Some novel techniques of parameter estimation for the dynamical models in biological systems

Inverse problems based on using experimental data to estimate unknown parameters of a system often arise in biological and chaotic systems. In this paper, we consider parameter estimation in systems biology involving linear and non-linear complex dynamical models, including the Michaelis–Menten enzyme kinetic system, a dynamical model of competence induction in Bacillus subtilis bacteria and a model of feedback bypass in B. subtilis bacteria. We propose some novel techniques for inverse problems. Firstly, we establish an approximation of a non-linear differential algebraic equation that corresponds to the given biological systems. Secondly, we use the Picard contraction mapping, collage methods and numerical integration techniques to convert the parameter estimation into a minimization problem of the parameters. We propose two optimization techniques: a grid approximation method and a modified hybrid Nelder–Mead simplex search and particle swarm optimization (MH-NMSS-PSO) for non-linear parameter estimation. The two techniques are used for parameter estimation in a model of competence induction in B. subtilis bacteria with noisy data. The MH-NMSS-PSO scheme is applied to a dynamical model of competence induction in B. subtilis bacteria based on experimental data and the model for feedback bypass. Numerical results demonstrate the effectiveness of our approach.

Linear models for endocytic transformations from live cell imaging

Endocytosis is the process by which cells internalise molecules including nutrient proteins from the extracellular media. In one form, macropinocytosis, the membrane at the cell surface ruffles and folds over to give rise to an internalised vesicle. Negatively charged phospholipids within the membrane called phosphoinositides then undergo a series of transformations that are critical for the correct trafficking of the vesicle within the cell, and which are often pirated by pathogens such as Salmonella. Advanced fluorescent video microscopy imaging now allows the detailed observation and quantification of these events in live cells over time. Here we use these observations as a basis for building differential equation models of the transformations. An initial investigation of these interactions was modelled with reaction rates proportional to the sum of the concentrations of the individual constituents. A first order linear system for the concentrations results. The structure of the system enables analytical expressions to be obtained and the problem becomes one of determining the reaction rates which generate the observed data plots. We present results with reaction rates which capture the general behaviour of the reactions so that we now have a complete mathematical model of phosphoinositide transformations that fits the experimental observations. Some excellent fits are obtained with modulated exponential functions; however, these are not solutions of the linear system. The question arises as to how the model may be modified to obtain a system whose solution provides a more accurate fit.

Mapping the language of science and science teaching practices : a case study of early childhood school science

Concerns raised in educational reports about school science in terms of students. outcomes and attitudes, as well as science teaching practices prompted investigation into science learning and teaching practices at the foundational level of school science. Without science content and process knowledge, understanding issues of modern society and active participation in decision-making is difficult. This study contended that a focus on the development of the language of science could enable learners to engage more effectively in learning science and enhance their interest and attitudes towards science. Furthermore, it argued that explicit teaching practices where science language is modelled and scaffolded would facilitate the learning of science by young children at the beginning of their formal schooling. This study aimed to investigate science language development at the foundational level of school science learning in the preparatory-school with students aged five and six years. It focussed on the language of science and science teaching practices in early childhood. In particular, the study focussed on the capacity for young students to engage with and understand science language. Previous research suggests that students have difficulty with the language of science most likely because of the complexities and ambiguities of science language. Furthermore, literature indicates that tensions transpire between traditional science teaching practices and accepted early childhood teaching practices. This contention prompted investigation into means and models of pedagogy for learning foundational science language, knowledge and processes in early childhood. This study was positioned within qualitative assumptions of research and reported via descriptive case study. It was located in a preparatory-school classroom with the class teacher, teacher-aide, and nineteen students aged four and five years who participated with the researcher in the study. Basil Bernstein.s pedagogical theory coupled with Halliday.s Systemic Functional Linguistics (SFL) framed an examination of science pedagogical practices for early childhood science learning. Students. science learning outcomes were gauged by focussing a Hallydayan lens on their oral and reflective language during 12 science-focussed episodes of teaching. Data were collected throughout the 12 episodes. Data included video and audio-taped science activities, student artefacts, journal and anecdotal records, semi-structured interviews and photographs. Data were analysed according to Bernstein.s visible and invisible pedagogies and performance and competence models. Additionally, Halliday.s SFL provided the resource to examine teacher and student language to determine teacher/student interpersonal relationships as well as specialised science and everyday language used in teacher and student science talk. Their analysis established the socio-linguistic characteristics that promoted science competencies in young children. An analysis of the data identified those teaching practices that facilitate young children.s acquisition of science meanings. Positive indications for modelling science language and science text types to young children have emerged. Teaching within the studied setting diverged from perceived notions of common early childhood practices and the benefits of dynamic shifting pedagogies were validated. Significantly, young students demonstrated use of particular specialised components of school-science language in terms of science language features and vocabulary. As well, their use of language demonstrated the students. knowledge of science concepts, processes and text types. The young students made sense of science phenomena through their incorporation of a variety of science language and text-types in explanations during both teacher-directed and independent situations. The study informs early childhood science practices as well as practices for foundational school science teaching and learning. It has exposed implications for science education policy, curriculum and practices. It supports other findings in relation to the capabilities of young students. The study contributes to Systemic Functional Linguistic theory through the development of a specific resource to determine the technicality of teacher language used in teaching young students. Furthermore, the study contributes to methodology practices relating to Bernsteinian theoretical perspectives and has demonstrated new ways of depicting and reporting teaching practices. It provides an analytical tool which couples Bernsteinian and Hallidayan theoretical perspectives. Ultimately, it defines directions for further research in terms of foundation science language learning, ongoing learning of the language of science and learning science, science teaching and learning practices, specifically in foundational school science, and relationships between home and school science language experiences.

Hypothetical model of hydrophilic lubrication in synovial joints

This paper presents a new insight into the mechanism of biolubrication of articulating mammalian joints that includes the function of surface-active phospholipids (SAPLs). SAPLs can be adsorbed on surface of cartilage membranes as a hydrophobic monolayer (H-phobic-M Madel or Hills' Model) or as a newly proposed hydrophilic bilayer (H-philic-B Model). With respect to the synovial joint's frictionless work, three processes are identified namely: monolayer/bilayer phospholipids binding to cartilage with lubricin interaction; influence of induced-pressure on interaction of hyaluronan with phospholipids; and biolubrication arising from two gliding articular hydrophilic surfaces acting as reverse micelle. Lubricin is considered to play critical role as a supplier of phospholipids, which overlay the articular surface of articular cartilage. Hyaluronic acid is considered to play a critical mediating role in the interaction between the hydrophilic part of phospholipids, the articular surface and water (hydration) in facilitating the lubrication process. Tivo models of frictionless lubrication processes, namely hydrophobic (H-phobic-M Model) and our conceptual hydrophilic (H-philic-B Model), are compared. © Institution of Engineers Australia, 2008.

Large scale participatory acoustic sensor data analysis : tools and reputation models to enhance effectiveness

Acoustic sensors play an important role in augmenting the traditional biodiversity monitoring activities carried out by ecologists and conservation biologists. With this ability however comes the burden of analysing large volumes of complex acoustic data. Given the complexity of acoustic sensor data, fully automated analysis for a wide range of species is still a significant challenge. This research investigates the use of citizen scientists to analyse large volumes of environmental acoustic data in order to identify bird species. Specifically, it investigates ways in which the efficiency of a user can be improved through the use of species identification tools and the use of reputation models to predict the accuracy of users with unidentified skill levels. Initial experimental results are reported.

Modelling the activation of words in human memory : the spreading activation, spooky-activation-at-a-distance and the entanglement models compared

Modelling how a word is activated in human memory is an important requirement for determining the probability of recall of a word in an extra-list cueing experiment. The spreading activation, spooky-action-at-a-distance and entanglement models have all been used to model the activation of a word. Recently a hypothesis was put forward that the mean activation levels of the respective models are as follows: Spreading � Entanglment � Spooking-action-at-a-distance This article investigates this hypothesis by means of a substantial empirical analysis of each model using the University of South Florida word association, rhyme and word norms.

Computer-intensive simulations for cellular models

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Library and information science education 2.0 : guiding principles and models of best practice. Interview with Hilary Hughes.

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS education as it strives to foster web 2.0 professionals.

Library and information science education 2.0 : guiding principles and models of best practice. Interview with Bob Pymm.

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS education as it strives to foster web 2.0 professionals.

Library and information science education 2.0 : guiding principles and models of best practice. Interview with Jake Wallis.

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS education as it strives to foster web 2.0 professionals.

Library and information science education 2.0 : guiding principles and models of best practice. Interview with Lyn Hay.

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS education as it strives to foster web 2.0 professionals.

Library and information science education 2.0 : guiding principles and models of best practice. Interview with Roy Crotty.

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS education as it strives to foster web 2.0 professionals.

Library and information science education 2.0 : guiding principles and models of best practice. Interview with Mary Anne Kennan.

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS education as it strives to foster web 2.0 professionals.

Library and information science education 2.0 : guiding principles and models of best practice. Interview with Huan Vo-Tran.

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS education as it strives to foster web 2.0 professionals.

Library and information science education 2.0 : guiding principles and models of best practice ALTC Fellowship Report

This ALTC Teaching Fellowship aimed to establish Guiding Principles for Library and Information Science Education 2.0. The aim was achieved by (i) identifying the current and anticipated skills and knowledge required by successful library and information science (LIS) professionals in the age of web 2.0 (and beyond), (ii) establishing the current state of LIS education in Australia in supporting the development of librarian 2.0, and in doing so, identify models of best practice. The fellowship has contributed to curriculum renewal in the LIS profession. It has helped to ensure that LIS education in Australia continues to meet the changing skills and knowledge requirements of the profession it supports. It has also provided a vehicle through which LIS professionals and LIS educators may find opportunities for greater collaboration and more open communication. This will help bridge the gap between LIS theory and practice and will foster more authentic engagement between LIS education and other parts of the LIS industry in the education of the next generation of professionals. Through this fellowship the LIS discipline has become a role model for other disciplines who will be facing similar issues in the coming years. Eighty-one members of the Australian LIS profession participated in a series of focus groups exploring the current and anticipated skills and knowledge needed by the LIS professional in the web 2.0 world and beyond. Whilst each focus group tended to draw on specific themes of interest to that particular group of people, there was a great deal of common ground. Eight key themes emerged: technology, learning and education, research or evidence-based practice, communication, collaboration and team work, user focus, business savvy and personal traits. It was acknowledged that the need for successful LIS professionals to possess transferable skills and interpersonal attributes was not new. It was noted however that the speed with which things are changing in the web 2.0 world was having a significant impact and that this faster pace is placing a new and unexpected emphasis on the transferable skills and knowledge. It was also acknowledged that all librarians need to possess these skills, knowledge and attributes and not just the one or two role models who lead the way. The most interesting finding however was that web 2.0, library 2.0 and librarian 2.0 represented a ‘watershed’ for the LIS profession. Almost all the focus groups spoke about how they are seeing and experiencing a culture change in the profession. Librarian 2.0 requires a ‘different mindset or attitude’. The Levels of Perspective model by Daniel Kim provides one lens by which to view this finding. The focus group findings suggest that we are witnessing a re-awaking of the Australian LIS profession as it begins to move towards the higher levels of Kim’s model (ie mental models, vision). Thirty-six LIS educators participated in telephone interviews aimed at exploring the current state of LIS education in supporting the development of librarian 2.0. Skills and knowledge of LIS professionals in a web 2.0 world that were identified and discussed by the LIS educators mirrored those highlighted in the focus group discussions with LIS professionals. Similarly it was noted that librarian 2.0 needed a focus less on skills and knowledge and more on attitude. However, whilst LIS professionals felt that there was a paradigm shift within the profession. LIS educators did not speak with one voice on this matter with quite a number of the educators suggesting that this might be ‘overstating it a bit’. This study provides evidence for “disparate viewpoints” (Hallam, 2007) between LIS educators and LIS professionals that can have a significant implications for the future of not just LIS professional education specifically but for the profession generally. Library and information science education 2.0: guiding principles and models of best practice 1 Inviting the LIS academics to discuss how their teaching and learning activities support the development of librarian 2.0 was a core part of the interviews conducted. The strategies used and the challenges faced by LIS educators in developing their teaching and learning approaches to support the formation of librarian 2.0 are identified and discussed. A core part of the fellowship was the identification of best practice examples on how LIS educators were developing librarian 2.0. Twelve best practice examples were identified. Each educator was recorded discussing his or her approach to teaching and learning. Videos of these interviews are available via the Fellowship blog at .The LIS educators involved in making the videos felt uncomfortable with the term ‘best practice’. Many acknowledged that there simply seeking to do the best by their students and that there was always room for improvement. For this reason these videos are offered as examples of “great practice”. The videos are a tool for other educators to use, regardless of discipline, in developing their teaching and learning approaches to supporting web 2.0 professionals. It has been argued that the main purpose of professional education is transformation (Dall’ Alba, 2009; Dall’Alba & Barnacle, 2007). As such professional education should focus not just on skills and knowledge acquisition but also on helping students to develop ways of being the professionals in question (ie LIS professionals, teachers, lawyers, engineers).The aim of this fellowship was to establish Guidelines for Library and Information Science Education 2.0 it has however become apparent that at this point in time it is not yet possible to fulfil this aim. The fellowship has clearly identified skills and knowledge needed by the LIS professional in web 2.0 world (and beyond). It has also identified examples of ‘great practice’ by LIS educators as they endeavour to develop LIS professionals who will be successful in a web 20 world. The fellowship however has also shown that the LIS profession is currently undergoing significant attitudinal and conceptual change. Consequently, before a philosophy of LIS education 2.0 can be expressed, the Australian LIS profession must first explore and articulate what it means to be an LIS professional in the 21st century (ie a world of web 2.0 and beyond). In short, the LIS profession in Australia must take stock not of “what we know and can do” but on “who we are becoming” (Dall’Alba, 2009, p 34).