may indeed mask any catalysis by the oligonucleotides.

Contrast summation across eyes and space is revealed along the entire dipper function by a "Swiss cheese" stimulus.

Previous contrast discrimination experiments have shown that luminance contrast is summed across ocular (T. S. Meese, M. A. Georgeson, & D. H. Baker, 2006) and spatial (T. S. Meese & R. J. Summers, 2007) dimensions at threshold and above. However, is this process sufficiently general to operate across the conjunction of eyes and space? Here we used a "Swiss cheese" stimulus where the blurred "holes" in sine-wave carriers were of equal area to the blurred target ("cheese") regions. The locations of the target regions in the monocular image pairs were interdigitated across eyes such that their binocular sum was a uniform grating. When pedestal contrasts were above threshold, the monocular neural images contained strong evidence that the high-contrast regions in the two eyes did not overlap. Nevertheless, sensitivity to dual contrast increments (i.e., to contrast increments in different locations in the two eyes) was a factor of ∼1.7 greater than to single increments (i.e., increments in a single eye), comparable with conventional binocular summation. This provides evidence for a contiguous area summation process that operates at all contrasts and is influenced little, if at all, by eye of origin. A three-stage model of contrast gain control fitted the results and possessed the properties of ocularity invariance and area invariance owing to its cascade of normalization stages. The implications for a population code for pattern size are discussed.

The development of the visual system in pre-term infants as assessed by electrophysiological techniques

In an endeavour to provide further insight into the maturation of the human visual system, the contiguous development of the pattern reversal VEP, flash VEP and flash ERG was studied in a group of neurologically normal pre-term infants, born between 28 and 35 weeks gestation. Maturational changes were observed in all the evoked electrophysiological responses recorded, these were mainly characterised by an increase in the complexity of the waveform and a shortening in the latency of the response. Initially the ERG was seen to consist of a broad b-wave only, with the a-wave emerging at an average age of 40 weeks PMA. The a-wave showed only a slight reduction in latency and a modest increase in amplitude as the infant grows older, whereas the changes seen in the ERG b-wave were much more dramatic. Pattern reversal VEPs were successfully recorded for the first time during the pre-term period. Flash VEPs were also recorded for comparison. The neonatal pattern reversal VEP consistently showed a major positive component (P1) of long latency. As the infant grew older, the latency of the P1 component decreased and was found to be negatively correlated with PMA at recording. The appearance of the N1 and N2 components became more frequent as the infant matured. The majority of infants were found to be myopic at birth and refractive error was correlated with PMA, with emmetropisation occurring at about 45 weeks PMA. The pattern reversal VEP in response to 2o checks was apparently unaffected by refractive error.

A multivariate spatial analysis of vowel formants in American English

This paper presents the results of a multivariate spatial analysis of 38 vowel formant variables in the language of 402 informants from 236 cities from across the contiguous United States, based on the acoustic data from the Atlas of North American English (Labov, Ash & Boberg, 2006). The results of the analysis both confirm and challenge the results of the Atlas. Most notably, while the analysis identifies similar patterns as the Atlas in the West and the Southeast, the analysis finds that the Midwest and the Northeast are distinct dialect regions that are considerably stronger than the traditional Midland and Northern dialect region indentified in the Atlas. The analysis also finds evidence that a western vowel shift is actively shaping the language of the Western United States.

Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through next generation sequencing

We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR) in antibody fragment libraries and next generation sequencing (NGS) analysis of their quality and diversity.