A Mammalian Circadian Clock Model Incorporating Daytime Expression Elements

Models of the mammalian clock have traditionally been based around two feedback loops-the self-repression of Per/Cry by interfering with activation by BMAL/CLOCK, and the repression of Bmal/Clock by the REV-ERB proteins. Recent experimental evidence suggests that the D-box, a transcription factor binding site associated with daytime expression, plays a larger role in clock function than has previously been understood. We present a simplified clock model that highlights the role of the D-box and illustrate an approach for finding maximum-entropy ensembles of model parameters, given experimentally imposed constraints. Parameter variability can be mitigated using prior probability distributions derived from genome-wide studies of cellular kinetics. Our model reproduces predictions concerning the dual regulation of Cry1 by the D-box and Rev-ErbA/ROR response element (RRE) promoter elements and allows for ensemble-based predictions of phase response curves (PRCs). Nonphotic signals such as Neuropeptide Y (NPY) may act by promoting Cry1 expression, whereas photic signals likely act by stimulating expression from the E/E' box. Ensemble generation with parameter probability restraints reveals more about a model's behavior than a single optimal parameter set.

Learning through feedback loop metaphors

The metaphor of a feedback loop underpinned a significant curriculum change in a first year teacher-education unit. Assessment for Learning (AfL) practices such as discussing examples of previous student work and giving peer feedback were embedded within the curriculum design. The metaphor of a feedback loop connected these AfL practices into a purposeful process that informed student learning as well as tutor learning about student understanding, that then informed the next teaching episode. Student teachers (n=350) in twelve tutorial groups taught by eight university tutors were able to develop a shared understanding of quality performances before completing each assessment task. As well as providing ongoing insights to improve teaching, data from this action research project enabled the participant tutor-researchers to interrogate the concept of feedback loops. The researchers theorised sociocultural feedback loops as emergent, entangled and dynamic moves in a dance of knowing during which participants negotiated meaning and identities of capability.

A natural model for architecture : the nature of the evolutionary model 1995

John Frazer's architectural work is inspired by living and generative processes. Both evolutionary and revolutionary, it explores informatin ecologies and the dynamics of the spaces between objects. Fuelled by an interest in the cybernetic work of Gordon Pask and Norbert Wiener, and the possibilities of the computer and the "new science" it has facilitated, Frazer and his team of collaborators have conducted a series of experiments that utilize genetic algorithms, cellular automata, emergent behaviour, complexity and feedback loops to create a truly dynamic architecture. Frazer studied at the Architectural Association (AA) in London from 1963 to 1969, and later became unit master of Diploma Unit 11 there. He was subsequently Director of Computer-Aided Design at the University of Ulter - a post he held while writing An Evolutionary Architecture in 1995 - and a lecturer at the University of Cambridge. In 1983 he co-founded Autographics Software Ltd, which pioneered microprocessor graphics. Frazer was awarded a person chair at the University of Ulster in 1984. In Frazer's hands, architecture becomes machine-readable, formally open-ended and responsive. His work as computer consultant to Cedric Price's Generator Project of 1976 (see P84)led to the development of a series of tools and processes; these have resulted in projects such as the Calbuild Kit (1985) and the Universal Constructor (1990). These subsequent computer-orientated architectural machines are makers of architectural form beyond the full control of the architect-programmer. Frazer makes much reference to the multi-celled relationships found in nature, and their ongoing morphosis in response to continually changing contextual criteria. He defines the elements that describe his evolutionary architectural model thus: "A genetic code script, rules for the development of the code, mapping of the code to a virtual model, the nature of the environment for the development of the model and, most importantly, the criteria for selection. In setting out these parameters for designing evolutionary architectures, Frazer goes beyond the usual notions of architectural beauty and aesthetics. Nevertheless his work is not without an aesthetic: some pieces are a frenzy of mad wire, while others have a modularity that is reminiscent of biological form. Algorithms form the basis of Frazer's designs. These algorithms determine a variety of formal results dependent on the nature of the information they are given. His work, therefore, is always dynamic, always evolving and always different. Designing with algorithms is also critical to other architects featured in this book, such as Marcos Novak (see p150). Frazer has made an unparalleled contribution to defining architectural possibilities for the twenty-first century, and remains an inspiration to architects seeking to create responsive environments. Architects were initially slow to pick up on the opportunities that the computer provides. These opportunities are both representational and spatial: computers can help architects draw buildings and, more importantly, they can help architects create varied spaces, both virtual and actual. Frazer's work was groundbreaking in this respect, and well before its time.

The impact of corporate venturing on a firm's competence modes

In this conceptual paper we investigate how corporate venturing influences an organization's competences. The impact of various types of corporate ventures on the portfolio of strategic options of a firm's competence modes (Sanchez, 2004a; Sanchez & Heene, 2002) will be assessed by distinguishing two fundamentally different dimensions of corporate venturing: technology and product (Block & MacMillan, 1993). We argue that the level of product and factor market dynamism mediates the effect of corporate venturing on a firm's competence modes. Corporate ventures that significantly increase the level of product or factor market dynamics will increase the flexibility in all five competence modes. These ventures have a direct effect on the lower-order competence modes and an indirect, lagged effect on higher-order competence modes through feedback loops. The developed framework and the propositions contribute to managing the ability of a firm to change its coordination, resource, and operating flexibility in order to sustain value creation.

Controller structure and design of firing angle controllers for (unit connected) HVDC systems

This paper investigates the control of a HVDC link, fed from an AC source through a controlled rectifier and feeding an AC line through a controlled inverter. The overall objective is to maintain maximum possible link voltage at the inverter while regulating the link current. In this paper the practical feedback design issues are investigated with a view of obtaining simple, robust designs that are easy to evaluate for safety and operability. The investigations are applicable to back-to-back links used for frequency decoupling and to long DC lines. The design issues discussed include: (i) a review of overall system dynamics to establish the time scale of different feedback loops and to highlight feedback design issues; (ii) the concept of using the inverter firing angle control to regulate link current when the rectifier firing angle controller saturates; and (iii) the design issues for the individual controllers including robust design for varying line conditions and the trade-off between controller complexity and the reduction of nonlinearity and disturbance effects

Innovation in construction : a case study of the Australian context

The dominant economic paradigm currently guiding industry policy making in Australia and much of the rest of the world is the neoclassical approach. Although neoclassical theories acknowledge that growth is driven by innovation, such innovation is exogenous to their standard models and hence often not explored. Instead the focus is on the allocation of scarce resources, where innovation is perceived as an external shock to the system. Indeed, analysis of innovation is largely undertaken by other disciplines, such as evolutionary economics and institutional economics. As more has become known about innovation processes, linear models, based on research and development or market demand, have been replaced by more complex interactive models which emphasise the existence of feedback loops between the actors and activities involved in the commercialisation of ideas (Manley 2003). Currently dominant among these approaches is the national or sectoral innovation system model (Breschi and Malerba 2000; Nelson 1993), which is based on the notion of increasingly open innovation systems (Chesbrough, Vanhaverbeke, and West 2008). This chapter reports on the ‘BRITE Survey’ funded by the Cooperative Research Centre for Construction Innovation which investigated the open sectoral innovation system operating in the Australian construction industry. The BRITE Survey was undertaken in 2004 and it is the largest construction innovation survey ever conducted in Australia. The results reported here give an indication of how construction innovation processes operate, as an example that should be of interest to international audiences interested in construction economics. The questionnaire was based on a broad range of indicators recommended in the OECD’s Community Innovation Survey guidelines (OECD/Eurostat 2005). Although the ABS has recently begun to undertake regular innovation surveys that include the construction industry (2006), they employ a very narrow definition of the industry and only collect very basic data compared to that provided by the BRITE Survey, which is presented in this chapter. The term ‘innovation’ is defined here as a new or significantly improved technology or organisational practice, based broadly on OECD definitions (OECD/Eurostat 2005). Innovation may be technological or organisational in nature and it may be new to the world, or just new to the industry or the business concerned. The definition thus includes the simple adoption of existing technological and organisational advancements. The survey collected information about respondents’ perceptions of innovation determinants in the industry, comprising various aspects of business strategy and business environment. It builds on a pilot innovation survey undertaken by PricewaterhouseCoopers (PWC) for the Australian Construction Industry Forum on behalf of the Australian Commonwealth Department of Industry Tourism and Resources, in 2001 (PWC 2002). The survey responds to an identified need within the Australian construction industry to have accurate and timely innovation data upon which to base effective management strategies and public policies (Focus Group 2004).

Spatiotemporal investigations of DNA damage repair using microbeams

Cellular response to radiation damage is made by a complex network of pathways and feedback loops whose spatiotemporal organisation is still unclear despite its decisive role in determining the fate of the damaged cell. Revealing the dynamic sequence of the repair proteins is therefore critical in understanding how the DNA repair mechanisms work. There are also still open questions regarding the possible movement of damaged chromatin domains and its role as trigger for lesion recognition and signalling in the DNA repair context. The single-cell approach and the high spatial resolution offered by microbeams provide the perfect tool to study and quantify the dynamic processes associated with the induction and repair of DNA damage. We have followed the development of radiation-induced foci for three DNA damage markers (i.e. γ-H2AX, 53BP1 and hSSB1) using normal fibroblasts (AG01522), human breast adenocarcinoma cells (MCF7) and human fibrosarcoma cells (HT1080) stably transfected with yellow fluorescent protein fusion proteins following irradiation with the QUB X-ray microbeam (carbon X-rays <2 µm spot). The size and intensity of the foci has been analysed as a function of dose and time post-irradiation to investigate the dynamics of the above-mentioned DNA repair processes and monitor the remodelling of chromatin structure that the cell undergoes to deal with DNA damage.

Evolving noisy oscillatory dynamics in genetic regulatory networks

We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.

Modeling as a means for making powerful ideas accessible to children at an early age

The SimCalc Vision and Contributions Advances in Mathematics Education 2013, pp 419-436 Modeling as a Means for Making Powerful Ideas Accessible to Children at an Early Age Richard Lesh, Lyn English, Serife Sevis, Chanda Riggs … show all 4 hide » Look Inside » Get Access Abstract In modern societies in the 21st century, significant changes have been occurring in the kinds of “mathematical thinking” that are needed outside of school. Even in the case of primary school children (grades K-2), children not only encounter situations where numbers refer to sets of discrete objects that can be counted. Numbers also are used to describe situations that involve continuous quantities (inches, feet, pounds, etc.), signed quantities, quantities that have both magnitude and direction, locations (coordinates, or ordinal quantities), transformations (actions), accumulating quantities, continually changing quantities, and other kinds of mathematical objects. Furthermore, if we ask, what kind of situations can children use numbers to describe? rather than restricting attention to situations where children should be able to calculate correctly, then this study shows that average ability children in grades K-2 are (and need to be) able to productively mathematize situations that involve far more than simple counts. Similarly, whereas nearly the entire K-16 mathematics curriculum is restricted to situations that can be mathematized using a single input-output rule going in one direction, even the lives of primary school children are filled with situations that involve several interacting actions—and which involve feedback loops, second-order effects, and issues such as maximization, minimization, or stabilizations (which, many years ago, needed to be postponed until students had been introduced to calculus). …This brief paper demonstrates that, if children’s stories are used to introduce simulations of “real life” problem solving situations, then average ability primary school children are quite capable of dealing productively with 60-minute problems that involve (a) many kinds of quantities in addition to “counts,” (b) integrated collections of concepts associated with a variety of textbook topic areas, (c) interactions among several different actors, and (d) issues such as maximization, minimization, and stabilization.

Rice ragged stunt oryzavirus genome segment S4 could encode an RNA dependent RNA polymerase and a second protein of unknown function

The complete nucleotide sequence of genome segment S4 of rice ragged stunt oryzavirus (RRSV, Thai-isolate) was determined. The 3823 bp sequence contains two large open reading frames (ORFs). ORF1, spanning nucleotides 12 to 3776, is capable of encoding a protein of M(r) 141,380 (P4a). The P4a amino acid sequence predicted from the nucleotide sequence contains sequence motifs conserved in RNA-dependent RNA polymerases (RDRPs). When compared for evolutionary relationships with RDRPs of other reoviruses using the amino acid sequences around the conserved GDD motif, P4a was shown to be more related to Nilaparvata lugens reovirus and reovirus serotype 3 than to rice dwarf phytoreovirus, bovine rotavirus or bluetongue virus. The ORF2, spanning nucleotides 491 to 1468, is out of frame with ORF1 and is capable of encoding a protein of 36, 920 (P4b). Coupled in vitro transcription-translation from cloned ORF2 in wheat germ extract confirmed the existence of ORF2 but in vivo production and possible function of P4b is yet to be determined.

Rice ragged stunt oryzavirus genome segments S7 and S10 encode non-structural proteins of M(r) 68 025 (Pns7) and M(r) 32364 (Pns10) : brief report

The nucleotide sequences of genome segments S7 and S10 of a Thai-isolate of rice ragged stunt virus (RRSV) were determined. The 1938 bp S7 sequence contains a single large open reading frame (ORF) spanning nucleotides 20 to 1 843 that is predicted to encode a protein of M(r) 68 025. The 1 162 bp S10 sequence has a major ORF spanning nucleotides 142 to 1 032 that is predicted to encode a protein of M(r) 32364. This S10 ORF is preceded by a small ORF (nt 20-55) which is probably a minicistron. Coupled in vitro transcription-translation from the two major ORFs gave protein products of the expected sizes. However, no protein was visualised from S10 when the small ORF sequence was included. Proteins were expressed in Escherichia coli from the full length ORF of S7 (P7) and from a segment of the S10 ORF (P10) fused to the ORF of glutathione S-transferase (GST). Neither fusion protein was recognised by polyclonal antibodies raised against RRSV particles. Furthermore, polyclonal antibodies raised against GST-P7 fusion protein did not recognise any virion structural polypeptides. These data strongly suggest that the proteins P7 and P10 do not form part of RRSV particle. This is further supported by observed sequence homology (though very weak) of predicted.

Mathematical modeling of the cancer cell’s control circuitry : paving the way to individualized therapeutic strategies

Cancer is a disease of signal transduction in which the dysregulation of the network of intracellular and extracellular signaling cascades is sufficient to thwart the cells finely-tuned biochemical control mechanisms. A keen interest in the mathematical modeling of cell signaling networks and the regulation of signal transduction has emerged in recent years, and has produced a glimmer of insight into the sophisticated feedback control and network regulation operating within cells. In this review, we present an overview of published theoretical studies on the control aspects of signal transduction, emphasizing the role and importance of mechanisms such as ‘ultrasensitivity’ and feedback loops. We emphasize that these exquisite and often subtle control strategies represent the key to orchestrating ‘simple’ signaling behaviors within the complex intracellular network, while regulating the trade-off between sensitivity and robustness to internal and external perturbations. Through a consideration of these apparent paradoxes, we explore how the basic homeostasis of the intracellular signaling network, in the face of carcinogenesis, can lead to neoplastic progression rather than cell death. A simple mathematical model is presented, furnishing a vivid illustration of how ‘control-oriented’ models of the deranged signaling networks in cancer cells may enucleate improved treatment strategies, including patient-tailored combination therapies, with the potential for reduced toxicity and more robust and potent antitumor activity.

Service-learning through multiple client-sponsored projects in an MBA marketing course

This paper outlines an approach for teaching Marketing Principles in an MBA course through service-learning to enable adult learners to connect the lectures’ marketing content to a real-world marketing project. During the course, 40 students in groups of four to five individuals were involved in eight different client-sponsored marketing projects executed simultaneously. The rationale, planning and management of this approach utilised current research on service-learning, living cases and client-sponsored projects in marketing education. The experimental curriculum design is presented in a timeline that mirrors the preparation and management of the group projects and the considerations to be taken into account when initiating and facilitating the projects. Reflections from this iteration of the service-learning design suggest the importance of: detailed project planning, the involvement of students in choosing the projects, the introduction of forms and feedback loops, the role of the instructor in facilitating the students and managing expectations, and the role of the company representative in supporting the groups.

Association of sporadic chondrocalcinosis with a -4-basepair G-to-A transition in the 5′-untranslated region of ANKH that promotes enhanced expression of ANKH protein and excess generation of extracellular inorganic pyrophosphate

Objective Certain mutations in ANKH, which encodes a multiple-pass transmembrane protein that regulates inorganic pyrophosphate (PPi) transport, are linked to autosomal-dominant familial chondrocalcinosis. This study investigated the potential for ANKH sequence variants to promote sporadic chondrocalcinosis. Methods ANKH variants identified by genomic sequencing were screened for association with chondrocalcinosis in 128 patients with severe sporadic chondrocalcinosis or pseudogout and in ethnically matched healthy controls. The effects of specific variants on expression of common markers were evaluated by in vitro transcription/translation. The function of these variants was studied in transfected human immortalized CH-8 articular chondrocytes. Results Sporadic chondrocalcinosis was associated with a G-to-A transition in the ANKH 5′-untranslated region (5′-UTR) at 4 bp upstream of the start codon (in homozygotes of the minor allele, genotype relative risk 6.0, P = 0.0006; overall genotype association P = 0.02). This -4-bp transition, as well as 2 mutations previously linked with familial and sporadic chondrocalcinosis (+14 bp C-to-T and C-terminal GAG deletion, respectively), but not the French familial chondrocalcinosis kindred 143-bp T-to-C mutation, increased reticulocyte ANKH transcription/ANKH translation in vitro. Transfection of complementary DNA for both the wild-type ANKH and the -4-bp ANKH protein variant promoted increased extracellular PPi in CH-8 cells, but unexpectedly, these ANKH mutants had divergent effects on the expression of extracellular PPi and the chondrocyte hypertrophy marker, type X collagen. Conclusion A subset of sporadic chondrocalcinosis appears to be heritable via a -4-bp G-to-A ANKH 5′-UTR transition that up-regulates expression of ANKH and extracellular PPi in chondrocyte cells. Distinct ANKH mutations associated with heritable chondrocalcinosis may promote disease by divergent effects on extracellular PPi and chondrocyte hypertrophy, which is likely to mediate differences in the clinical phenotypes and severity of the disease.