Interpreting scratch assays using pair density dynamics and approximate Bayesian computation

Quantifying the impact of biochemical compounds on collective cell spreading is an essential element of drug design, with various applications including developing treatments for chronic wounds and cancer. Scratch assays are a technically simple and inexpensive method used to study collective cell spreading; however, most previous interpretations of scratch assays are qualitative and do not provide estimates of the cell diffusivity, D, or the cell proliferation rate,l. Estimating D and l is important for investigating the efficacy of a potential treatment and provides insight into the mechanism through which the potential treatment acts. While a few methods for estimating D and l have been proposed, these previous methods lead to point estimates of D and l, and provide no insight into the uncertainty in these estimates. Here, we compare various types of information that can be extracted from images of a scratch assay, and quantify D and l using discrete computational simulations and approximate Bayesian computation. We show that it is possible to robustly recover estimates of D and l from synthetic data, as well as a new set of experimental data. For the first time, our approach also provides a method to estimate the uncertainty in our estimates of D and l. We anticipate that our approach can be generalized to deal with more realistic experimental scenarios in which we are interested in estimating D and l, as well as additional relevant parameters such as the strength of cell-to-cell adhesion or the strength of cell-to-substrate adhesion.

An observational analysis of the impact of board dynamics and directors’ participation on perceived board effectiveness

This study addresses calls for closer examination of board dynamics by offering an inside view of director interactions. Video-observations of three board meetings at each of two Australian corporations matched with director interviews and secondary data reveal distinct patterns of director interactions, their sources of variation and impact on perceived board effectiveness. Our data reveal that director interactions are multi-dimensional and dynamic: while group interactions across agenda items are similar, with a few directors leading the discussion, the contributing directors change across items. Moreover, directors’ inclusiveness and evenness of participation are associated with higher perceptions of board effectiveness. Last, we find that director interactions change with the nature of the items, board climate and board meeting arrangements. The study contributes to the literature by moving beyond the individual-level analysis of directors’ skills or independence, and offering a detailed view of how the joint group and individual dimensions of board dynamics affect board functioning.

eARTh : the dynamics of ontological representation

This Australian Indigenous creactive work and its Treatise promote ways of thinking about practice and research that extend well beyond the current discourse. It invites re-thinking on how research can be practice-led in new ways, and what that might mean for future students. When discussing the challenges of today, this work signifies how "Western Style" thinking and theory is wanting in so many ways. It engages a new dynamic and innovative way of theorising, encouraging future students to apply their full capacity of energy and wisdom. (Extract from examiners' reports.)

A review of pedestrian group dynamics and methodologies in modelling pedestrian group behaviours

Observations conducted by researchers revealed that the group interaction within crowds is a common phenomenon and has great influence on pedestrian behaviour. However, most research currently undertaken by various researchers failed to consider the group dynamics when developing pedestrian flow models. This paper presented a critical review of pedestrian models that incorporates group behaviour. Models reviewed in this paper are mainly created by microscopic modelling approaches such as social force, cellular automata, and agent-based method. The purpose of this literature review is to improve the understanding of group dynamics among pedestrians and highlight the need for considering group dynamics when developing pedestrian simulation models.

System dynamics model of the knowledge management process

To effectively manage the challenges being faced by construction organisations in a fast changing business environment, many organisations are attempting to integrate knowledge management (KM) into their business operations. KM activities interact with each other and form a process which receives input from its internal business environment and produces outputs that should be justified by its business performance. This paper aims to provide further understanding on the dynamic nature of the KM process. Through a combination of path analysis and system dynamic simulation, this study found that: 1) an improved business performance enables active KM activities and provide feedback and guidance for formulating learning-based policies; and 2) effective human resource recruitment policies can enlarge the pool of individual knowledge, which lead to a more conducive internal business environment, as well as a higher KM activity level. Consequently, the desired business performance level can be reached within a shorter time frame.

The pattern of coupling dynamics between postural motion, isotonic hand movements and physiological tremor

This study was designed to examine differences in the coupling dynamics between upper limb motion, physiological tremor and whole body postural sway in young healthy adults. Acceleration of the hand and fingers, forearm EMG activity and postural sway data were recorded. Estimation of the degree of bilateral and limb motion-postural sway coupling was determined by cross correlation, coherence and Cross-ApEn analyses. The results of the analysis revealed that, under postural tremor conditions, there was no significant coupling between limbs, muscles or sway across all metrics of coupling. In contrast, performing a rapid alternating flexion/extension movement about the wrist joint (with one or both limbs) resulted in stronger coupling between limb motion and postural sway. These results support the view that, for physiological tremor responses, the control of postural sway is maintained independent to tremor in the upper limb. However, increasing the level of movement about a distal segment of one arm (or both) leads to increased coupling throughout the body. The basis for this increased coupling would appear to be related to the enhanced neural drive to task-specific muscles within the upper limb.

Formation of carbon nanoscrolls from graphene nanoribbons : a molecular dynamics study

Carbon nanoscrolls (CNSs) are one of the carbon-based nanomaterials similar to carbon nanotubes (CNTs) but are not widely studied in spite of their great potential applications. Their practical applications are hindered by the challenging fabrication of the CNSs. A physical approach has been proposed recently to fabricate the CNS by rolling up a monolayer graphene nanoribbon (GNR) around a CNT driven by the interaction energy between them. In this study, we perform extensive molecular dynamics (MD) simulations to investigate the various factors that impact the formation of the CNS from GNR. Our simulation results show that the formation of the CNS is sensitive to the length of the CNT and temperature. When the GNR is functionalized with hydrogen, the formation of the CNS is determined by the density and distribution of the hydrogen atoms. Graphyne, the allotrope of graphene, is inferior to graphene in the formation of the CNS due to the weaker bonds and the associated smaller atom density. The mechanism behind the rolling of GNR into CNS lies in the balance between the GNR–CNT van der Waals (vdW) interactions and the strain energy of GNR. The present work reveals new important insights and provides useful guidelines for the fabrication of the CNS.

Targeting and transport : how microtubules control focal adhesion dynamics

Directional cell migration requires force generation that relies on the coordinated remodeling of interactions with the extracellular matrix (ECM), which is mediated by integrin-based focal adhesions (FAs). Normal FA turnover requires dynamic microtubules, and three members of the diverse group of microtubule plus-end-tracking proteins are principally involved in mediating microtubule interactions with FAs. Microtubules also alter the assembly state of FAs by modulating Rho GTPase signaling, and recent evidence suggests that microtubule-mediated clathrin-dependent and -independent endocytosis regulates FA dynamics. In addition, FA-associated microtubules may provide a polarized microtubule track for localized secretion of matrix metalloproteases (MMPs). Thus, different aspects of the molecular mechanisms by which microtubules control FA turnover in migrating cells are beginning to emerge.

Imaging intracellular protein dynamics by spinning disk confocal microscopy

The palette of fluorescent proteins (FPs) has grown exponentially over the past decade, and as a result, live imaging of cells expressing fluorescently tagged proteins is becoming more and more mainstream. Spinning disk confocal (SDC) microscopy is a high-speed optical sectioning technique and a method of choice to observe and analyze intracellular FP dynamics at high spatial and temporal resolution. In an SDC system, a rapidly rotating pinhole disk generates thousands of points of light that scan the specimen simultaneously, which allows direct capture of the confocal image with low-noise scientific grade-cooled charge-coupled device cameras, and can achieve frame rates of up to 1000 frames per second. In this chapter, we describe important components of a state-of-the-art spinning disk system optimized for live cell microscopy and provide a rationale for specific design choices. We also give guidelines of how other imaging techniques such as total internal reflection microscopy or spatially controlled photoactivation can be coupled with SDC imaging and provide a short protocol on how to generate cell lines stably expressing fluorescently tagged proteins by lentivirus-mediated transduction.

In the right space : exploring the dynamics between design, environment and pedagogy

The environments that we inhabit shape our everyday lives, influencing our behaviors and responses (Manu, 2013). As we enter an immersive phase of education in which physical and digital environments become inseparable, should we reconsider the role and importance of design on pedagogical practice? This paper explores the reciprocal cause and effect of space, technology and pedagogy in shaping the design of educational experiences within Queensland University of Technology's collaborative learning spaces.