An analytical tool that quantifies cellular morphology changes from three-dimensional fluorescence images

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for inclusion and exclusion of data points, and computer-aided pattern recognition to support the interpretation and findings of the analysis. It has become increasingly important to be able to measure fluorescence images constructed from three-dimensional (3D) datasets in order to be able to capture the complexity of cellular dynamics and understand the basis of cellular plasticity within biological systems. Sophisticated microscopy instruments have permitted the visualization of 3D fluorescence images through the acquisition of multispectral fluorescence images and powerful analytical software that reconstructs the images from confocal stacks that then provide a 3D representation of the collected 2D images. Advanced design-based stereology methods have progressed from the approximation and assumptions of the original model-based stereology(1) even in complex tissue sections(2). Despite these scientific advances in microscopy, a need remains for an automated analytic method that fully exploits the intrinsic 3D data to allow for the analysis and quantification of the complex changes in cell morphology, protein localization and receptor trafficking. Current techniques available to quantify fluorescence images include Meta-Morph (Molecular Devices, Sunnyvale, CA) and Image J (NIH) which provide manual analysis. Imaris (Andor Technology, Belfast, Northern Ireland) software provides the feature MeasurementPro, which allows the manual creation of measurement points that can be placed in a volume image or drawn on a series of 2D slices to create a 3D object. This method is useful for single-click point measurements to measure a line distance between two objects or to create a polygon that encloses a region of interest, but it is difficult to apply to complex cellular network structures. Filament Tracer (Andor) allows automatic detection of the 3D neuronal filament-like however, this module has been developed to measure defined structures such as neurons, which are comprised of dendrites, axons and spines (tree-like structure). This module has been ingeniously utilized to make morphological measurements to non-neuronal cells(3), however, the output data provide information of an extended cellular network by using a software that depends on a defined cell shape rather than being an amorphous-shaped cellular model. To overcome the issue of analyzing amorphous-shaped cells and making the software more suitable to a biological application, Imaris developed Imaris Cell. This was a scientific project with the Eidgenössische Technische Hochschule, which has been developed to calculate the relationship between cells and organelles. While the software enables the detection of biological constraints, by forcing one nucleus per cell and using cell membranes to segment cells, it cannot be utilized to analyze fluorescence data that are not continuous because ideally it builds cell surface without void spaces. To our knowledge, at present no user-modifiable automated approach that provides morphometric information from 3D fluorescence images has been developed that achieves cellular spatial information of an undefined shape (Figure 1). We have developed an analytical platform using the Imaris core software module and Imaris XT interfaced to MATLAB (Mat Works, Inc.). These tools allow the 3D measurement of cells without a pre-defined shape and with inconsistent fluorescence network components. Furthermore, this method will allow researchers who have extended expertise in biological systems, but not familiarity to computer applications, to perform quantification of morphological changes in cell dynamics.

Are you telling the truth? Psychopathy assessment and impression management in a community sample

Objectives: Researchers have suggested that approximately 1% of individuals within the community have psychopathic tendencies (Neumann and Hare, 2008), although confirmatory evidence is scant. Design: The current study aimed to extend previous research beyond university student samples to explore the effect of impression management and self-deception on the identification of psychopathic traits. Methods: A non-incarcerated community sample comprising of 300 adults completed the Self-Reported Psychopathy scale – version 3 (SRP-III; Paulhus, Hemphill & Hare, in press) as well as the Paulhus Deception Scales (PDS; Paulhus, 1998). Results: Results indicated that at least 1% of the current community sample had clear psychopathic tendencies, and that such tendencies were found in younger males who mis-used alcohol. Conclusions: Importantly, individuals with psychopathic traits did not present with an inflated propensity to distort assessment responses, which provides support for future research endeavours that aim to conduct larger-scale psychopathy assessments within the community. This paper further outlines the study implications in regards to the practical assessment of psychopathy.

Optimal image sample size for corneal nerve morphometry

Purpose Arbitrary numbers of corneal confocal microscopy images have been used for analysis of corneal subbasal nerve parameters under the implicit assumption that these are a representative sample of the central corneal nerve plexus. The purpose of this study is to present a technique for quantifying the number of random central corneal images required to achieve an acceptable level of accuracy in the measurement of corneal nerve fiber length and branch density. Methods Every possible combination of 2 to 16 images (where 16 was deemed the true mean) of the central corneal subbasal nerve plexus, not overlapping by more than 20%, were assessed for nerve fiber length and branch density in 20 subjects with type 2 diabetes and varying degrees of functional nerve deficit. Mean ratios were calculated to allow comparisons between and within subjects. Results In assessing nerve branch density, eight randomly chosen images not overlapping by more than 20% produced an average that was within 30% of the true mean 95% of the time. A similar sampling strategy of five images was 13% within the true mean 80% of the time for corneal nerve fiber length. Conclusions The “sample combination analysis” presented here can be used to determine the sample size required for a desired level of accuracy of quantification of corneal subbasal nerve parameters. This technique may have applications in other biological sampling studies.

A practical signal processing approach for condition monitoring of low speed machinery using Peak-Hold-Down-Sample algorithm

A simple and effective down-sample algorithm, Peak-Hold-Down-Sample (PHDS) algorithm is developed in this paper to enable a rapid and efficient data transfer in remote condition monitoring applications. The algorithm is particularly useful for high frequency Condition Monitoring (CM) techniques, and for low speed machine applications since the combination of the high sampling frequency and low rotating speed will generally lead to large unwieldy data size. The effectiveness of the algorithm was evaluated and tested on four sets of data in the study. One set of the data was extracted from the condition monitoring signal of a practical industry application. Another set of data was acquired from a low speed machine test rig in the laboratory. The other two sets of data were computer simulated bearing defect signals having either a single or multiple bearing defects. The results disclose that the PHDS algorithm can substantially reduce the size of data while preserving the critical bearing defect information for all the data sets used in this work even when a large down-sample ratio was used (i.e., 500 times down-sampled). In contrast, the down-sample process using existing normal down-sample technique in signal processing eliminates the useful and critical information such as bearing defect frequencies in a signal when the same down-sample ratio was employed. Noise and artificial frequency components were also induced by the normal down-sample technique, thus limits its usefulness for machine condition monitoring applications.

Factor analysis of the Self Report Version of the Strengths and Difficulties Questionnaire in a sample of children with intellectual disability

The rate of emotional and behavioral disturbance in children with intellectual disability (ID) is up to four times higher than that of their typically developing peers. It is important to identify these difficulties in children with ID as early as possible to prevent the chronic co-morbidity of ID and psychopathology. Children with ID have traditionally been assessed via proxy reporting, but appropriate and psychometrically rigorous instruments are needed so that children can report on their own emotions and behaviors. In this study, the factor structure of the self-report version of the Strengths and Difficulties Questionnaire (SDQ) was examined in a population of 128 children with ID (mean age = 12 years). Exploratory and Confirmatory Factor Analysis showed a three factor model (comprising Positive Relationships, Negative Behavior and Emotional Competence) to be a better measure than the original five factor SDQ model in this population.

Using optical coherence tomography to assess corneoscleral morphology after soft contact lens wear

Purpose. To evaluate the use of optical coherence tomography (OCT) to assess the effect of different soft contact lenses on corneoscleral morphology. Methods. Ten subjects had anterior segment OCT B-scans taken in the morning and again after six hours of soft contact lens wear. For each subject, three different contact lenses were used in the right eye on non-consecutive days, including a hydrogel sphere, a silicone hydrogel sphere and a silicone hydrogel toric. After image registration and layer segmentation, analyses were performed of the first hyper-reflective layer (HRL), the epithelial basement membrane (EBL) and the epithelial thickness (HRL to EBL). A root mean square difference (RMSD) of the layer profiles and the thickness change between the morning and afternoon measurements, was used to assess the effect of the contact lens on the corneoscleral morphology. Results. The soft contact lenses had a statistically significant effect on the morphology of the anterior segment layers (p <0.001). The average amounts of change for the three lenses (average RMSD values) for the corneal region were lower (3.93±1.95 µm for the HRL and 4.02±2.14 µm for the EBL) than those measured in the limbal/scleral region (11.24±6.21 µm for the HRL and 12.61±6.42 µm for the EBL). Similarly, averaged across the three lenses, the RMSD in epithelial thickness was lower in the cornea (2.84±0.84 µm) than the limbal/scleral (5.47±1.71 µm) region. Post-hoc analysis showed that ocular surface changes were significantly smaller with the silicone hydrogel sphere lens than both the silicone hydrogel toric (p<0.005) and hydrogel sphere (p<0.02) for the combined HRL and EBL data. Conclusions. In this preliminary study, we have shown that soft contact lenses can produce small but significant changes in the morphology of the limbal/scleral region and that OCT technology is useful in assessing these changes. The clinical significance of these changes is yet to be determined.

Malnutrition in a sample of community-dwelling people with Parkinson’s disease

Objective: Malnutrition results in poor health outcomes, and people with Parkinson’s disease may be more at risk of malnutrition. However, the prevalence of malnutrition in Parkinson’s disease is not yet well defined. The aim of this study is to provide an estimate of the extent of malnutrition in community-dwelling people with Parkinson’s disease. Methods: This is a cross-sectional study of people with Parkinson’s disease residing within a 2 hour driving radius of Brisbane, Australia. The Subjective Global Assessment (SGA) and scored Patient Generated Subjective Global Assessment (PG-SGA) were used to assess nutritional status. Body weight, standing or knee height, mid-arm circumference and waist circumference were measured. Results: Nineteen (15%) of the participants were moderately malnourished (SGA-B). The median PG-SGA score of the SGA-B group was 8 (4 – 15), significantly higher than the SGA-A group, U=1860.5,p<.05. The symptoms most influencing intake were loss of appetite, constipation, early satiety and problems swallowing. Conclusions: As with other populations, malnutrition remains under-recognised and undiagnosed in people with Parkinson’s disease. Regular screening of nutritional status in people with Parkinson’s disease by health professionals with whom they have regular contact should occur to identify those who may benefit from further nutrition assessment and intervention.

Fresh water and acid sensitivity of authigenic clays in sandstone reservoirs

Authigenic illite-smectite and chlorite in reservoir sandstones from several Pacific rim sedimentary basins in Australia and New Zealand have been examined using an Electroscan Environmental Scanning Electron Microscope (ESEM) before, during, and after treatment with fresh water and HCl, respectively. These dynamic experiments are possible in the ESEM because, unlike conventional SEMs that require a high vacuum in the sample chamber (10-6 torr), the ESEM will operate at high pressures up to 20 torr. This means that materials and processes can be examined at high magnifications in their natural states, wet or dry, and over a range of temperatures (-20 to 1000 degrees C) and pressures. Sandstones containing the illite-smectite (60-70% illite interlayers) were flushed with fresh water for periods of up to 12 hours. Close examination of the same illite-smectite lines or filled pores, both before and after freshwater treatments, showed that the morphology of the illite-smectite was not changed by prolonged freshwater treatment. Chlorite-bearing sandstones (Fe-rich chlorite) were reacted with 1M to 10M HCl at temperatures of up to 80 degrees C and for periods of up to 48 hours. Before treatment the chlorites showed typically platy morphologies. After HCl treatment the chlorite grains were coated with an amorphous gel composed of Ca, Cl, and possibly amorphous Si, as determined by EDS analyses on the freshly treated rock surface. Brief washing in water removed this surface coating and revealed apparently unchanged chlorite showing no signs of dissolution or acid attack. However, although the chlorite showed no morphological changes, elemental analysis only detected silicon and oxygen.

Executive function development and stress effects on driving performance : preliminary findings from a young adult sample.

This chapter presents a pilot study examining the interactive contributions of executive function development/impairment and psychosocial stress to young adults’ (17-30 years old) driving behaviour in a simulator city scenario.

The factor structure of the COPE Questionnaire in a sample of clinically depressed and anxious adults

The Coping Orientation to Problems Experienced is a multidimensional scale designed to assess how people respond to stress. The COPE has been validated in a variety of populations displaying variations in factor structure. However, in terms of mental health populations, it has only been validated in alcohol-dependent samples. This paper investigated the factor structure of the COPE in a sample of adults diagnosed with depression and anxiety. Two hundred and seventy-one patients attending cognitive behaviour therapy for anxiety and depression completed the COPE. Confirmatory factor analysis found a poor fit for both lower order and higher order factors based upon the Lyne and Roger (2000) study. Exploratory factor analyses identified six primary subscales (Active Planning, Social Support, Denial, Acceptance, Disengagement, Restraint) which explained approximately 60% of the variance in coping. These 6 subscales may assist researchers and clinicians to validly measure coping in anxious and depressed adults.

Discrimination experienced by HIV/AIDS infected persons and its associations with mental health in an Indian sample

Purpose The purpose of this study was to investigate the nature and prevalence of discrimination against people living with HIV/AIDS in West Bengal, India, and how discrimination is associated with depression, suicidal ideation and suicidal attempts. Method Semi-structured interviews and the Beck Depression Inventory were administered to 105 HIV infected persons recruited by incidental sampling, at an Integrated Counseling and Testing Center (ICTC) and through Networks of People Living with HIV/AIDS, in the West Bengal area. Results Findings showed that 40.8% of the sample has experienced discrimination at least in one social setting – such as family (29.1%), health centers (18.4%), community (17.5%) and workplace (6.8%). About two-fifths (40.8%) reported experiencing discrimination in multiple social settings. Demographic factors associated with discrimination were gender, age, occupation, education, and current residence. More than half of the sample was suffering from severe depression while 8.7% had attempted suicide. Discrimination in most areas was significantly associated with suicidal ideation and suicidal attempts. Conclusions Prevalence of discrimination associated with HIV/AIDS is high in our sample from West Bengal. While discrimination was not associated with depressive symptomatology, discrimination was associated with suicidal ideation and attempts. These findings suggest that there is an urgent need for interventions to reduce discrimination of HIV/AIDS in the West Bengal region.

Teacher Reporting Attitudes Scale (TRAS): confirmatory and exploratory factor analyses with a Malaysian sample.

The Teacher Reporting Attitude Scale (TRAS) is a newly developed tool to assess teachers’ attitudes toward reporting child abuse and neglect. This article reports on an investigation of the factor structure and psychometric properties of the short form Malay version of the TRAS. A self-report cross-sectional survey was conducted with 667 teachers in 14 randomly selected schools in Selangor state, Malaysia. Analyses were conducted in a 3-stage process using both confirmatory (stages 1 and 3) and exploratory factor analyses (stage 2) to test, modify, and confirm the underlying factor structure of the TRAS in a non-Western teacher sample. Confirmatory factor analysis did not support a 3-factor model previously reported in the original TRAS study. Exploratory factor analysis revealed an 8-item, 4-factor structure. Further confirmatory factor analysis demonstrated appropriateness of the 4-factor structure. Reliability estimates for the four factors—commitment, value, concern, and confidence—were moderate. The modified short form TRAS (Malay version) has potential to be used as a simple tool for relatively quick assessment of teachers’ attitudes toward reporting child abuse and neglect. Cross-cultural differences in attitudes toward reporting may exist and the transferability of newly developed instruments to other populations should be evaluated.

Preservice teachers’ perceptions of their middle schooling teacher preparation : a sample of the Australian context

Reviews into teacher education and reform measures, such as implementing professional standards for teachers, are designed to raise the quality of education. Such reviews and reforms also target preservice teachers; hence universities examine their teacher education programs to address these issues, including developing programs that are current with the literature. Over the past fifteen years, concerns have arisen about Australian early adolescents and their disengagement from the schooling system, their “at risk” behaviour and their need for social, emotional and academic support. These concerns have prompted a middle schooling movement in Australia with the literature recognising a need for specialised middle school teachers. As a result, various universities have responded by developing courses specifically designed to graduate teachers who possess the theoretical and pedagogical knowledge for engaging early adolescent learners. This mixed-method study analysed the responses of preservice teachers from three universities across two states in Australia near the completion of their middle years teacher preparation program. The three aims of the study were to: (1) investigate final-year preservice teachers’ perceptions of their confidence to teach in the middle years of schooling; (2) analyse the experiences included in their teacher preparation course that made them feel confident; and (3) describe strategies for enhancing middle schooling teacher education preparation. Data were gathered from final-year preservice teachers (n=142) using a survey that was developed in response to middle schooling literature and the Professional Standards for Queensland Teachers (Queensland College of Teachers, 2006). A questionnaire collected extended information about the participants’ (n=142) experiences that made them feel confident. It also gathered information about strategies for enhancing middle years teacher preparation. One-to-one, 45-minute interviews (n=10) were conducted to elicit in-depth responses aligned with the research aims. Quantitative results indicated that the majority of preservice teachers (n=142) claimed confidence associated with survey items relating to creating a positive classroom environment (range: 70-97%), developing positive relationships for teaching (71-98%), pedagogical knowledge for teaching (72-95%), and implementation of teaching (70-91%). Qualitative findings suggested that the experiences that assisted them to be confident for teaching were practicum and associated field studies coursework, a positive mentor teacher, specifically designed middle years subjects, the pedagogical approaches of university staff, and other real-world experiences such as volunteering in schools and participating in professional development alongside their mentors. This study demonstrated that universities presenting middle years teacher preparation need to consider: the quality of the practicum experience; the suitability of mentor teachers; the significance and practicalities of middle years subjects; university lecturers’ modelling of pedagogical practices; and the inclusion of real-world learning experiences. Although the findings of this study provided evidence as to how preservice teacher confidence for teaching has been influenced by their middle schooling teacher preparation, further research is required to investigate how confidence translates into practice within their first years of teaching.

Morphology-based model for predicting osteocyte-like cell line (MLO-Y4) growth process

This work has led to the development of empirical mathematical models to quantitatively predicate the changes of morphology in osteocyte-like cell lines (MLO-Y4) in culture. MLO-Y4 cells were cultured at low density and the changes in morphology recorded over 11 hours. Cell area and three dimensional shape features including aspect ratio, circularity and solidity were then determined using widely accepted image analysis software (ImageJTM). Based on the data obtained from the imaging analysis, mathematical models were developed using the non-linear regression method. The developed mathematical models accurately predict the morphology of MLO-Y4 cells for different culture times and can, therefore, be used as a reference model for analyzing MLO-Y4 cell morphology changes within various biological/mechanical studies, as necessary.

Combustion products of bulk aluminum rods burning in high pressure oxygen

Characterization of the combustion products released during the burning of commonly used engineering metallic materials may aid in material selection and risk assessment for the design of oxygen systems. The characterization of combustion products in regards to size distribution and morphology gives useful information for systems addressing fire detection. Aluminum rods (3.2-mm diameter cylinders) were vertically mounted inside a combustion chamber and ignited in pressurized oxygen by resistively heating an aluminum/palladium igniter wire attached to the bottom of the test sample. This paper describes the experimental work conducted to establish the particle size distribution and morphology of the resultant combustion products collected after the burning was completed and subsequently analyzed. In general, the combustion products consisted of a re-solidified oxidized slag and many small hollow spheres of size ranging from about 500 nm to 1000 µm in diameter, surfaced with quenched dendritic and grain-like structures. The combustion products were characterized using optical and scanning electron microscopy.