Using the canonical modelling approach to simplify the simulation of function in functional-structural plant models

Functional-structural plant models that include detailed mechanistic representation of underlying physiological processes can be expensive to construct and the resulting models can also be extremely complicated. On the other hand, purely empirical models are not able to simulate plant adaptability and response to different conditions. In this paper, we present an intermediate approach to modelling plant function that can simulate plant response without requiring detailed knowledge of underlying physiology. Plant function is modelled using a 'canonical' modelling approach, which uses compartment models with flux functions of a standard mathematical form, while plant structure is modelled using L-systems. Two modelling examples are used to demonstrate that canonical modelling can be used in conjunction with L-systems to create functional-structural plant models where function is represented either in an accurate and descriptive way, or in a more mechanistic and explanatory way. We conclude that canonical modelling provides a useful, flexible and relatively simple approach to modelling plant function at an intermediate level of abstraction.

Resolving the organization of the New World monkey third visual complex: The dorsal extrastriate cortex of the marmoset (Callithrix jacchus)

We tested current hypotheses on the functional organization of the third visual complex, a particularly controversial region of the primate extrastriate cortex. In anatomical experiments, injections of retrograde tracers were placed in the dorsal cortex immediately rostral to the second visual area (V2) of New World monkeys (Callithrix jacchus), revealing the topography of interconnections between the third tier cortex and the primary visual area (V1). The data indicate the presence of a dorsomedial area (DM), which represents the entire upper and lower quadrants of the visual field, and which receives strong, topographically organized projections from the superficial layers of V1. The visuotopic organization and boundaries of DM were confirmed by electrophysiological recordings in the same animals and by architectural characteristics which were distinct from those found in ventral extrastriate cortex rostral to V2. There was no electrophysiological or histological evidence for a transitional area between V2 and DM. In particular, the central representation of the upper quadrant in DM was directly adjacent to the representation of the horizontal meridian that marks the rostral border of V2. The present results argue in favor of the hypothesis that the third visual complex in New World monkeys contains different areas in its dorsal and ventral components: area DM, near the dorsal midline, and a homolog of area 19 of other mammals, located more lateral and ventrally. The characteristics of DM suggest that it may correspond to visual area 6 (V6) of Old World monkeys. (C) 2005 Wiley-Liss, Inc.

The applicability of recurrent neural networks for biological sequence analysis

Selection of machine learning techniques requires a certain sensitivity to the requirements of the problem. In particular, the problem can be made more tractable by deliberately using algorithms that are biased toward solutions of the requisite kind. In this paper, we argue that recurrent neural networks have a natural bias toward a problem domain of which biological sequence analysis tasks are a subset. We use experiments with synthetic data to illustrate this bias. We then demonstrate that this bias can be exploitable using a data set of protein sequences containing several classes of subcellular localization targeting peptides. The results show that, compared with feed forward, recurrent neural networks will generally perform better on sequence analysis tasks. Furthermore, as the patterns within the sequence become more ambiguous, the choice of specific recurrent architecture becomes more critical.

The nomenclature of style: Brutalism, Minimalism, art history and visual style in architecture journals

The naming of styles or movements is a basic mechanism of the architectural journals. The announcement of new tendencies, groups or philosophies, gives a journal its character as ‘news’, and if such terms are taken up in general discourse this demonstrates the prescience of the editor and enhances the repute of the journal. The announcement of phenomenon such as ‘critical regionalism’ or ‘deconstructivism’ referred architectural developments to a context in socio-politics or philosophy, and thus aimed to provide at least an initial resistance to their understanding as the formal styles which they quickly became. A different strategy, or occasion, which this paper will discuss, is where the name of an architectural moment is given in the traditional form of an art historical style. Here the nomenclature of style and a certain attitude to form is introduced as the starting point for a more open ended critical inquiry. Two examples of this strategy will be given. The first is Peter Reyner Banham and the Architecture Review’s promotion of ‘Brutalism’ as an anti-aesthetic which took its conceptual form from early twentieth century art movements, particularly Futurism. The second, identified with Architectural Design in the 1990’s is ‘Minimalism’, a term describing a strand of the visual arts of the 1960’s which can be understood as an attempt to nuance and add seriousness to the present rampant nostalgia for the style of the architecture of the 1960’s.

Specific morphological features predictive for the basal phenotype in grade 3 invasive ductal carcinoma of breast

Aims: Cytokeratin (CK) 14, a myoepithelial marker, is also expressed in a proportion of breast carcinomas. There is evidence that these tumours show a differing metastatic pattern and clinical outcome from other invasive ductal carcinomas (IDCs) and may need different management. Currently, they are not identified in routine practice and no morphological guidelines exist to aid their identification. The aim of this study was to analyse the histological features of CK14+ IDC. Methods and results: A detailed histological review of 453 grade 3 IDCs revealed 88 (19.4%) that expressed CK14. Assessment was made independently by two pathologists using a standardized 'tick-box' proforma covering grade, architectural and cytological features. The results were analysed using logistic regression to identify features that predicted for basal phenotype. Concordance between the two pathologists was fair to good for most parameters (kappa 0.4-0.6). On multiple logistic regression, the basal phenotype was highly significantly associated with the presence of a central scar (P = 0.005), tumour necrosis (P < 0.0001), presence of spindle cells (P = 0.006) or squamous metaplasia (P < 0.0001), high total mitotic count (> 40 per 10 high-power field) (P = 0.0002) and high nuclear-cytoplasmic ratio (P = 0.0002). Conclusions: Specific morphological features are strongly associated with basal-like breast carcinoma. These could be used in routine diagnostic practice to identify this important subset of tumours.

A rapidly evolving secretome builds and patterns a sea shell

Background: Instructions to fabricate mineralized structures with distinct nanoscale architectures, such as seashells and coral and vertebrate skeletons, are encoded in the genomes of a wide variety of animals. In mollusks, the mantle is responsible for the extracellular production of the shell, directing the ordered biomineralization of CaCO3 and the deposition of architectural and color patterns. The evolutionary origins of the ability to synthesize calcified structures across various metazoan taxa remain obscure, with only a small number of protein families identified from molluskan shells. The recent sequencing of a wide range of metazoan genomes coupled with the analysis of gene expression in non-model animals has allowed us to investigate the evolution and process of biomineralization in gastropod mollusks. Results: Here we show that over 25% of the genes expressed in the mantle of the vetigastropod Haliotis asinina encode secreted proteins, indicating that hundreds of proteins are likely to be contributing to shell fabrication and patterning. Almost 85% of the secretome encodes novel proteins; remarkably, only 19% of these have identifiable homologues in the full genome of the patellogastropod Lottia scutum. The spatial expression profiles of mantle genes that belong to the secretome is restricted to discrete mantle zones, with each zone responsible for the fabrication of one of the structural layers of the shell. Patterned expression of a subset of genes along the length of the mantle is indicative of roles in shell ornamentation. For example, Has-sometsuke maps precisely to pigmentation patterns in the shell, providing the first case of a gene product to be involved in molluskan shell pigmentation. We also describe the expression of two novel genes involved in nacre (mother of pearl) deposition. Conclusion: The unexpected complexity and evolvability of this secretome and the modular design of the molluskan mantle enables diversification of shell strength and design, and as such must contribute to the variety of adaptive architectures and colors found in mollusk shells. The composition of this novel mantle-specific secretome suggests that there are significant molecular differences in the ways in which gastropods synthesize their shells.

Oase: Tijdschrift voor Architectuur = Oase: Architecture Journal

In recent years, both architectural historiography and architectural design practice have been characterized by significant shifts. These new perspectives and methodologies did not merely bring about internal changes, but also called into question the boundaries and relations between the two disciplines. This issue of OASE investigates the impact of these changes for both disciplines in a series of dialogues between historians, architects, designers and photographers, exploring themes such as the everyday, the landscape, heritage and visual culture.

Relationships between quality of experience and participation in diverse performance settingshttp://espace.library.uq.edu.au/workflow/edit_metadata.php?id=382160&wfs_id=778

The flow concept describes a model of enjoyment that has relevance for understanding participation and experience across a wide range of activities (Csikszentmihalyi, 1997). The basic premise of the flow concept is that when challenges and skills are simultaneously balanced and extending the individual, a state of total absorption can occur. Research by Jackson and colleagues has examined the utility of the flow concept to understanding participation and performance in sport settings. Recently, Jackson and Eklund have examined flow in a range of performance settings: sport, exercise, dance, creative and performing arts, and music. In this paper, we present descriptive and construct validity data on how participants in these activities experienced flow, as assessed by the recently revised flow scales: The Dispositional Flow Scale-2 (DFS-2) and Flow State Scale-2 (FSS-2) (Jackson & Eklund, 2002). The fmdings will be discussed in relation to the utility of the flow concept to understanding participation across performance settings.

Suit keen renovator: Alternate reality design

Virtual territories and their theme parks are more akin to the physical world of real estate than they might at first appear. The trick in triggering the designer's imagination, is to find a 'nice renovator' (cottage/ house) at a low price, with loads of potential, and by doing it on the cheap to add character, and engage the imagination. Here the designer can construct changes from an imagined space. Vision is more important than how the actual place presents.This work describes a case study involving undergraduate students in the Creative Industries who needed a place to explore, so as to create their own visions and projects. The place had to inspire, trigger engagement, and their imaginations. At the same time it was important that the place did not coerce activity, or distract from the task by confusing tools with task, or architectural navigation with conceptual skills.The solution was an alternate reality.

A reference architecture for instructional educational software

Our extensive research has indicated that high-school teachers are reluctant to make use of existing instructional educational software (Pollard, 2005). Even software developed in a partnership between a teacher and a software engineer is unlikely to be adopted by teachers outside the partnership (Pollard, 2005). In this paper we address these issues directly by adopting a reusable architectural design for instructional educational software which allows easy customisation of software to meet the specific needs of individual teachers. By doing this we will facilitate more teachers regularly using instructional technology within their classrooms. Our domain-specific software architecture, Interface-Activities-Model, was designed specifically to facilitate individual customisation by redefining and restructuring what constitutes an object so that they can be readily reused or extended as required. The key to this architecture is the way in which the software is broken into small generic encapsulated components with minimal domain specific behaviour. The domain specific behaviour is decoupled from the interface and encapsulated in objects which relate to the instructional material through tasks and activities. The domain model is also broken into two distinct models - Application State Model and Domainspecific Data Model. This decoupling and distribution of control gives the software designer enormous flexibility in modifying components without affecting other sections of the design. This paper sets the context of this architecture, describes it in detail, and applies it to an actual application developed to teach high-school mathematical concepts.