PathGrid: a service-orientated architecture for microscopy image analysis.

This paper describes 'PathGrid'--an analysis and data integration system, developed initially to meet the demands in the analysis of medical microscopy imaging data. An overview of the current system is given, describing the techniques used in developing the data handling infrastructure and the analysis algorithm development. The use of software created in the context of systems designed for the astronomy domain is noted, specifically infrastructure from the astronomy virtual observatory movement for data discovery, access and workflow management, and astronomical image analysis software adapted for the analysis of high-throughput astronomy imaging surveys. This paper notes the applicability of the techniques from the astronomy domain. The testbed infrastructure deployment is described, emphasizing its speed and ease of use and support. The validity of the analysis techniques is confirmed through the pilot study described here--with the application to a large sample of immunohistochemistry microscopy data obtained in part for assessing the oestrogen receptor status of breast cancers. The analysis showed that the specificity and sensitivity values for the automatic scoring using PathGrid were within the errors of those obtained via a 'gold standard' manual pathologist scoring.

Scaling the structure--function relationship for clinical perimetry.

PURPOSE: The full ranges of glaucomatous visual field defects and retinal ganglion cell losses extend over several orders of magnitude and therefore an interpretation of the structure-function relationship for clinical perimetry requires scaling of both variables. However, the most appropriate scale has not been determined. The present study was undertaken to compare linear and logarithmic transformations, which have been proposed for correlating the perimetric defects and neural losses of glaucoma. METHODS: Perimetry, by behavioural testing, and retinal histology data were obtained from rhesus monkeys with significant visual field defects caused by experimental glaucoma. Ganglion cell densities were measured in histologic sections of retina that corresponded to specific perimetry test locations for the treated and control eyes. The linear (percentage) and logarithmic (decibel) relationships for sensitivity loss as a function of ganglion cell loss were analysed. RESULTS: With decibel scaling, visual sensitivity losses and ganglion cell densities were linearly correlated with high coefficients of determination (r(2)), although the parameters of the functions varied with eccentricity. The structure-function relationships expressed as linear percentage-loss functions were less systematic in two respects. Firstly, the relationship exhibited considerable scatter in the data for small losses in visual sensitivity and, secondly, visual sensitivity losses became saturated with larger losses in ganglion cell density. The parameters of the percentage-loss functions also varied with eccentricity, but the variation was less than for the decibel-loss functions. CONCLUSIONS: Linear scaling of perimetric defects and ganglion cell losses might potentially improve the structure-function relationship for visual defects associated with small amounts of cell loss, but the usefulness of the relationship is limited because of the high variability in that range. With log--log co-ordinates, the structure--function relationship for clinical perimetry is relatively more accurate and precise for cell losses greater than about 3 dB. The comparatively greater accuracy and precision of decibel loss functions are a likely consequence of the logarithmic scale of stimulus intensities for perimetry measurements and because the relationship between visual sensitivity and the number of neural detectors is a form of probability summation.

Ocular dominance column width and contrast sensitivity in monkeys reared with strabismus or anisometropia.

PURPOSE: To study the relationship between the width of ocular dominance columns in primary visual cortex and spatial contrast sensitivity functions in monkeys with strabismus or anisometropia during infancy. METHODS: Adult monkeys having had monocular visual abnormalities induced in infancy were tested behaviorally for spatial contrast sensitivity and then subjected to functional enucleation of one eye to reveal the ocular dominance columns (ODCs) of the primary visual cortex by cytochrome oxidase (CO) staining. The relative widths of the left and right eyes' ODCs were measured and related to the contrast sensitivity functions. RESULTS: The relative widths of the ODCs having input from eyes with strabismic or anisometropic amblyopia were reduced in proportion to the age of onset and the duration of the early visual abnormality. The relative losses in contrast sensitivity were in ordinal agreement with the losses in relative width of the ODCs. CONCLUSIONS: Amblyopia induced by the early monocular abnormalities of strabismus or anisometropia is proportional to the loss in cortical afference as reflected in the reduction in width of the respective ODCs in the primary visual cortex.

Neural losses correlated with visual losses in clinical perimetry.

PURPOSE: The validity of clinical perimetry for evaluation of the pathology of glaucoma is based on correlated losses in retinal ganglion cells and visual sensitivity, but procedures to quantify neural losses from visual field defects have not been developed. The purpose of the present study was to investigate the neural and sensitivity losses from experimental glaucoma to establish the framework for a quantitative model for the structure-function relationships of standard clinical perimetry. METHODS: Perimetry, by behavioral testing, and retinal histology data were obtained from rhesus monkeys with significant visual field defects caused by experimental glaucoma. Ganglion cell densities were obtained from sections of retina that corresponded to 16 perimetry test locations. Perimetry sensitivity as a function of ganglion cell density at corresponding retina/visual field locations was analyzed. RESULTS: The structure-function relationships were linear on log-log coordinates, with parameters that varied systematically with eccentricity. The slope value varied from 1.25 dB/dB at 4.2 degrees from fixation to a value of 2.32 dB/dB at 24 degrees from fixation, whereas the intercept value varied from -25.2 dB to -55.7 dB over the same range of eccentricities. The structure-function relationships produced a model to predict the ganglion cell density underlying a given level of visual sensitivity and location in the visual field. The model, with no free parameters, produced an accurate and relatively precise quantification of retinal ganglion cell losses caused by experimental glaucoma in monkeys. However, because the early detection of glaucoma is limited by intersubject variability, ganglion cell losses of 40% to 50% were necessary before visual sensitivity losses exceeded the normal 95% confidence limits. CONCLUSIONS: With retinal eccentricity as a factor, the neural losses from glaucoma are predictable from visual sensitivity measurements by clinical perimetry. The relationships derived from experimental glaucoma in monkeys also accurately predict the rate of age-related losses of retinal ganglion cells in humans, based on the normative perimetry data for age-related reductions in visual sensitivity. The success of the model in this study suggested that it is potentially applicable to the clinical interpretation of the state of glaucomatous optic neuropathy.

Vitreal glutamate concentration in monkeys with experimental glaucoma.

PURPOSE: To investigate the hypothesis that the pathophysiology for the death of retinal ganglion cells in glaucoma involves excitotoxic effects from elevated concentrations of vitreal glutamate. METHODS: Experimental glaucoma was induced in the right eyes of 18 rhesus monkeys by argon laser treatments to the trabecular meshwork. After significant visual field defects and/or typical clinical glaucomatous changes had developed (1.5-13 months), the eyes were removed, and a sample (0.1-0.2 mL) of posterior vitreous was collected. Similar vitreous samples also were collected from eight untreated monkeys. The vitreous samples were analyzed in a masked fashion by high-pressure liquid chromatography in two independent laboratories. Mean levels of vitreal glutamate were determined for the treated and control eyes and differences between groups of eyes were evaluated by Student's t-test. RESULTS: The mean level (+/- SD) of vitreal glutamate in the eight untreated monkeys was 5.0 +/- 2.0 microM. A similar level of 5.7 +/- 1.8 microM was measured in the untreated eyes of monkeys with experimental glaucoma. In the glaucomatous eyes, the mean concentration of vitreal glutamate was 5.7 +/- 2.6 microM, which was not significantly different from the concentrations in the control eyes. CONCLUSIONS: Vitreal glutamate concentrations were not elevated in eyes with anatomic and functional damage from experimental glaucoma. This finding is in contradiction to previous reports that vitreal glutamate increases to toxic levels and probably contributes to glaucomatous damage of retinal ganglion cells.

Effects of hearing protectors on auditory localization in azimuth and elevation.

An experiment was conducted to determine the effects of two types of hearing protectors on auditory localization performance. Six listeners localized a 750-ms broadband noise from loudspeakers ranging in azimuth from -180 degrees to +180 degrees and in elevation from -75 degrees to +90 degrees. Independent variables included the type of hearing protector and the elevation of the source. Dependent measures included azimuth error, elevation error, and the percentage of trials resulting in a front-back confusion. Performance on each of the dependent measures was found to be mediated by one or more of the independent variables. Actual or potential applications include the generation of improved design guidelines for hearing protectors and workplace alarms.

Effects of CIC hearing aids on auditory localization by listeners with normal hearing.

An experiment was conducted to determine the effects of completely-in-the-canal (CIC) hearing aids on auditory localization performance. Six normal-hearing listeners localized a 750-ms broadband noise from loudspeakers ranging in azimuth from -180 degrees to +180 degrees and in elevation from -75 degrees to +90 degrees. Independent variables included the presence or absence of the hearing aid and the elevation of the source. Dependent measures included azimuth error, elevation error, and the percentage of trials resulting in a front-back confusion. The findings indicate a statistically significant decrement in localization acuity, both in azimuth and elevation, occasioned by the wearing of CIC hearing aids. However, the magnitude of this decrement was small compared to those typically caused by other ear-canal occlusions, such as earplugs, and would probably not engender mislocalization of real-world sounds.

Female voice communications in high levels of aircraft cockpit noises--Part I: spectra, levels, and microphones.

HYPOTHESIS: Female produced speech, although more intelligible than male speech in some noise spectra, may be more vulnerable to degradation by high levels of some military aircraft cockpit noises. The acoustic features of female speech are higher in frequency, lower in power, and appear more susceptible than male speech to masking by some of these military noises. Current military aircraft voice communication systems were optimized for the male voice and may not adequately accommodate the female voice in these high level noises. METHODS: This applied study investigated the intelligibility of female and male speech produced in the noise spectra of four military aircraft cockpits at levels ranging from 95 dB to 115 dB. The experimental subjects used standard flight helmets and headsets, noise-canceling microphones, and military aircraft voice communications systems during the measurements. RESULTS: The intelligibility of female speech was lower than that of male speech for all experimental conditions; however, differences were small and insignificant except at the highest levels of the cockpit noises. Intelligibility for both genders varied with aircraft noise spectrum and level. Speech intelligibility of both genders was acceptable during normal cruise noises of all four aircraft, but improvements are required in the higher levels of noise created during aircraft maximum operating conditions. CONCLUSIONS: The intelligibility of female speech was unacceptable at the highest measured noise level of 115 dB and may constitute a problem for other military aviators. The intelligibility degradation due to the noise can be neutralized by use of an available, improved noise-canceling microphone, by the application of current active noise reduction technology to the personal communication equipment, and by the development of a voice communications system to accommodate the speech produced by both female and male aviators.

Fourier transform infrared spectroscopy of dysplastic, papillomavirus-positive cervicovaginal lavage specimens.

To assess the utility of a new, rapid, economical procedure that may prove valuable in cervical screening, Fourier transform infrared (ir) spectroscopy was performed on 25 cervicovaginal lavage specimens from women referred for colposcopy on the basis of a cytological abnormality detected on their Pap smear and whose lavage specimen was positive for human papillomavirus. Of the 18 classed as CIN I or less by histopathology, 11 showed band frequencies that deviated only slightly from spectra that characterize normal cervical cells and 3 of 5 "atypia" specimens had spectra identical to normal. Two of 3 classed as CIN II had spectra only slightly more abnormal to these 11. In the case of 2 graded as CIN I, several bands were similarly altered in the direction of the pattern seen for 4 CIN III specimens. A further CIN I sample gave a spectrum that was even further shifted toward the latter and the remaining CIN I sample had a pattern that matched the 4 CIN IIIs. The most obvious change in each of the CIN IIIs was an additional peak at 972 cm-1 and this has been suggested as a key indicator for malignancy. One of the 3 CIN IIs had this peak. Other characteristic spectral changes were seen as well in the CIN III samples. High-risk HPV18 was present in 3 of the CIN III samples, as well as in one specimen classed as atypia, but having an abnormal ir spectrum. Low-risk HPV 6 or 11 was seen along in samples with a normal or slightly abnormal ir spectrum, but never in those that showed an ir pattern that was abnormal. The current study has therefore shown complete concordance between ir spectral findings and histopathology result in the case of CIN III specimens, but less precise matching for other grades of CIN. The spectral differences revealed by ir spectroscopy are likely to characterize molecular abnormalities in cervical cells during progression to cancer and may therefore have potential in assisting with clinical decision making. More studies will, however, be required to establish the place of this technique in cervical screening.

Identification and characterization of the human lactoferrin-binding protein from Neisseria meningitidis.

Lactoferrin-binding activity in Neisseria meningitidis was detected by a solid-phase binding assay with horseradish peroxidase-conjugated human lactoferrin (HRP-lactoferrin). Expression of lactoferrin-binding activity was regulated by the level of iron in the medium, so that growth in the presence of the iron chelator EDDA (ethylenediamine di-ortho-hydroxyphenylacetic acid) resulted in a greater than 350-fold increase in binding activity, which was reversed by addition of excess iron. A maximal level of expression could be obtained at reasonable culture densities by using either intermediate levels of EDDA or high levels of EDDA and moderate levels of complexed iron sources such as hemoglobin and transferrin. Competition binding assays demonstrated that the binding of lactoferrin was specific for human lactoferrin in that neither bovine lactoferrin, human transferrin, nor human hemoglobin was able to block binding of HRP-lactoferrin. The binding specificity for human lactoferrin correlated with growth studies in which human but not bovine lactoferrin could support the growth of iron-starved cells. Binding of lactoferrin was not dependent on its level of iron saturation, since iron-saturated lactoferrin and apolactoferrin were equally effective at blocking binding of HRP-lactoferrin in competitive binding assays. The lactoferrin-binding protein was identified as a 105,000-molecular-weight iron-regulated outer membrane protein in three different meningococcal strains by a batch affinity method with biotinylated human lactoferrin and streptavidin-agarose.

Identification and characterization of the transferrin receptor from Neisseria meningitidis.

Expression of the meningococcal transferrin receptor, detected by assay with human transferrin conjugated to peroxidase, was regulated by the level of iron in the medium. The transferrin receptor was identified by SDS-PAGE and Western blot analysis, as a 71,000 molecular weight iron-regulated outer membrane protein in Neisseria meningitidis B16B6. Growth studies with iron-deficient cells and competition binding experiments demonstrated that the meningococcal receptor was species-specific for human transferrin. Reciprocal competitive binding experiments and limited proteolysis of intact cells indicated that the transferrin and lactoferrin receptors are distinct.

The delta 5 and delta 6 desaturation of fatty acids of varying chain length by rat liver: a preliminary report.

The delta 6 desaturase of rat liver can accommodate substrates with a wide range of chain length. delta 9-cis, 12-cis-Dienoic acids of chain lengths 14-22 carbon atoms were all desaturated at the delta 6 position by microsmal preparations from rat liver. By contrast, the delta 5 desaturase appeared much more chain-length sensitive. The percentage delta 5 desaturation of a series of delta 8-cis- and delta 9-trans-monoenoic acids increased with increasing chain length (from C16 to C20).

Desaturation of positional and geometric isomers of monoenoic fatty acids by microsomal preparations from rat liver.

A range of cis- and trans-monoenoic fatty acids was tested as substrates for desaturation in microsomal preparations from rat liver. Trans-monoenoic acids were generally desaturated in the delta 9 position to the same extent as stearic acid. Acids with delta 7-trans- and delta 11-trans-olefinic unsaturation produced delta 7-trans, 9-cis- and delta 9-cis, 11-trans-conjugated dienoic acids, respectively, but the delta 8-trans-and delta 10-trans-monoenoic acids did not give delta 8,9- or delta 9,10-allenes. Of the cis-monoenoic acids examined, only those with double bonds at or beyond the delta 14 position gave any measurable delta 9 desaturation. When delta 9 desaturation of long chain saturated acids was inhibited by adding sterculic acid, these saturated acids were desaturated at the delta 5 and delta 6 positions. Many of the monoenoic acids tested were also desaturated at the delta 5 and/or delta 6 positions, although the percentage conversions were always low. delta 9-cis, 11-trans-, delta 9-cis, 12-trans- and delta 9-cis, 13-trans-dienoic acids, produced in situ by delta 9 desaturation of the corresponding monoenoic acids, were extensively desaturated in the delta 6 position. These results are discussed in terms of: (a) the various models proposed to explain the substrate specificities of the desaturases, and (b) the metabolism of unnatural fatty acids ingested from dietary sources.

Cystic fibrosis: making a correct and early diagnosis.

Cystic fibrosis is detected with increasing frequency in older children, adolescents, and even young adults. The quality of life and longevity in patients with cystic fibrosis is more favorable the earlier a diagnosis is made and a therapeutic regimen begun. This report presents and reviews five cases in chich the diagnosis of cystic fibrosis was made after the age of six years. Emphasis is placed on the variability of presenting signs and symptoms and the problems that can arise in confirming a suspected diagnosis of cystic fibrosis.