Bridging experiments, models and simulations : an integrative approach to validation in computational cardiac electrophysiology

Computational models in physiology often integrate functional and structural information from a large range of spatio-temporal scales from the ionic to the whole organ level. Their sophistication raises both expectations and scepticism concerning how computational methods can improve our understanding of living organisms and also how they can reduce, replace and refine animal experiments. A fundamental requirement to fulfil these expectations and achieve the full potential of computational physiology is a clear understanding of what models represent and how they can be validated. The present study aims at informing strategies for validation by elucidating the complex interrelations between experiments, models and simulations in cardiac electrophysiology. We describe the processes, data and knowledge involved in the construction of whole ventricular multiscale models of cardiac electrophysiology. Our analysis reveals that models, simulations, and experiments are intertwined, in an assemblage that is a system itself, namely the model-simulation-experiment (MSE) system. Validation must therefore take into account the complex interplay between models, simulations and experiments. Key points for developing strategies for validation are: 1) understanding sources of bio-variability is crucial to the comparison between simulation and experimental results; 2) robustness of techniques and tools is a pre-requisite to conducting physiological investigations using the MSE system; 3) definition and adoption of standards facilitates interoperability of experiments, models and simulations; 4) physiological validation must be understood as an iterative process that defines the specific aspects of electrophysiology the MSE system targets, and is driven by advancements in experimental and computational methods and the combination of both.

A computational model for BMP movement in sea urchin embryos

Bone morphogen proteins (BMPs) are distributed along a dorsal-ventral (DV) gradient in many developing embryos. The spatial distribution of this signaling ligand is critical for correct DV axis specification. In various species, BMP expression is spatially localized, and BMP gradient formation relies on BMP transport, which in turn requires interactions with the extracellular proteins Short gastrulation/Chordin (Chd) and Twisted gastrulation (Tsg). These binding interactions promote BMP movement and concomitantly inhibit BMP signaling. The protease Tolloid (Tld) cleaves Chd, which releases BMP from the complex and permits it to bind the BMP receptor and signal. In sea urchin embryos, BMP is produced in the ventral ectoderm, but signals in the dorsal ectoderm. The transport of BMP from the ventral ectoderm to the dorsal ectoderm in sea urchin embryos is not understood. Therefore, using information from a series of experiments, we adapt the mathematical model of Mizutani et al. (2005) and embed it as the reaction part of a one-dimensional reaction–diffusion model. We use it to study aspects of this transport process in sea urchin embryos. We demonstrate that the receptor-bound BMP concentration exhibits dorsally centered peaks of the same type as those observed experimentally when the ternary transport complex (Chd-Tsg-BMP) forms relatively quickly and BMP receptor binding is relatively slow. Similarly, dorsally centered peaks are created when the diffusivities of BMP, Chd, and Chd-Tsg are relatively low and that of Chd-Tsg-BMP is relatively high, and the model dynamics also suggest that Tld is a principal regulator of the system. At the end of this paper, we briefly compare the observed dynamics in the sea urchin model to a version that applies to the fly embryo, and we find that the same conditions can account for BMP transport in the two types of embryos only if Tld levels are reduced in sea urchin compared to fly.

Biceps femoris long-head architecture: A reliability and retrospective injury study

Purpose: To determine i) the reliability of two-dimensional ultrasonography for the assessment of biceps femoris long head (BFlh) architectural characteristics; ii) if limbs with a history of strain injury in the BFlh display different architecture and eccentric strength compared to uninjured limbs. Methods: This case-control study (control [n=20], injured group [n=16], males) assessed the BFlh architecture at rest and during graded isometric contractions using two-dimensional ultrasonography. The control group were assessed three times (>24hrs apart) to determine reliability. Previously injured individuals were evaluated once. Results The assessment of BFlh architecture was highly reliable (intraclass correlations >0.90). Fascicle length (p<0.001; d range: 0.67 to 1.34) and fascicle length relative to muscle thickness (p<0.001; d range: 0.58 to 0.85) of the previously injured BFlh were significantly less than the contralateral uninjured BFlh at all intensities. Pennation angle of the previously injured BFlh was significantly greater (p<0.001; d range: 0.62 to 0.88) than the contralateral uninjured BFlh at all intensities. Eccentric strength in the previously injured limb was significantly lower than the contralateral limb (-15.4%; -52.5N; 95% CI=-28.45 to -76.23; p<0.001, d=0.56). Conclusion These data indicate that two-dimensional ultrasonography is reliable for assessing BFlh architecture at rest and during graded isometric contractions. Fascicle length, fascicle length relative to muscle thickness and pennation angle are significantly different in previously injured BFlh compared to an uninjured contralateral BFlh. Eccentric strength of the previously injured limb is also significantly lower than the uninjured contralateral limb. These findings have implications for rehabilitation and injury prevention practices which should consider altered architectural characteristics.

In pursuit of an architecture realism

The noble idea of studying seminal works to ‘see what we can learn’ has turned in the 1990s into ‘let’s see what we can take’ and in the last decade a more toxic derivative ‘what else can’t we take’. That is my observation as a student of architecture in the 1990s, and as a practitioner in the 2000s. In 2010, the sense that something is ending is clear. The next generation is rising and their gaze has shifted. The idea of classification (as a means of separation) was previously rejected by a generation of Postmodernists; the usefulness of difference declined. It’s there in the presence of plurality in the resulting architecture, a decision to mine history and seize in a willful manner. This is a process of looking back but never forward. It has been a mono-culture of absorption. The mono-culture rejected the pursuit of the realistic. It is a blanket suffocating all practice of architecture in this country from the mercantile to the intellectual. Independent reviews of Australia’s recent contributions to the Venice Architecture Biennales confirm the malaise. The next generation is beginning to reconsider classification as a means of unification. By acknowledging the characteristics of competing forces it is possible to bring them into a state of tension. Seeking a beautiful contrast is a means to a new end. In the political setting, this is described by Noel Pearson as the radical centre[1]. The concept transcends the political and in its most essential form is a cultural phenomenon. It resists the compromised position and suggests that we can look back while looking forward. The radical centre is the only demonstrated opportunity where it is possible to pursue a realistic architecture. A realistic architecture in Australia may be partially resolved by addressing our anxiety of permanence. Farrelly’s built desires[2] and Markham’s ritual demonstrations[3] are two ways into understanding the broader spectrum of permanence. But I think they are downstream of our core problem. Our problem, as architects, is that we are yet to come to terms with this place. Some call it landscape others call it country. Australian cities were laid out on what was mistaken for a blank canvas. On some occasions there was the consideration of the landscape when it presented insurmountable physical obstacles. The architecture since has continued to work on its piece of a constantly blank canvas. Even more ironic is the commercial awards programs that represent a claim within this framework but at best can only establish a dialogue within itself. This is a closed system unable to look forward. It is said that Melbourne is the most European city in the southern hemisphere but what is really being described there is the limitation of a senseless grid. After all, if Dutch landscape informs Dutch architecture why can’t the Australian landscape inform Australian architecture? To do that, we would have to acknowledge our moribund grasp of the meaning of the Australian landscape. Or more precisely what Indigenes call Country[4]. This is a complex notion and there are different ways into it. Country is experienced and understood through the senses and seared into memory. If one begins design at that starting point it is not unreasonable to think we can arrive at an end point that is a counter trajectory to where we have taken ourselves. A recent studio with Masters students confirmed this. Start by finding Country and it would be impossible to end up with a building looking like an Aboriginal man’s face. To date architecture in Australia has overwhelmingly ignored Country on the back of terra nullius. It can’t seem to get past the picturesque. Why is it so hard? The art world came to terms with this challenge, so too did the legal establishment, even the political scene headed into new waters. It would be easy to blame the budgets of commerce or the constraints of program or even the pressure of success. But that is too easy. Those factors are in fact the kind of limitations that opportunities grow out of. The past decade of economic plenty has, for the most part, smothered the idea that our capitals might enable civic settings or an architecture that is able to looks past lot line boundaries in a dignified manner. The denied opportunities of these settings to be prompted by the Country they occupy is criminal. The public realm is arrested in its development because we refuse to accept Country as a spatial condition. What we seem to be able to embrace is literal and symbolic gestures usually taking the form of a trumped up art installations. All talk – no action. To continue to leave the public realm to the stewardship of mercantile interests is like embracing derivative lending after the global financial crisis.Herein rests an argument for why we need a resourced Government Architect’s office operating not as an isolated lobbyist for business but as a steward of the public realm for both the past and the future. New South Wales is the leading model with Queensland close behind. That is not to say both do not have flaws but current calls for their cessation on the grounds of design parity poorly mask commercial self interest. In Queensland, lobbyists are heavily regulated now with an aim to ensure integrity and accountability. In essence, what I am speaking of will not be found in Reconciliation Action Plans that double as business plans, or the mining of Aboriginal culture for the next marketing gimmick, or even discussions around how to make buildings more ‘Aboriginal’. It will come from the next generation who reject the noxious mono-culture of absorption and embrace a counter trajectory to pursue an architecture of realism.

Dataset validation within big data security architecture

In recent years, increasing focus has been made on making good business decisions utilizing the product of data analysis. With the advent of the Big Data phenomenon, this is even more apparent than ever before. But the question is how can organizations trust decisions made on the basis of results obtained from analysis of untrusted data? Assurances and trust that data and datasets that inform these decisions have not been tainted by outside agency. This study will propose enabling the authentication of datasets specifically by the extension of the RESTful architectural scheme to include authentication parameters while operating within a larger holistic security framework architecture or model compliant to legislation.

Thermal conductivity of configurable two-dimensional carbon nanotube architecture and strain modulation

We reported the thermal conductivity of the two-dimensional carbon nanotube (CNT)-based architecture, which can be constructed through welding of single-wall CNTs by electron beam. Using large-scale nonequilibrium molecular dynamics simulations, the thermal conductivity is found to vary with different junction types due to their different phonon scatterings at the junction. The strong length and strain dependence of the thermal conductivity suggests an effective avenue to tune the thermal transport properties of the CNT-based architecture, benefiting the design of nanoscale thermal rectifiers or phonon engineering.

DIY media architecture: Open and participatory approaches to community engagement

Media architecture’s combination of the digital and the physical can trigger, enhance, and amplify urban experiences. In this paper, we examine how to bring about and foster more open and participatory approaches to engage communities through media architecture by identifying novel ways to put some of the creative process into the hands of laypeople. We review technical, spatial, and social aspects of DIY phenomena with a view to better understand maker cultures, communities, and practices. We synthesise our findings and ask if and how media architects as a community of practice can encourage the ‘open-sourcing’ of information and tools allowing laypeople to not only participate but become active instigators of change in their own right. We argue that enabling true DIY practices in media architecture may increase citizen control. Seeking design strategies that foster DIY approaches, we propose five areas for further work and investigation. The paper begs many questions indicating ample room for further research into DIY Media Architecture.

Figuras de Espaço na Arquitectura de um Vazio [Figures of space in the architecture of a void]

This text discusses the production of space as performance, space as the architecture of a void in relation to Fernanda Fragateiro's art work 'Caixa para Guardar o Vazio'

High efficiency quantum dot-sensitised solar cells by material science and device architecture

This thesis studied cadmium sulfide and cadmium selenide quantum dots and their performance as light absorbers in quantum dot-sensitised solar cells. This research has made contributions to the understanding of size dependent photodegradation, passivation and particle growth mechanism of cadmium sulfide quantum dots using SILAR method and the role of ZnSe shell coatings on solar cell performance improvement.

Manuel Aires Mateus : an architecture for the art of life [曼努埃尔·艾利斯·马特乌斯：建筑，为了生活的艺术]

This text is the outcome of a conversation with Manuel Aires Mateus (Aires Mateus Arquitectos) and discusses the importance of architecture and memory in contemporary architectural productions

A critical realist perspective of Enterprise Architecture evolution : conditioning and outcomes

This paper investigates how Enterprise Architecture (EA) evolves due to emerging trends. It specifically explores how EA integrates the Service-oriented Architecture (SOA). Archer’s Morphogenetic theory is used as an analytical approach to distinguish the architectural conditions under which SOA is introduced, to study the relationships between these conditions and SOA introduction, and to reflect on EA evolution (elaborations) that then take place. The paper focuses on reasons for why EA evolution could take place, or not and what architectural changes could happen due to SOA integration. The research builds on sound theoretical foundations to discuss EA evolution in a field that often lacks a solid theoretical groundwork. Specifically, it proposes that critical realism, using the morphogenetic theory, can provide a useful theoretical foundation to study enterprise architecture (EA) evolution. The initial results of a literature review (a-priori model) were extended using explorative interviews. The findings of this study are threefold. First, there are five different levels of EA-SOA integration outcomes. Second, a mature EA, flexible and well-defined EA framework and comprehensive objectives of EA improve the integration outcomes. Third, the analytical separation using Archer’s theory is helpful in order to understand how these different integration outcomes are generated.

Aesthetics of urban media façades

This paper sets out to develop and extend current literature on design practices for ambient media façades. It does this by bringing together theories of ambient media, computational aesthetics, and urban aesthetics. This unique theoretical combination has informed the design of several exemplars produced by the author, which are discussed as case studies.

Easy data, hard data : the politics and pragmatics of Twitter research after the computational turn

In this chapter, we draw out the relevant themes from a range of critical scholarship from the small body of digital media and software studies work that has focused on the politics of Twitter data and the sociotechnical means by which access is regulated. We highlight in particular the contested relationships between social media research (in both academic and non-academic contexts) and the data wholesale, retail, and analytics industries that feed on them. In the second major section of the chapter we discuss in detail the pragmatic edge of these politics in terms of what kinds of scientific research is and is not possible in the current political economy of Twitter data access. Finally, at the end of the chapter we return to the much broader implications of these issues for the politics of knowledge, demonstrating how the apparently microscopic level of how the Twitter API mediates access to Twitter data actually inscribes and influences the macro level of the global political economy of science itself, through re-inscribing institutional and traditional disciplinary privilege We conclude with some speculations about future developments in data rights and data philanthropy that may at least mitigate some of these negative impacts.