Cell invasion with proliferation mechanisms motivated by time-lapse data

Cell invasion involves a population of cells which are motile and proliferative. Traditional discrete models of proliferation involve agents depositing daughter agents on nearest- neighbor lattice sites. Motivated by time-lapse images of cell invasion, we propose and analyze two new discrete proliferation models in the context of an exclusion process with an undirected motility mechanism. These discrete models are related to a family of reaction- diffusion equations and can be used to make predictions over a range of scales appropriate for interpreting experimental data. The new proliferation mechanisms are biologically relevant and mathematically convenient as the continuum-discrete relationship is more robust for the new proliferation mechanisms relative to traditional approaches.

Hydrological consequences of land-cover change: Quantifying the influence of plants on soil moisture with time-lapse electrical resistivity

Electrical resistivity of soils and sediments is strongly influenced by the presence of interstitial water. Taking advantage of this dependency, electrical-resistivity imaging (ERI) can be effectively utilized to estimate subsurface soil-moisture distributions. The ability to obtain spatially extensive data combined with time-lapse measurements provides further opportunities to understand links between land use and climate processes. In natural settings, spatial and temporal changes in temperature and porewater salinity influence the relationship between soil moisture and electrical resistivity. Apart from environmental factors, technical, theoretical, and methodological ambiguities may also interfere with accurate estimation of soil moisture from ERI data. We have examined several of these complicating factors using data from a two-year study at a forest-grassland ecotone, a boundary between neighboring but different plant communities.At this site, temperature variability accounts for approximately 20-45 of resistivity changes from cold winter to warm summer months. Temporal changes in groundwater conductivity (mean=650 S/cm =57.7) and a roughly 100-S/cm spatial difference between the forest and grassland had only a minor influence on the moisture estimates. Significant seasonal fluctuations in temperature and precipitation had negligible influence on the basic measurement errors in data sets. Extracting accurate temporal changes from ERI can be hindered by nonuniqueness of the inversion process and uncertainties related to time-lapse inversion schemes. The accuracy of soil moisture obtained from ERI depends on all of these factors, in addition to empirical parameters that define the petrophysical soil-moisture/resistivity relationship. Many of the complicating factors and modifying variables to accurately quantify soil moisture changes with ERI can be accounted for using field and theoretical principles.

Visualising the 48 hour game making challenge

We have always felt that “something very special” was happening in the 48hr and other similar game jams. This “something” is more than the intensity and challenge of the experience, although this certainly has appeal for the participants. We had an intuition that these intense 48 hour game jams exposed something pertinent to the changing shape of the Australian games industry where we see the demise of the late 20th century large studio - the “Night Elf” model and the growth of the small independent model. There are a large number of wider economic and cultural factors around this evolution but our interest is specifically in the change from “industry” to “creative industry” and the growth of games as a cultural media and art practice. If we are correct in our intuition, then illuminating this something also has important ramifications for those courses which teach game and interaction design and development. Rather than undertake a formal ethno-methodological approach, we decided to track as many of the actors in the event as possible. We documented the experience (Keith Novak’s beautiful B&W photography), the individual and their technology (IOGraph mouse tracking), the teams as a group (Time lapse photography) and movement tracking throughout the whole space (Blue tooth phone tracking). The raw data collected has given us opportunity to start a commentary on the “something special” happening in the 48hr.

Service condition of railroad corridors around the insulated rail joints

Railroad corridors contain large number of Insulated Rail Joints (IRJs) that act as safety critical elements in the circuitries of the signaling and broken rail identification systems. IRJs are regarded as sources of excitation for the passage of loaded wheels leading to high impact forces; these forces in turn cause dips, cross levels and twists to the railroad geometry in close proximity to the sections containing the IRJs in addition to the local damages to the railhead of the IRJs. Therefore, a systematic monitoring of the IRJs in railroad is prudent to mitigate potential risk of their sudden failure (e.g., broken tie plates) under the traffic. This paper presents a simple method of periodic recording of images using time-lapse photography and total station surveying measurements to understand the ongoing deterioration of the IRJs and their surroundings. Over a 500 day period, data were collected to examine the trends in narrowing of the joint gap due to plastic deformation the railhead edges and the dips, cross levels and twists caused to the railroad geometry due to the settlement of ties (sleepers) around the IRJs. The results reflect that the average progressive settlement beneath the IRJs is larger than that under the continuously welded rail, which leads to excessive deviation of railroad profile, cross levels and twists.

Monitoring mesenchymal stem cell cultures using image processing and pattern recognition techniques

Stem cells have attracted tremendous interest in recent times due to their promise in providing innovative new treatments for a great range of currently debilitating diseases. This is due to their potential ability to regenerate and repair damaged tissue, and hence restore lost body function, in a manner beyond the body's usual healing process. Bone marrow-derived mesenchymal stem cells or bone marrow stromal cells are one type of adult stem cells that are of particular interest. Since they are derived from a living human adult donor, they do not have the ethical issues associated with the use of human embryonic stem cells. They are also able to be taken from a patient or other donors with relative ease and then grown readily in the laboratory for clinical application. Despite the attractive properties of bone marrow stromal cells, there is presently no quick and easy way to determine the quality of a sample of such cells. Presently, a sample must be grown for weeks and subject to various time-consuming assays, under the direction of an expert cell biologist, to determine whether it will be useful. Hence there is a great need for innovative new ways to assess the quality of cell cultures for research and potential clinical application. The research presented in this thesis investigates the use of computerised image processing and pattern recognition techniques to provide a quicker and simpler method for the quality assessment of bone marrow stromal cell cultures. In particular, aim of this work is to find out whether it is possible, through the use of image processing and pattern recognition techniques, to predict the growth potential of a culture of human bone marrow stromal cells at early stages, before it is readily apparent to a human observer. With the above aim in mind, a computerised system was developed to classify the quality of bone marrow stromal cell cultures based on phase contrast microscopy images. Our system was trained and tested on mixed images of both healthy and unhealthy bone marrow stromal cell samples taken from three different patients. This system, when presented with 44 previously unseen bone marrow stromal cell culture images, outperformed human experts in the ability to correctly classify healthy and unhealthy cultures. The system correctly classified the health status of an image 88% of the time compared to an average of 72% of the time for human experts. Extensive training and testing of the system on a set of 139 normal sized images and 567 smaller image tiles showed an average performance of 86% and 85% correct classifications, respectively. The contributions of this thesis include demonstrating the applicability and potential of computerised image processing and pattern recognition techniques to the task of quality assessment of bone marrow stromal cell cultures. As part of this system, an image normalisation method has been suggested and a new segmentation algorithm has been developed for locating cell regions of irregularly shaped cells in phase contrast images. Importantly, we have validated the efficacy of both the normalisation and segmentation method, by demonstrating that both methods quantitatively improve the classification performance of subsequent pattern recognition algorithms, in discriminating between cell cultures of differing health status. We have shown that the quality of a cell culture of bone marrow stromal cells may be assessed without the need to either segment individual cells or to use time-lapse imaging. Finally, we have proposed a set of features, that when extracted from the cell regions of segmented input images, can be used to train current state of the art pattern recognition systems to predict the quality of bone marrow stromal cell cultures earlier and more consistently than human experts.

Multimodal and monomodal discourses of marketization in higher education : power, ideology, and the absence of the image

The ubiquity of multimodality in hypermedia environments is undeniable. Bezemer and Kress (2008) have argued that writing has been displaced by image as the central mode for representation. Given the current technical affordances of digital technology and user-friendly interfaces that enable the ease of multimodal design, the conspicuous absence of images in certain domains of cyberspace is deserving of critical analysis. In this presentation, I examine the politics of discourses implicit within hypertextual spaces, drawing textual examples from a higher education website. I critically examine the role of writing and other modes of production used in what Fairclough (1993) refers to as discourses of marketisation in higher education, tracing four pervasive discourses of teaching and learning in the current economy: i) materialization, ii) personalization, iii) technologisation, and iv) commodification (Fairclough, 1999). Each of these arguments is supported by the critical analysis of multimodal texts. The first is a podcast highlighting the new architectonic features of a university learning space. The second is a podcast and transcript of a university Open Day interview with prospective students. The third is a time-lapse video showing the construction of a new science and engineering precinct. These three multimodal texts contrast a final web-based text that exhibits a predominance of writing and the powerful absence or silencing of the image. I connect the weightiness of words and the function of monomodality in the commodification of discourses, and its resistance to the multimodal affordances of web-based technologies, and how this is used to establish particular sets of subject positions and ideologies through which readers are constrained to occupy. Applying principles of critical language study by theorists that include Fairclough, Kress, Lemke, and others whose semiotic analysis of texts focuses on the connections between language, power, and ideology, I demonstrate how the denial of image and the privileging of written words in the multimodality of cyberspace is an ideological effect to accentuate the dominance of the institution.

Reproductive behavioural differences between wild-caught and pond-reared Penaeus monodon prawn broodstock

Ongoing problems exist with the commercial scale domestication of Penaeus monodon. One of the major issues, in terms of reproductive performance, is the low egg hatch rate of eggs from these captive bred prawns. The current study investigated the related issue of mating success. Time lapse video observations were conducted to compare the mating behaviour of pond-reared (domesticated) and wild-caught prawn P. monodon broodstock. Mating success of the pond-reared prawns was found to be low relative to wild-caught. It was determined that both male and female prawns contributed to this low mating rate suggesting both genders were impacted negatively by the domestication process. The causative factors for the low mating success are yet to be determined, however external physical abnormalities and lack of sexual maturity did not appear to play a role. The most notable behavioural difference between wild-caught and domesticated prawns was a reduced level of pursuit behaviour by domesticated males. This and other behavioural differences are discussed in relation to an increasing body of evidence that male prawns respond to sex pheromones produced by receptive females and that males detect these chemical signals in part, via their second antennal flagella. Accordingly we hypothesise that pond-reared (domesticated) females may have a reduced ability to produce or release sex pheromones and males, a reduced ability to detect them when compared to their wild-caught counterparts.

Quantifying alterations in cell migration : tracking fluorescently-tagged migrating cells by FACs and live-imaging

Cell migration is fundamental to many different physiological processes including embryonic development, inflammation and wound healing. Given the range and importance cell migration plays a number of assays have been developed to measure different aspects of cell migration. Here we describe two different methods to analyze cell migration. The first method analyzes the migration of fluorescently tagged cells using Boyden chambers and FACs and the second looks at migration properties using time-lapse microscopy.

Electrical imaging and fluid modeling of convective fingering in a shallow water-table aquifer

Unstable density-driven flow can lead to enhanced solute transport in groundwater. Only recently has the complex fingering pattern associated with free convection been documented in field settings. Electrical resistivity (ER) tomography has been used to capture a snapshot of convective instabilities at a single point in time, but a thorough transient analysis is still lacking in the literature. We present the results of a 2 year experimental study at a shallow aquifer in the United Arab Emirates that was designed to specifically explore the transient nature of free convection. ER tomography data documented the presence of convective fingers following a significant rainfall event. We demonstrate that the complex fingering pattern had completely disappeared a year after the rainfall event. The observation is supported by an analysis of the aquifer halite budget and hydrodynamic modeling of the transient character of the fingering instabilities. Modeling results show that the transient dynamics of the gravitational instabilities (their initial development, infiltration into the underlying lower-density groundwater, and subsequent decay) are in agreement with the timing observed in the time-lapse ER measurements. All experimental observations and modeling results are consistent with the hypothesis that a dense brine that infiltrated into the aquifer from a surficial source was the cause of free convection at this site, and that the finite nature of the dense brine source and dispersive mixing led to the decay of instabilities with time. This study highlights the importance of the transience of free convection phenomena and suggests that these processes are more rapid than was previously understood.

Menstrual effluent induces epithelial-mesenchymal transitions in mesothelial cells

Background Menstrual effluent affects mesothelial cell (MC) morphology. We evaluated whether these changes were consistent with epithelial-mesenchymal transitions (EMT). Methods Monolayer cultures of MC were incubated overnight in conditioned media, prepared from cells isolated form menstrual effluent, with or without kinase and ATP inhibitors. Changes in cell morphology were monitored using time-lapse video microscopy and immunohistochemistry. Effects on the expression of EMT-associated molecules were evaluated using real-time RT-PCR and/or Western blot analysis. Results Incubation in conditioned media disrupted cell-cell contacts, and increased MC motility. The changes were reversible. During the changes the distribution of cytokeratins, fibrillar actin and α-tubulin changed. Sodium azide, an inhibitor of ATP production, and Genistein, a general tyrosine kinase inhibitor, antagonized these effects. Wortmannin, a phosphatidylinositol 3-kinase inhibitor, and SU6656, an Src tyrosine kinase inhibitor, only partially antagonized the effect. The expression of Snail and vimentin was markedly up-regulated, whereas the expression of E-cadherin was decreased and cytokeratins were altered. Conclusions In MC, menstrual effluent initiates a reversible, energy-dependent transition process from an epithelial to a mesenchymal phenotype. Involvement of the (Src) tyrosine kinase signalling pathway and the changes in the expression of cytokeratins, Snail, vimentin and E-cadherin demonstrate that the morphological changes are EMT.

Landform characterization using geophysics—Recent advances, applications, and emerging tools

This paper presents an overview of the strengths and limitations of existing and emerging geophysical tools for landform studies. The objectives are to discuss recent technical developments and to provide a review of relevant recent literature, with a focus on propagating field methods with terrestrial applications. For various methods in this category, including ground-penetrating radar (GPR), electrical resistivity (ER), seismics, and electromagnetic (EM) induction, the technical backgrounds are introduced, followed by section on novel developments relevant to landform characterization. For several decades, GPR has been popular for characterization of the shallow subsurface and in particular sedimentary systems. Novel developments in GPR include the use of multi-offset systems to improve signal-to-noise ratios and data collection efficiency, amongst others, and the increased use of 3D data. Multi-electrode ER systems have become popular in recent years as they allow for relatively fast and detailed mapping. Novel developments include time-lapse monitoring of dynamic processes as well as the use of capacitively-coupled systems for fast, non-invasive surveys. EM induction methods are especially popular for fast mapping of spatial variation, but can also be used to obtain information on the vertical variation in subsurface electrical conductivity. In recent years several examples of the use of plane wave EM for characterization of landforms have been published. Seismic methods for landform characterization include seismic reflection and refraction techniques and the use of surface waves. A recent development is the use of passive sensing approaches. The use of multiple geophysical methods, which can benefit from the sensitivity to different subsurface parameters, is becoming more common. Strategies for coupled and joint inversion of complementary datasets will, once more widely available, benefit the geophysical study of landforms.Three cases studies are presented on the use of electrical and GPR methods for characterization of landforms in the range of meters to 100. s of meters in dimension. In a study of polygonal patterned ground in the Saginaw Lowlands, Michigan, USA, electrical resistivity tomography was used to characterize differences in subsurface texture and water content associated with polygon-swale topography. Also, a sand-filled thermokarst feature was identified using electrical resistivity data. The second example is on the use of constant spread traversing (CST) for characterization of large-scale glaciotectonic deformation in the Ludington Ridge, Michigan. Multiple CST surveys parallel to an ~. 60. m high cliff, where broad (~. 100. m) synclines and narrow clay-rich anticlines are visible, illustrated that at least one of the narrow structures extended inland. A third case study discusses internal structures of an eolian dune on a coastal spit in New Zealand. Both 35 and 200. MHz GPR data, which clearly identified a paleosol and internal sedimentary structures of the dune, were used to improve understanding of the development of the dune, which may shed light on paleo-wind directions.

4D GPR tracking of water infiltration in fractured high-porosity limestone

Three thousand liters of water were infiltrated from a 4 m diameter pond to track flow and transport inside fractured carbonates with 20-40 % porosity. Sixteen time-lapse 3D Ground Penetrating Radar (GPR) surveys with repetition intervals between 2 hrs and 5 days monitored the spreading of the water bulb in the subsurface. Based on local travel time shifts between repeated GPR survey pairs, localized changes of volumetric water content can be related to the processes of wetting, saturation and drainage. Deformation bands consisting of thin sub vertical sheets of crushed grains reduce the magnitude of water content changes but enhance flow in sheet parallel direction. This causes an earlier break through across a stratigraphic boundary compared to porous limestone without deformation bands. This experiment shows how time-lapse 3D GPR or 4D GPR can non-invasively track ongoing flow processes in rock-volumes of over 100 m3.

Tracking Alzheimer's disease

Population-based brain mapping provides great insight into the trajectory of aging and dementia, as well as brain changes that normally occur over the human life span.We describe three novel brain mapping techniques, cortical thickness mapping, tensor-based morphometry (TBM), and hippocampal surface modeling, which offer enormous power for measuring disease progression in drug trials, and shed light on the neuroscience of brain degeneration in Alzheimer's disease (AD) and mild cognitive impairment (MCI).We report the first time-lapse maps of cortical atrophy spreading dynamically in the living brain, based on averaging data from populations of subjects with Alzheimer's disease and normal subjects imaged longitudinally with MRI. These dynamic sequences show a rapidly advancing wave of cortical atrophy sweeping from limbic and temporal cortices into higher-order association and ultimately primary sensorimotor areas, in a pattern that correlates with cognitive decline. A complementary technique, TBM, reveals the 3D profile of atrophic rates, at each point in the brain. A third technique, hippocampal surface modeling, plots the profile of shape alterations across the hippocampal surface. The three techniques provide moderate to highly automated analyses of images, have been validated on hundreds of scans, and are sensitive to clinically relevant changes in individual patients and groups undergoing different drug treatments. We compare time-lapse maps of AD, MCI, and other dementias, correlate these changes with cognition, and relate them to similar time-lapse maps of childhood development, schizophrenia, and HIV-associated brain degeneration. Strengths and weaknesses of these different imaging measures for basic neuroscience and drug trials are discussed.

Mapping cortical change in Alzheimer's disease, brain development, and schizophrenia

This paper describes algorithms that can identify patterns of brain structure and function associated with Alzheimer's disease, schizophrenia, normal aging, and abnormal brain development based on imaging data collected in large human populations. Extraordinary information can be discovered with these techniques: dynamic brain maps reveal how the brain grows in childhood, how it changes in disease, and how it responds to medication. Genetic brain maps can reveal genetic influences on brain structure, shedding light on the nature-nurture debate, and the mechanisms underlying inherited neurobehavioral disorders. Recently, we created time-lapse movies of brain structure for a variety of diseases. These identify complex, shifting patterns of brain structural deficits, revealing where, and at what rate, the path of brain deterioration in illness deviates from normal. Statistical criteria can then identify situations in which these changes are abnormally accelerated, or when medication or other interventions slow them. In this paper, we focus on describing our approaches to map structural changes in the cortex. These methods have already been used to reveal the profile of brain anomalies in studies of dementia, epilepsy, depression, childhood- and adult-onset schizophrenia, bipolar disorder, attention-deficit/hyperactivity disorder, fetal alcohol syndrome, Tourette syndrome, Williams syndrome, and in methamphetamine abusers. Specifically, we describe an image analysis pipeline known as cortical pattern matching that helps compare and pool cortical data over time and across subjects. Statistics are then defined to identify brain structural differences between groups, including localized alterations in cortical thickness, gray matter density (GMD), and asymmetries in cortical organization. Subtle features, not seen in individual brain scans, often emerge when population-based brain data are averaged in this way. Illustrative examples are presented to show the profound effects of development and various diseases on the human cortex. Dynamically spreading waves of gray matter loss are tracked in dementia and schizophrenia, and these sequences are related to normally occurring changes in healthy subjects of various ages.

Time alone

Time Alone is the introductory image to the exhibition Lightsite, which toured Western Australian galleries from February 2006 to November 2007. It is a five-minute-long exposure photographic image captured inside an abandoned building which the author converted into a camera obscura. It depicts an inverted image of the outside environment and the text 'time' - which is constructed by torch-light within the building interior and during the photographic exposure. The image evokes isolation and the temporality of inhabitation within the remote farmlands of the Great Southern Region of Western Australia: the region of focus for all of the twelve works in Lightsite. Indeed the owner of this now-abandoned house passed away and was not found for a week - bringing poignancy to the central theme of this creative work.