Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

Knowledge management for enterprise systems: observations from small, medium and large organizations

Anecdotal evidence suggests that the lifecycle-wide management of Enterprise System (ES) related knowledge is critical for ES health and longevity. At a time where many ES-vendors now offering solutions to Small and Medium size organizations, this paper investigates the ability of Small and Medium size organizations to maintain a lifecycle-wide knowledge management strategy. The paper explores the alleged differences in the knowledge management practices across 27 small, medium and large organizations that had implemented a market-leading ES. Results suggest that: (1) despite similar knowledge creation efforts in all three organizational sizes, small organizations struggle with retaining, transferring and applying the knowledge. The study also reveals that, (2) the overall goodness of the knowledge management process in larger organizations remains higher than their small and medium counterparts.

Least-squares congealing for large numbers of images

In this paper we pursue the task of aligning an ensemble of images in an unsupervised manner. This task has been commonly referred to as “congealing” in literature. A form of congealing, using a least-squares criteria, has been recently demonstrated to have desirable properties over conventional congealing. Least-squares congealing can be viewed as an extension of the Lucas & Kanade (LK)image alignment algorithm. It is well understood that the alignment performance for the LK algorithm, when aligning a single image with another, is theoretically and empirically equivalent for additive and compositional warps. In this paper we: (i) demonstrate that this equivalence does not hold for the extended case of congealing, (ii) characterize the inherent drawbacks associated with least-squares congealing when dealing with large numbers of images, and (iii) propose a novel method for circumventing these limitations through the application of an inverse-compositional strategy that maintains the attractive properties of the original method while being able to handle very large numbers of images.

The contribution of leadership attributes to large scale, complex project success

Mismanagement of large-scale, complex projects has resulted in spectacular failures, cost overruns, time blowouts, and stakeholder dissatisfaction. We focus discussion on the interaction of key management and leadership attributes which facilitate leaders’ adaptive behaviors. These behaviors should in turn influence adaptive team member behavior, stakeholder engagement and successful project outcomes, outputs and impacts. An understanding of this type of management will benefit from a perspective based in managerial and organizational cognition. The research question we explore is whether successful leaders of large-scale complex projects have an internal process leading to a display of administrative, adaptive, and enabling behaviors that foster adaptive processes and enabling behaviors within their teams and with external stakeholders. At the core of the model we propose interactions of key attributes, namely cognitive flexibility, affect, and emotional intelligence. The result of these cognitive-affective attribute interactions is leadership leading to enhanced likelihood of complex project success.

Towards an automatic system for road lane marking extraction in large-scale aerial images acquired over rural areas by hierarchical image analysis and Gabor filter

An automatic approach to road lane marking extraction from high-resolution aerial images is proposed, which can automatically detect the road surfaces in rural areas based on hierarchical image analysis. The procedure is facilitated by the road centrelines obtained from low-resolution images. The lane markings are further extracted on the generated road surfaces with 2D Gabor filters. The proposed method is applied on the aerial images of the Bruce Highway around Gympie, Queensland. Evaluation of the generated road surfaces and lane markings using four representative test fields has validated the proposed method.

Room ventilation and the risk of airborne infection transmission in three health care settings within a large teaching hospital

Background: Room ventilation is a key determinant of airborne disease transmission. Despite this, ventilation guidelines in hospitals are not founded on robust scientific evidence related to prevention of airborne transmission. Methods: We sought to assess the effect of ventilation rates on influenza, tuberculosis (TB) and rhinovirus infection risk within three distinct rooms in a major urban hospital; a Lung Function Laboratory, Emergency Department (ED) Negative-pressure Isolation Room and an Outpatient Consultation Room were investigated. Air exchange rate measurements were performed in each room using CO2 as a tracer. Gammaitoni and Nucci’s model was employed to estimate infection risk. Results: Current outdoor air exchange rates in the Lung Function Laboratory and ED Isolation Room limited infection risks to between 0.1 and 3.6%. Influenza risk for individuals entering an Outpatient Consultation Room after an infectious individual departed ranged from 3.6 to 20.7%, depending on the duration for which each person occupied the room. Conclusions: Given the absence of definitive ventilation guidelines for hospitals, air exchange measurements combined with modelling afford a useful means of assessing, on a case-by-case basis, the suitability of room ventilation at preventing airborne disease transmission.

Evaluating automatic road detection across a large aerial imagery collection

The automated extraction of roads from aerial imagery can be of value for tasks including mapping, surveillance and change detection. Unfortunately, there are no public databases or standard evaluation protocols for evaluating these techniques. Many techniques are further hindered by a reliance on manual initialisation, making large scale application of the techniques impractical. In this paper, we present a public database and evaluation protocol for the evaluation of road extraction algorithms, and propose an improved automatic seed finding technique to initialise road extraction, based on a combination of geometric and colour features.

Tissue engineering bone - reconstruction of critical sized segmental bone defects in a large animal model

Currently, well established clinical therapeutic approaches for bone reconstruction are restricted to the transplantation of autografts and allografts, and the implantation of metal devices or ceramic-based implants to assist bone regeneration. Bone grafts possess osteoconductive and osteoinductive properties, their application, however, is associated with disadvantages. These include limited access and availability, donor site morbidity and haemorrhage, increased risk of infection, and insufficient transplant integration. As a result, recent research focuses on the development of complementary therapeutic concepts. The field of tissue engineering has emerged as an important alternative approach to bone regeneration. Tissue engineering unites aspects of cellular biology, biomechanical engineering, biomaterial sciences and trauma and orthopaedic surgery. To obtain approval by regulatory bodies for these novel therapeutic concepts the level of therapeutic benefit must be demonstrated rigorously in well characterized, clinically relevant animal models. Therefore, in this PhD project, a reproducible and clinically relevant, ovine, critically sized, high load bearing, tibial defect model was established and characterized as a prerequisite to assess the regenerative potential of a novel treatment concept in vivo involving a medical grade polycaprolactone and tricalciumphosphate based composite scaffold and recombinant human bone morphogenetic proteins.

Managing large collections of business process models - Current techniques and challenges

Nowadays, business process management is an important approach for managing organizations from an operational perspective. As a consequence, it is common to see organizations develop collections of hundreds or even thousands of business process models. Such large collections of process models bring new challenges and provide new opportunities, as the knowledge that they encapsulate requires to be properly managed. Therefore, a variety of techniques for managing large collections of business process models is being developed. The goal of this paper is to provide an overview of the management techniques that currently exist, as well as the open research challenges that they pose.

Using turning technologies to engage tutors and facilitate effective marking and moderation in large classes

Audience Response Systems (ARS) have been successfully used by academics to facilitate student learning and engagement, particularly in large lecture settings. However, in large core subjects a key challenge is not only to engage students, but also to engage large and diverse teaching teams in order to ensure a consistent approach to grading assessments. This paper provides an insight into the ways in which ARS can be used to encourage participation by tutors in marking and moderation meetings. It concludes that ARS can improve the consistency of grading and the quality of feedback provided to students.

When the shoe doesn't quite fit: Regulating large commercial airports with expanding roles

Airports, whether publicly or privately owned or operated fill both public and private roles. They need to act as public infrastructure providers and as businesses which cover their operating costs. That leads to special governance concerns with respect to consumers and competitors which are only beginning to be addressed. These challenges are highlighted both by shifts in ownership status and by the expansion of roles performed by airports as passenger and cargo volumes continue to increase and as nearby urban areas expand outward towards airports. We survey five ways in which the regulatory shoe doesn‟t quite fit the needs. Our findings suggest that, while ad hoc measures limit political tension, new governance measures are needed.

Screening to identify large truck potential blackspots : methodological issues and concerns

1. Overview of hotspot identification (HSID)methods 2. Challenges with HSID 3. Bringing crash severity into the ‘mix’ 4. Case Study: Truck Involved Crashes in Arizona 5. Conclusions • Heavy duty trucks have different performance envelopes than passenger cars and have more difficulty weaving, accelerating, and braking • Passenger vehicles have extremely limited sight distance around trucks • Lane and shoulder widths affect truck crash risk more than passenger cars • Using PDOEs to model truck crashes results in a different set of locations to examine for possible engineering and behavioral problems • PDOE models point to higher societal cost locations, whereas frequency models point to higher crash frequency locations • PDOE models are less sensitive to unreported crashes • PDOE models are a great complement to existing practice

Using technology to facilitate grading consistency in large classes

University classes in marketing are often large, and therefore require teams of teachers to cover all of the necessary activities. A major problem with teaching teams is the inconsistency that results from myriad individuals offering subjective opinions. This innovation uses the latest moderation techniques along with Audience Response Technology (ART) to enhance the learning experience by providing more consistent and reliable grading in large classes. Assessment items are moderated before they are graded in meetings that employ ART. Results show the process is effective when the teaching team is very large, or there is a diverse range of experienced and inexperienced teachers. This “behind the scenes” innovation is not immediately apparent to students, but results in more consistent grades, more useful feedback for students, and more confident graders.

Ocular surface changes with short-term contact lens wear

Contact lenses are a common method for the correction of refractive errors of the eye. While there have been significant advancements in contact lens designs and materials over the past few decades, the lenses still represent a foreign object in the ocular environment and may lead to physiological as well as mechanical effects on the eye. When contact lenses are placed in the eye, the ocular anatomical structures behind and in front of the lenses are directly affected. This thesis presents a series of experiments that investigate the mechanical and physiological effects of the short-term use of contact lenses on anterior and posterior corneal topography, corneal thickness, the eyelids, tarsal conjunctiva and tear film surface quality. The experimental paradigm used in these studies was a repeated measures, cross-over study design where subjects wore various types of contact lenses on different days and the lenses were varied in one or more key parameters (e.g. material or design). Both, old and newer lens materials were investigated, soft and rigid lenses were used, high and low oxygen permeability materials were tested, toric and spherical lens designs were examined, high and low powers and small and large diameter lenses were used in the studies. To establish the natural variability in the ocular measurements used in the studies, each experiment also contained at least one “baseline” day where an identical measurement protocol was followed, with no contact lenses worn. In this way, changes associated with contact lens wear were considered in relation to those changes that occurred naturally during the 8 hour period of the experiment. In the first study, the regional distribution and magnitude of change in corneal thickness and topography was investigated in the anterior and posterior cornea after short-term use of soft contact lenses in 12 young adults using the Pentacam. Four different types of contact lenses (Silicone hydrogel/ Spherical/–3D, Silicone Hydrogel/Spherical/–7D, Silicone Hydrogel/Toric/–3D and HEMA/Toric/–3D) of different materials, designs and powers were worn for 8 hours each, on 4 different days. The natural diurnal changes in corneal thickness and curvature were measured on two separate days before any contact lens wear. Significant diurnal changes in corneal thickness and curvature within the duration of the study were observed and these were taken into consideration for calculating the contact lens induced corneal changes. Corneal thickness changed significantly with lens wear and the greatest corneal swelling was seen with the hydrogel (HEMA) toric lens with a noticeable regional swelling of the cornea beneath the stabilization zones, the thickest regions of the lenses. The anterior corneal surface generally showed a slight flattening with lens wear. All contact lenses resulted in central posterior corneal steepening, which correlated with the relative degree of corneal swelling. The corneal swelling induced by the silicone hydrogel contact lenses was typically less than the natural diurnal thinning of the cornea over this same period (i.e. net thinning). This highlights why it is important to consider the natural diurnal variations in corneal thickness observed from morning to afternoon to accurately interpret contact lens induced corneal swelling. In the second experiment, the relative influence of lenses of different rigidity (polymethyl methacrylate – PMMA, rigid gas permeable – RGP and silicone hydrogel – SiHy) and diameters (9.5, 10.5 and 14.0) on corneal thickness, topography, refractive power and wavefront error were investigated. Four different types of contact lenses (PMMA/9.5, RGP/9.5, RGP/10.5, SiHy/14.0), were worn by 14 young healthy adults for a period of 8 hours on 4 different days. There was a clear association between fluorescein fitting pattern characteristics (i.e. regions of minimum clearance in the fluorescein pattern) and the resulting corneal shape changes. PMMA lenses resulted in significant corneal swelling (more in the centre than periphery) along with anterior corneal steepening and posterior flattening. RGP lenses, on the other hand, caused less corneal swelling (more in the periphery than centre) along with opposite effects on corneal curvature, anterior corneal flattening and posterior steepening. RGP lenses also resulted in a clinically and statistically significant decrease in corneal refractive power (ranging from 0.99 to 0.01 D), large enough to affect vision and require adjustment in the lens power. Wavefront analysis also showed a significant increase in higher order aberrations after PMMA lens wear, which may partly explain previous reports of "spectacle blur" following PMMA lens wear. We further explored corneal curvature, thickness and refractive changes with back surface toric and spherical RGP lenses in a group of 6 subjects with toric corneas. The lenses were worn for 8 hours and measurements were taken before and after lens wear, as in previous experiments. Both lens types caused anterior corneal flattening and a decrease in corneal refractive power but the changes were greater with the spherical lens. The spherical lens also caused a significant decrease in WTR astigmatism (WRT astigmatism defined as major axis within 30 degrees of horizontal). Both the lenses caused slight posterior corneal steepening and corneal swelling, with a greater effect in the periphery compared to the central cornea. Eyelid position, lid-wiper and tarsal conjunctival staining were also measured in Experiment 2 after short-term use of the rigid and SiHy contact lenses. Digital photos of the external eyes were captured for lid position analysis. The lid-wiper region of the marginal conjunctiva was stained using fluorescein and lissamine green dyes and digital photos were graded by an independent masked observer. A grading scale was developed in order to describe the tarsal conjunctival staining. A significant decrease in the palpebral aperture height (blepharoptosis) was found after wearing of PMMA/9.5 and RGP/10.5 lenses. All three rigid contact lenses caused a significant increase in lid-wiper and tarsal staining after 8 hours of lens wear. There was also a significant diurnal increase in tarsal staining, even without contact lens wear. These findings highlight the need for better contact lens edge design to minimise the interactions between the lid and contact lens edge during blinking and more lubricious contact lens surfaces to reduce ocular surface micro-trauma due to friction and for. Tear film surface quality (TFSQ) was measured using a high-speed videokeratoscopy technique in Experiment 2. TFSQ was worse with all the lenses compared to baseline (PMMA/9.5, RGP/9.5, RGP/10.5, and SiHy/14) in the afternoon (after 8 hours) during normal and suppressed blinking conditions. The reduction in TFSQ was similar with all the contact lenses used, irrespective of their material and diameter. An unusual pattern of change in TFSQ in suppressed blinking conditions was also found. The TFSQ with contact lens was found to decrease until a certain time after which it improved to a value even better than the bare eye. This is likely to be due to the tear film drying completely over the surface of the contact lenses. The findings of this study also show that there is still a scope for improvement in contact lens materials in terms of better wettability and hydrophilicity in order to improve TFSQ and patient comfort. These experiments showed that a variety of changes can occur in the anterior eye as a result of the short-term use of a range of commonly used contact lens types. The greatest corneal changes occurred with lenses manufactured from older HEMA and PMMA lens materials, whereas modern SiHy and rigid gas permeable materials caused more subtle changes in corneal shape and thickness. All lenses caused signs of micro-trauma to the eyelid wiper and palpebral conjunctiva, although rigid lenses appeared to cause more significant changes. Tear film surface quality was also significantly reduced with all types of contact lenses. These short-term changes in the anterior eye are potential markers for further long term changes and the relative differences between lens types that we have identified provide an indication of areas of contact lens design and manufacture that warrant further development.

Morphological design control for large-scale city development : a new proposal

Whereas many good examples can be found of the study of urban morphology informing the design of new residential areas in Europe, it is much more difficult to find examples relating to other land uses and outside of Europe. This paper addresses a particular issue, the control and coordination of large and complex development schemes within cities, and, in doing so, considers commercial and mixed-use schemes outside of Europe. It is argued that urban morphology has much to offer for both the design of such development and its implementation over time. Firstly, lessons are drawn from the work of Krier and Rossi in Berlin, the form-based guidance developed in Chelmsford, UK, and the redesign and coordination of the Melrose Arch project in Johannesburg, SA. A recent development at Boggo Road in Brisbane, Australia, is then subjected to a more detailed examination. It is argued that the scheme has been unsatisfactory in terms of both design and implementation. An alternative framework based on historical morphological studies is proposed that would overcome these deficiencies. It is proposed that this points the way to a general approach that could be incorporated within the planning process internationally.