BLAST Atlas : a function based multiple genome browser

BLAST Atlas is a visual analysis system for comparative genomics that supports genome-wide gene characterisation, functional assignment and function-based browsing of one or more chromosomes. Inspired by applications such as the WorldWide Telescope, Bing Maps 3D and Google Earth, BLAST Atlas uses novel three-dimensional gene and function views that provide a highly interactive and intuitive way for scientists to navigate, query and compare gene annotations. The system can be used for gene identification and functional assignment or as a function-based multiple genome comparison tool which complements existing position based comparison and alignment viewers.

Water drinking influences eye length and IOP in young healthy subjects

This study aimed to investigate the influence of water loading upon intraocular pressure (IOP), ocular pulse amplitude (OPA) and axial length. Twenty one young adult subjects who were classified based on their spherical equivalent refraction as either myopes (n=11), or emmetropes (n=10) participated. Measures of IOP, OPA and ocular biometrics were collected before, and then 10, 15, 25 and 30 minutes following the ingestion of 1000 ml of water. Significant increases in both IOP and OPA were found to occur following water loading (p<0.0001), with peaks in both parameters occurring at 10 minutes after water loading (mean ± SEM increase of 2.24 ± 0.31 mmHg in IOP and 0.46 ± 0.06 mmHg in OPA). Axial length was found to reduce significantly following water loading (p=0.0005), with the largest reduction in axial length evident 10 minutes after water drinking (mean decrease 12 ± 3 µm). A significant time by refractive error group interaction (p=0.048) was found in axial length, indicative of a different pattern of change in eye length following water loading between the myopic and emmetropic populations. The largest difference in axial length change was evident at 10 minutes after water loading with a 17 ± 5 µm reduction in axial length evident in the myopes and only a 6 ± 2 µm reduction in the emmetropes. These findings illustrate significant changes in ocular parameters in young adult subjects following water loading.

Predicting dry eye using non-invasive techniques of tear film surface assessment

PURPOSE. To measure tear film surface quality in healthy and dry eye subjects using three noninvasive techniques of tear film quality assessment and to establish the ability of these noninvasive techniques to predict dry eye. METHODS. Thirty four subjects participated in the study, and were classified as dry eye or normal, based on standard clinical assessments. Three non-invasive techniques were applied for measurement of tear film surface quality: dynamic-area high-speed videokeratoscopy (HSV), wavefront sensing (DWS) and lateral shearing interferometry (LSI). The measurements were performed in both natural blinking conditions (NBC) and in suppressed blinking conditions (SBC). RESULTS. In order to investigate the capability of each method to discriminate dry eye subjects from normal subjects, the receiver operating curve (ROC) was calculated and then the area under the curve (AUC) was extracted. The best result was obtained for the LSI technique (AUC=0.80 in SBC and AUC=0.73 in NBC), which was followed by HSV (AUC=0.72 in SBC and AUC=0.71 in NBC). The best result for DWS was AUC=0.64 obtained for changes in vertical coma in suppressed blinking conditions, while for normal blinking conditions the results were poorer. CONCLUSIONS. Non-invasive techniques of tear film surface assessment can be used for predicting dry eye and this can be achieved in natural blinking as well as suppressed blinking conditions. In this study, LSI showed the best detection performance, closely followed by the dynamic-area HSV. The wavefront sensing technique was less powerful, particularly in natural blinking conditions.

Lateral shearing interferometry, dynamic wavefront sensing, and high-speed videokeratoscopy for noninvasive assessment of tear film surface characteristics : a comparitive study

There are several noninvasive techniques for assessing the kinetics of tear film, but no comparative studies have been conducted to evaluate their efficacies. Our aim is to test and compare techniques based on high-speed videokeratoscopy (HSV), dynamic wavefront sensing (DWS), and lateral shearing interferometry (LSI). Algorithms are developed to estimate the tear film build-up time TBLD, and the average tear film surface quality in the stable phase of the interblink interval TFSQAv. Moderate but significant correlations are found between TBLD measured with LSI and DWS based on vertical coma (Pearson's r2=0.34, p<0.01) and higher order rms (r2=0.31, p<0.01), as well as between TFSQAv measured with LSI and HSV (r2=0.35, p<0.01), and between LSI and DWS based on the rms fit error (r2=0.40, p<0.01). No significant correlation is found between HSV and DWS. All three techniques estimate tear film build-up time to be below 2.5 sec, and they achieve a remarkably close median value of 0.7 sec. HSV appears to be the most precise method for measuring tear film surface quality. LSI appears to be the most sensitive method for analyzing tear film build-up.

Regional changes in corneal thickness and shape with soft contact lenses

Purpose: To investigate the influence of soft contact lenses on regional variations in corneal thickness and shape while taking account of natural diurnal variations in these corneal parameters. Methods: Twelve young, healthy subjects wore 4 different types of soft contact lenses on 4 different days. The lenses were of two different materials (silicone hydrogel, hydrogel), designs (spherical, toric) and powers (–3.00, –7.00 D). Corneal thickness and topography measurements were taken before and after 8 hours of lens wear and on two days without lens wear, using the Pentacam HR system. Results: The hydrogel toric contact lens caused the greatest level of corneal thickening in the central (20.3 ± 10.0 microns) as well as peripheral cornea (24.1 ± 9.1 microns) (p < 0.001) with an obvious regional swelling of the cornea beneath the stabilizing zones. The anterior corneal surface generally showed slight flattening. All contact lenses resulted in central posterior corneal steepening and this was weakly correlated with central corneal swelling (p = 0.03) and peripheral corneal swelling (p = 0.01). Conclusions: There was an obvious regional corneal swelling apparent after wear of the hydrogel soft toric lenses, due to the location of the thicker stabilization zones of the toric lenses. However with the exception of the hydrogel toric lens, the magnitude of corneal swelling induced by the contact lenses over the 8 hours of wear was less than the natural diurnal thinning of the cornea over this same period.

Deliberative assessment of surrogate consent in dementia research

Background Research involving incapacitated persons with dementia entails complex scientific, legal, and ethical issues, making traditional surveys of layperson views on the ethics of such research challenging. We therefore assessed the impact of democratic deliberation (DD), involving balanced, detailed education and peer deliberation, on the views of those responsible for persons with dementia. Methods One hundred and seventy-eight community-recruited caregivers or primary decision-makers for persons with dementia were randomly assigned to either an all-day DD session group or a control group. Educational materials used for the DD session were vetted for balance and accuracy by an interdisciplinary advisory panel. We assessed the acceptability of family-surrogate consent for dementia research (“surrogate-based research”) from a societal policy perspective as well as from the more personal perspectives of deciding for a loved one or for oneself (surrogate and self-perspectives), assessed at baseline, immediately post-DD session, and 1 month after DD date, for four research scenarios of varying risk-benefit profiles. Results At baseline, a majority in both the DD and control groups supported a policy of family consent for dementia research in all research scenarios. The support for a policy of family consent for surrogate-based research increased in the DD group, but not in the control group. The change in the DD group was maintained 1 month later. In the DD group, there were transient changes in attitudes from surrogate or self-perspectives. In the control group, there were no changes from baseline in attitude toward surrogate consent from any perspective. Conclusions Intensive, balanced, and accurate education, along with peer deliberation provided by democratic deliberation, led to a sustained increase in support for a societal policy of family consent in dementia research among those responsible for dementia patients.

Geographical information systems : an effective planning and decision-making platform for community health coalitions in Australia

The development of locally-based healthcare initiatives, such as community health coalitions that focus on capacity building programs and multi-faceted responses to long-term health problems, have become an increasingly important part of the public health landscape. As a result of their complexity and the level of investment, it has become necessary to develop innovative ways to help manage these new healthcare approaches. Geographical Information Systems (GIS) have been suggested as one of the innovative approaches that will allow community health coalitions to better manage and plan their activities. The focus of this paper is to provide a commentary on the use of GIS as a tool for community coalitions and discuss some of the potential benefits and issues surrounding the development of these tools.

Panel studies of new venture creation : a review and suggestions for future research

We review all journal articles based on “PSED-type” research, i.e., longitudinal, empirical studies of large probability samples of on-going, business start-up efforts. We conclude that the research stream has yielded interesting findings; sometimes by confirming prior research with a less bias-prone methodology and at other times by challenging whether prior conclusions are valid for the early stages of venture development. Most importantly, the research has addressed new, process-related research questions that prior research has shunned or been unable to study in a rigorous manner. The research has revealed an enormous and fascinating variability in new venture creation that also makes it challenging to arrive at broadly valid generalizations. An analysis of the findings across studies as well as an examination of those studies that have been relatively more successful at explaining outcomes give good guidance regarding what is required in order to achieve strong and credible results. We compile and present such advice to users of existing data sets and designers of new projects in the following areas: Statistically representative and/or theoretically relevant sampling; Level of analysis issues; Dealing with process heterogeneity; Dealing with other heterogeneity issues, and Choice and interpretation of dependent variables.

Pondering policy and parental perspectives : how parents view their role in shaping early childhood public policy

The focus of this paper is the role of Australian parents in early childhood education and care (ECEC), in particular, their role in shaping ECEC public policy. The paper reports the findings of a study investigating the different ways in which a group of parents viewed and experienced this role. Set against a policy backdrop where parents are positioned as 'consumers' and 'participants' in ECEC, the study employed a phenomenographic research approach to describe this role as viewed and experienced by parents. The study identified four logically related, qualitatively different ways of constituting this role among this group of parents, ranging from 'no role in shaping public policy' (the no role conception) to 'participating in policy decision-making, particularly where policy was likely to affect their child and family (the participating in policy decision-making conception). The study provides an insider-perspective on the role of parents in shaping policy and highlights variation in how this role is constituted by parents. The study also identifies factors perceived by parents as influencing their participation and discusses their implications for both policy and practice.

Contracting bubbles in Hele-Shaw cells with a power-law fluid

The problem of bubble contraction in a Hele-Shaw cell is studied for the case in which the surrounding fluid is of power-law type. A small perturbation of the radially symmetric problem is first considered, focussing on the behaviour just before the bubble vanishes, it being found that for shear-thinning fluids the radially symmetric solution is stable, while for shear-thickening fluids the aspect ratio of the bubble boundary increases. The borderline (Newtonian) case considered previously is neutrally stable, the bubble boundary becoming elliptic in shape with the eccentricity of the ellipse depending on the initial data. Further light is shed on the bubble contraction problem by considering a long thin Hele-Shaw cell: for early times the leading-order behaviour is one-dimensional in this limit; however, as the bubble contracts its evolution is ultimately determined by the solution of a Wiener-Hopf problem, the transition between the long-thin limit and the extinction limit in which the bubble vanishes being described by what is in effect a similarity solution of the second kind. This same solution describes the generic (slit-like) extinction behaviour for shear-thickening fluids, the interface profiles that generalise the ellipses that characterise the Newtonian case being constructed by the Wiener-Hopf calculation.

A two-compartment mechanochemical model of the roles of transforming growth factor-beta and tissue tension in dermal wound healing

The repair of dermal tissue is a complex process of interconnected phenomena, where cellular, chemical and mechanical aspects all play a role, both in an autocrine and in a paracrine fashion. Recent experimental results have shown that transforming growth factor-beta (TGF-beta) and tissue mechanics play roles in regulating cell proliferation, differentiation and the production of extracellular materials. We have developed a 1D mathematical model that considers the interaction between the cellular, chemical and mechanical phenomena, allowing the combination of TGF-beta and tissue stress to inform the activation of fibroblasts to myofibroblasts. Additionally, our model incorporates the observed feature of residual stress by considering the changing zero-stress state in the formulation for effective strain. Using this model, we predict that the continued presence of TGF-beta in dermal wounds will produce contractures due to the persistence of myofibroblasts; in contrast, early elimination of TGF-beta significantly reduces the myofibroblast numbers resulting in an increase in wound size. Similar results were obtained by varying the rate at which fibroblasts differentiate to myofibroblasts and by changing the myofibroblast apoptotic rate. Taken together, the implication is that elevated levels of myofibroblasts is the key factor behind wounds healing with excessive contraction, suggesting that clinical strategies which aim to reduce the myofibroblast density may reduce the appearance of contractures.

Modelling cell separation during plant organ abscission

A simple mathematical model is presented to describe the cell separation process that plants undertake in order to deliberately shed organs. The focus here is on modelling the production of the enzyme polygalacturonase, which breaks down pectin that provides natural cell-to-cell adhesion in the localised abscission zone. A coupled system of three ordinary differential equations is given for a single cell, and then extended to hold for a layer of cells in the abscission zone. Simple observations are made based on the results of this preliminary model and, furthermore, a number of opportunities for applied mathematicians to make contributions in this subject area are discussed.

Catch me if you can : the effective service of bankruptcy documents in a changing world

This article discusses some recent judicial decisions to assist legal practitioners to overcome some of the problems encountered when serving Bankruptcy Notices and Creditor’s Petitions. Some of the issues covered in the discussion are: What the valid last-known address of the debtor can be, whether a Bankruptcy Notice can be validly served by email on a debtor who is located outside Australia, whether service of a Bankruptcy Notice is valid when the debtor is outside Australia when service on the debtor occurs in Australia, whether the creditor’s failure to obtain leave for service of a Bankruptcy Notice can be excused, what can be done regarding personal service of a Creditor’s Petition when a debtor is outside Australia and whether the Court can set aside a sequestration order. The article goes on to place the issues in the context of broader bankruptcy policies noting that effective service of bankruptcy documents is challenging in a world where mobility of debtors is global and new modes of communication ever changing.

Models of collective cell spreading with variable cell aspect ratio : a motivation for degenerate diffusion models

Continuum diffusion models are often used to represent the collective motion of cell populations. Most previous studies have simply used linear diffusion to represent collective cell spreading, while others found that degenerate nonlinear diffusion provides a better match to experimental cell density profiles. In the cell modeling literature there is no guidance available with regard to which approach is more appropriate for representing the spreading of cell populations. Furthermore, there is no knowledge of particular experimental measurements that can be made to distinguish between situations where these two models are appropriate. Here we provide a link between individual-based and continuum models using a multi-scale approach in which we analyze the collective motion of a population of interacting agents in a generalized lattice-based exclusion process. For round agents that occupy a single lattice site, we find that the relevant continuum description of the system is a linear diffusion equation, whereas for elongated rod-shaped agents that occupy L adjacent lattice sites we find that the relevant continuum description is connected to the porous media equation (pme). The exponent in the nonlinear diffusivity function is related to the aspect ratio of the agents. Our work provides a physical connection between modeling collective cell spreading and the use of either the linear diffusion equation or the pme to represent cell density profiles. Results suggest that when using continuum models to represent cell population spreading, we should take care to account for variations in the cell aspect ratio because different aspect ratios lead to different continuum models.

Age, muscle fatigue, and walking endurance in pre-menopausal women

Aging is associated with loss of endurance; however, aging is also associated with decreased fatigue during maximal isometric contractions. The aims of this study were to examine the relationship between age and walking endurance (WE) and maximal isometric fatigue (MIF) and to determine which metabolic/fitness components explain the expected age effects on WE and MIF. Subjects were 96 pre-menopausal women. Oxygen uptake (walking economy) was assessed during a 3-mph walk; aerobic capacity and WE by progressive treadmill test; knee extension strength by isometric contractions, MIF during a 90-s isometric plantar flexion (muscle metabolism measured by 31P MRS). Age was related to increased walking economy (low VO2, r = −0.19, P < 0.03) and muscle metabolic economy (force/ATP, 0.34, P = 0.01), and reduced MIF (−0.26, P < 0.03). However, age was associated with reduced WE (−0.28, P < 0.01). Multiple regression showed that muscle metabolic economy explained the age-related decrease in MIF (partial r for MIF and age −0.13, P = 0.35) whereas walking economy did not explain the age-related decrease in WE (partial r for WE and age −0.25, P < 0.02). Inclusion of VO2max and knee endurance strength accounted for the age-related decreased WE (partial r for WE and age = 0.03, P > 0.80). In premenopausal women, age is related to WE and MIF. In addition, these results support the hypothesis that age-related increases in metabolic economy may decrease MIF. However, decreased muscle strength and oxidative capacity are related to WE.