Computational science for undergraduate biologists via QUT.Bio.Excel

Molecular biology is a scientific discipline which has changed fundamentally in character over the past decade to rely on large scale datasets – public and locally generated - and their computational analysis and annotation. Undergraduate education of biologists must increasingly couple this domain context with a data-driven computational scientific method. Yet modern programming and scripting languages and rich computational environments such as R and MATLAB present significant barriers to those with limited exposure to computer science, and may require substantial tutorial assistance over an extended period if progress is to be made. In this paper we report our experience of undergraduate bioinformatics education using the familiar, ubiquitous spreadsheet environment of Microsoft Excel. We describe a configurable extension called QUT.Bio.Excel, a custom ribbon, supporting a rich set of data sources, external tools and interactive processing within the spreadsheet, and a range of problems to demonstrate its utility and success in addressing the needs of students over their studies.

Role of serotonin via 5-HT2B receptors in the reinforcing effects of MDMA in mice

The amphetamine derivative 3,4-methylenedioxymethamphetamine (MDMA, ecstasy) reverses dopamine and serotonin transporters to produce efflux of dopamine and serotonin, respectively, in regions of the brain that have been implicated in reward. However, the role of serotonin/dopamine interactions in the behavioral effects of MDMA remains unclear. We previously showed that MDMA-induced locomotion, serotonin and dopamine release are 5-HT(2B) receptor-dependent. The aim of the present study was to determine the contribution of serotonin and 5-HT(2B) receptors to the reinforcing properties of MDMA. We show here that 5-HT(2B) (-/-) mice do not exhibit behavioral sensitization or conditioned place preference following MDMA (10 mg/kg) injections. In addition, MDMA-induced reinstatement of conditioned place preference after extinction and locomotor sensitization development are each abolished by a 5-HT(2B) receptor antagonist (RS127445) in wild type mice. Accordingly, MDMA-induced dopamine D1 receptor-dependent phosphorylation of extracellular regulated kinase in nucleus accumbens is abolished in mice lacking functional 5-HT(2B) receptors. Nevertheless, high doses (30 mg/kg) of MDMA induce dopamine-dependent but serotonin and 5-HT(2B) receptor-independent behavioral effects. These results underpin the importance of 5-HT(2B) receptors in the reinforcing properties of MDMA and illustrate the importance of dose-dependent effects of MDMA on serotonin/dopamine interactions.

The continuing decline of science and mathematics enrolments in Australian high schools

Is there a crisis in Australian science and mathematics education? Declining enrolments in upper secondary Science and Mathematics courses have gained much attention from the media, politicians and high-profile scientists over the last few years, yet there is no consensus amongst stakeholders about either the nature or the magnitude of the changes. We have collected raw enrolment data from the education departments of each of the Australian states and territories from 1992 to 2012 and analysed the trends for Biology, Chemistry, Physics, two composite subject groups (Earth Sciences and Multidisciplinary Sciences), as well as entry, intermediate and advanced Mathematics. The results of these analyses are discussed in terms of participation rates, raw enrolments and gender balance. We have found that the total number of students in Year 12 increased by around 16% from 1992 to 2012 while the participation rates for most Science and Mathematics subjects, as a proportion of the total Year 12 cohort, fell (Biology (-10%), Chemistry (-5%), Physics (-7%), Multidisciplinary Science (-5%), intermediate Mathematics (-11%), advanced Mathematics (-7%) in the same period. There were increased participation rates in Earth Sciences (+0.3%) and entry Mathematics (+11%). In each case the greatest rates of change occurred prior to 2001 and have been slower and steadier since. We propose that the broadening of curriculum offerings, further driven by students' self-perception of ability and perceptions of subject difficulty and usefulness, are the most likely cause of the changes in participation. While these continuing declines may not amount to a crisis, there is undoubtedly serious cause for concern.

Surface science of plasma exposed surfaces : a challenge for applied plasma science

This article introduces a deterministic approach to using low-temperature, thermally non-equilibrium plasmas to synthesize delicate low-dimensional nanostructures of a small number of atoms on plasma exposed surfaces. This approach is based on a set of plasma-related strategies to control elementary surface processes, an area traditionally covered by surface science. Major issues related to balanced delivery and consumption of building units, appropriate choice of process conditions, and account of plasma-related electric fields, electric charges and polarization effects are identified and discussed in the quantum dot nanoarray context. Examples of a suitable plasma-aided nanofabrication facility and specific effects of a plasma-based environment on self-organized growth of size- and position-uniform nanodot arrays are shown. These results suggest a very positive outlook for using low-temperature plasma-based nanotools in high-precision nanofabrication of self-assembled nanostructures and elements of nanodevices, one of the areas of continuously rising demand from academia and industry.

Emotional climate and high quality learning experiences in science teacher education

The role of emotion during learning encounters in science teacher education is under-researched and under-theorized. In this case study we explore the emotional climates, that is, the collective states of emotional arousal, of a preservice secondary science education class to illuminate practice for producing and reproducing high quality learning experiences for preservice science teachers. Theories related to the sociology of emotions informed our analyses from data sources such as preservice teachers’ perceptions of the emotional climate of their class, emotional facial expressions, classroom conversations, and cogenerative dialogue. The major outcome from our analyses was that even though preservice teachers reported high positive emotional climate during the professor’s science demonstrations, they also valued the professor’s in the moment reflections on her teaching that were associated with low emotional climate ratings. We co-relate emotional climate data and preservice teachers’ comments during cogenerative dialogue to expand our understanding of high quality experiences and emotional climate in science teacher education. Our study also contributes refinements to research perspectives on emotional climate.

Computational plasma nanoscience : where plasma physics meets surface science

Multiscale hybrid simulations that bridge the nine-order-of-magnitude spatial gap between the macroscopic plasma nanotools and microscopic surface processes on nanostructured solids are described. Two specific examples of carbon nanotip-like and semiconductor quantum dot nanopatterns are considered. These simulations are instrumental in developing physical principles of nanoscale assembly processes on solid surfaces exposed to low-temperature plasmas.

Theorizing in design science research : an abstraction layers framework

For Design Science Research (DSR) to gain wide credence as a research paradigm in Information Systems (IS), it must contribute to theory. “Theory cannot be improved until we improve the theorizing process, and we cannot improve the theorizing process until we describe it more explicitly, operate it more self-consciously, and decouple it from validation more deliberately” (Weick 1989, p. 516). With the aim of improved design science theorizing, we propose a DSR abstraction-layers framework that integrates, interlates, and harmonizes key methodological notions, primary of which are: 1) the Design Science (DS), Design Research (DR), and Routine Design (RD) distinction (Winter 2008); 2) Multi Grounding in IS Design Theory (ISDT) (Goldkuhl & Lind 2010); 3) the Idealized Model for Theory Development (IM4TD) (Fischer & Gregor 2011); and 4) the DSR Theorizing Framework (Lee et al. 2011). Though theorizing, or the abstraction process, has been the subject of healthy discussion in DSR, important questions remain. With most attention to date having focused on theorizing for Design Research (DR), a key stimulus of the layered view was the realization that Design Science (DS) produces abstract knowledge at a higher level of generality. The resultant framework includes four abstraction layers: (i) Design Research (DR) 1st Abstract Layer, (ii) Design Science (DS) 2nd Abstract Layer, (iii) DSR Incubation 3rd Layer, and (iv) Routine Design 4th Layer. Differentiating and inter-relating these layers will aid DSR researchers to discover, position, and amplify their DSR contributions. Additionally, consideration of the four layers can trigger creative perspectives that suggest unplanned outputs. The first abstraction layer, including its alternative patterns of activity, is well recognized in the literature. The other layers, however, are less well recognized; and the integrated representation of layers is novel.

The importance of science fiction and other STEM-related mass media in young people’s decisions to enrol in university STEM courses

This paper presents Australian results from the Interests and Recruitment in Science (IRIS) study with respect to the influence of STEM-related mass media, including science fiction, on students’ decisions to enrol in university STEM courses. The study found that across the full cohort (N=2999), students tended to attribute far greater influence to science-related documentaries/channels such as Life on Earth and the Discovery Channel, etc. than to science-fiction movies or STEM-related TV dramas. Males were more inclined than females to consider science fiction/fantasy books and films and popular science books/magazines as having been important in their decisions. Students taking physics/astronomy tended to rate the importance of science fiction/fantasy books and films higher than students in other courses. The implications of these results for our understanding of influences on STEM enrolments are discussed.

Changes in teachers’ behaviour in secondary science education : implementing a standards-referenced national curriculum

There is substantial attention worldwide to the quality of secondary school teaching in STEM in Education. This paper reports on the use of Outcome Mapping (OM) as an approach to guide and monitor change in teacher practice and a visual tool, shaped as a Star, to benchmark and monitor this behaviour. OM and the visual tool were employed to guide and document three secondary teachers’ behaviour as they planned, implemented and assessed a science unit in the new Australian standards-referenced curriculum. Five key outcome markers in the teachers’ behaviour were identified together with progress markers — cumulative qualitative indicators — leading to these outcomes. The use of a Star to benchmark and track teachers’ behaviours was particularly useful because it showed teacher behaviour on multiple dimensions simultaneously at various points in time. It also highlighted priorities in need of further attention and provided a pathway to achievement. Hence, OM and the Star representation provide both theoretical and pragmatic approaches to enhancing quality in STEM teaching.

The impact of diabetic ketoacidosis and age on behavior six months post-diagnosis in children with type 1 diabetes

Objectives: Children with type 1 diabetes mellitus (DM1) may be at increased risk of psychosocial and adjustment difficulties. We examined behavioral outcomes six months post-diagnosis in a group of children with newly diagnosed DM1. Methods: This study formed part of a larger longitudinal project examining pathophysiology and neuropsychological outcomes in diabetic patients with or without diabetic ketoacidosis (DKA). Participants were 61 children (mean age 11.8 years, SD 2.7 years) who presented with a new diagnosis of DM1 at the Royal Children’s Hospital, Melbourne. Twenty-three (11 female) presented in DKA and 38 (14 female) without DKA. Parents completed the behavior assessment system for children, second edition six months post-diagnosis. Results: There was a non-linear relationship between age and behavior. Internalising problems (i.e. anxiety depression, withdrawal) peaked in the transition from childhood to adolescence; children aged 10–13 years had elevated rates relative to the normal population (t = 2.55, P = 0.018). There was a non-significant trend for children under 10 to display internalising problems (P = 0.052), but rates were not elevated in children over 13 (P = 0.538). Externalising problems were not significantly elevated in any age group. Interestingly, children who presented in DKA were at lower risk of internalising problems than children without DKA (t = 3.83, P < 0.001). There was no effect of DKA on externalising behaviors. Conclusions: Children transitioning from childhood to adolescence are at significant risk for developing internalising problems such as anxiety and lowered mood after diagnosis of DM1. Somewhat counter-intuitively, parents of children presenting in DKA reported fewer internalising symptoms than parents of children without DKA. These results highlight the importance of monitoring and supporting psychosocial adjustment in newly diagnosed children even when they seem physically well.

Paradoxical enhancement of fear extinction memory and synaptic plasticity by inhibition of the histone acetyltransferase p300

It is well established that the coordinated regulation of activity-dependent gene expression by the histone acetyltransferase (HAT) family of transcriptional coactivators is crucial for the formation of contextual fear and spatial memory, and for hippocampal synaptic plasticity. However, no studies have examined the role of this epigenetic mechanism within the infralimbic prefrontal cortex (ILPFC), an area of the brain that is essential for the formation and consolidation of fear extinction memory. Here we report that a postextinction training infusion of a combined p300/CBP inhibitor (Lys-CoA-Tat), directly into the ILPFC, enhances fear extinction memory in mice. Our results also demonstrate that the HAT p300 is highly expressed within pyramidal neurons of the ILPFC and that the small-molecule p300-specific inhibitor (C646) infused into the ILPFC immediately after weak extinction training enhances the consolidation of fear extinction memory. C646 infused 6 h after extinction had no effect on fear extinction memory, nor did an immediate postextinction training infusion into the prelimbic prefrontal cortex. Consistent with the behavioral findings, inhibition of p300 activity within the ILPFC facilitated long-term potentiation (LTP) under stimulation conditions that do not evoke long-lasting LTP. These data suggest that one function of p300 activity within the ILPFC is to constrain synaptic plasticity, and that a reduction in the function of this HAT is required for the formation of fear extinction memory.

Building the science and innovation base: work, skills and employment issues

This Special Issue of New Technology, Work and Employment has been prompted by the increasing awareness in many countries of the need to maintain and grow their science and innovation base. The development of science, engineering, technology and mathematics (STEM) skills and capacity is seen as vital for economic development and prosperity through its impact on national and regional research and development (R&D), technological advancement, and innovation potential.

Emotional climate and behavioral management during sleep time in early childhood education settings

The majority of children cease napping between 3 and 5 years of age yet, internationally, the allocation of a sleep time during the day for children of this age remains a practice in many early childhood education (ECE) settings. These dual circumstances present a disjuncture between children's sleep needs and center practices, that may cause conflict for staff, increase stress for children and escalate negative emotional climate in the room. Testing this hypothesis requires observation of both the emotional climate and behavioral management used in ECE rooms that extends into the sleep time. This study was the first to apply the Classroom Assessment and Scoring System (CLASS) Pre-K (Pianta, La Paro, & Hamre, 2008) to observe the emotional climate and behavioral management during sleep time. Pilot results indicated that the CLASS Pre-K functioned reliably to measure emotional climate and behavioral management in sleep time. However, new sleep-specific examples of the dimensions used were developed, to help orient fieldworkers to the CLASS Pre-K rating system in the sleep time context. The CLASS was then used to assess emotional climate and behavior management between the non-sleep and sleep time sessions, in 113 ECE rooms in Queensland, Australia. In these rooms 2.114 children were observed. Of these children, 71% did not sleep at any point during the allotted sleep times. There was a significant drop in emotional climate and behavioral management between the non-sleep and sleep-time sessions. Furthermore, the duration of mandated sleep time (a period of time where no activities are provided to non-sleeping children) accounted for significant independent variance in the observed emotional climate during sleep-time. The CLASS Pre-K presents a valuable tool to assess the emotional climate and behavior management during sleep-time and draws attention to the need for further studies of sleep time in ECE settings.

Popular Science

Review of The Anatomist by Bill Hayes (Scribe, 2008). Bill Hayes wanted to write about Henry Gray, the author of Gray's Anatomy (1858), which at least until the television series connoted a standard text for anatomy students. Perhaps even more seductive for the biographer than the book's enduring appeal was a sense that Gray himself had partly disappeared from the historical record. Here was a scientist with the sort of brilliant young mind that seemed a specialty of the Victorian Age, and yet one who had not benefited from that period's compulsive documenting of the men of the moment and their deeds. Surely in that mystery there lay a narrative...

Deletions and other pleasures : Episode 1: The pleasures of science fiction

"Christy Dena’s online-remix-narrative takes iconic images of popular culture and builds with them a strange world where the human fallibility is programmatically deleted. Both dystopic and playful, Dena’s work is an ironic reimagining of pleasure as a state of robotic flatlining, using tropes of science fiction to critique processes of social normalisation and increasing alienation from emotionality." This creative response began as a completely different story and form. What excited me in the end was the concept of deletion and how it could be an interesting mechanic: where the only thing you can do in the world is delete. I thought about deleting parts of robots to make them better. Healing comes from taking away, from removing things. Memories of Joseph Weizenbaum’s chatbot ELIZA came flooding back: where the (human) player is a patient talking to a Rogerian psychotherapist. But in this work I’m switching the roles and making the player the doctor, a doctor to robots…a doctor that can only prescribe deletions. I conceived of the work as a branching narrative, and started writing it in Twine. With every robot patient, the player chose one of many deletions. But when I realised I wouldn’t be able to arrange an artist and sound designer I looked for another option. I played with Zeega and felt that I could get the mood I was after with that platform. So the piece transformed into a work where the player/viewer is imprisoned in the decisions of the deleting protagonist…which has its own effect on the experience and meaning.