Entry letter from a publisher 1969: Part 21

Entry letters for the Booker Prize from publisher

Impact of environmental inputs on reverse-engineering approach to network structures

Background: Uncovering complex network structures from a biological system is one of the main topic in system biology. The network structures can be inferred by the dynamical Bayesian network or Granger causality, but neither techniques have seriously taken into account the impact of environmental inputs. Results: With considerations of natural rhythmic dynamics of biological data, we propose a system biology approach to reveal the impact of environmental inputs on network structures. We first represent the environmental inputs by a harmonic oscillator and combine them with Granger causality to identify environmental inputs and then uncover the causal network structures. We also generalize it to multiple harmonic oscillators to represent various exogenous influences. This system approach is extensively tested with toy models and successfully applied to a real biological network of microarray data of the flowering genes of the model plant Arabidopsis Thaliana. The aim is to identify those genes that are directly affected by the presence of the sunlight and uncover the interactive network structures associating with flowering metabolism. Conclusion: We demonstrate that environmental inputs are crucial for correctly inferring network structures. Harmonic causal method is proved to be a powerful technique to detect environment inputs and uncover network structures, especially when the biological data exhibit periodic oscillations

Processing bodies are dynamically localised and associate with multiple organelles throughout the replicative lifespan of the yeast cell

Processing bodies (p-bodies) are cytoplasmic messenger ribonucleoprotein granules containing components of the mRNA degradation machinery, that form during stress conditions in the budding yeast Saccharomyces cerevisiae. P-bodies are conserved in eukaryotes and are related to other mRNP granules such as stress granules and neuronal granules. mRNP granules and their components self-assemble through a process of liquid-liquid phase separation, facilitated by protein-protein interaction by low complexity regions. Errors in this assembly process can cause a build-up of aggregated protein and have been implicated in the pathology of human neurodegenerative diseases such as amyotrophic lateral sclerosis. The exact role of p-bodies in normal cellular function is not known, but p-bodies are induced in conditions of stress, and can store mRNA that later re-enters translation, leading to the theory that they are sites of mRNA storage. A contrasting theory suggests them as sites of mRNA decay, due to the presence of deadenylation, decapping and exonuclease complexes within p-bodies. In this work, time-lapse fluorescence microscopy, using optimised high brightness, low photobleaching fluorescent protein fusions, was used to allow long term imaging of p-body localisation throughout the cell cycle of S. cerevisiae. Imaging was combined with microfluidic dissection of mother and daughter cells, to track single mother cells over their entire replicative lifespan (RLS) while continuing to monitor p body localisation. P-bodies were found to be localised in proximity to multiple different organelles with changes to localisation occurring through the cell cycle. Advanced replicative aged altered the profile of p-body localisation causing p-bodies to localise heavily to the mitochondria. P-bodies were also found to be inherited by daughter cells in a process dependent on the mRNA transport machinery and the p-body protein Dcp1. This inheritance was multigenerational with a single p-body moving between multiple daughter cells and was not lost in cells of advanced replicative age

Synthesis Study: Overview of Readily Available Culvert Inspection Technologies

Culverts, conduits that facilitate passage of water beneath roadways and other structures, represent important components of infrastructure systems, helping to drain, direct or divert surface water and prevent the disruption of roadways. Their efficient inspection and maintenance is thus critical to safe operation of Indiana’s transportation infrastructure. Although approximately 25% of culverts associated with INDOT managed roadways are inspected each year, inspectors face many challenges determining the actual condition of culverts, which can vary substantially in material type, form, length, depth of cover, accessibility, and age. This study was therefore performed to understand and synthesize technical culvert inspection alternatives with a focus on identifying and prioritizing readily available solutions. Research revealed that no standard inspection guidelines exist for small culverts, and that inspection practices vary significantly across states. DOT survey results indicate that DOTs primarily rely on visual examination conducted by field personnel, often from the open ends of the culvert, limiting the range of flaws and failure modes that can be identified, and the desired early warning benefits of inspection. While a range of technologies exist to facilitate inspection, most methods apply to only a limited set of culvert materials and operating conditions. This study thus provides a ranked recommendation of readily available culvert inspection solutions, segmented according to their applicability to varying culvert conditions and inspection needs. Techniques involving mobile visual camera systems and multi-sensing modes stand out for their potential to provide insight into the condition of a variety of culvert types at moderate cost

Editorial: Collaboration in higher education: Partnering with students, colleagues and external stakeholders

Welcome to this Special Issue of the Journal of University Teaching and Learning Practice (JUTLP). This editorial provides an overview of Collaboration in Higher Education. Humans are social, inter-dependent beings, needing to be and communicate with each other. Being with other people provides an opportunity to grow and develop, creating a sense of self and identity. Together we construct, structure and restructure the stories that build the larger narratives of who we are, what we do and how we live, act and behave as people, professionals and larger communities. It is through our collaborations that we come together, and construct meaning and ourselves. As Higher Education continues to exclude and sideline, as it constrains and removes spaces and places for collaboration between service staff, faculty and students within institutions, between institutions, and with other stakeholders, there is a need to rediscover the power of collaboration. The articles included, build on practical experience, research data, personal and collective reflections, to outline how the contributors have navigated this tension to create spaces of voice and hope. Presented are case studies that are boundary crossing: across disciplinary boundaries; cross-institution collaboration; cross-boundary working; pedagogical co-creation and the re-conceptualising of learning; and students as partners, co-researchers and co-authors. Together they showcase refreshed notions of collegiality and collaboration in Higher Education that support new and more nuanced, and dynamic models of co-creation. We hope the Special Issue helps seed an ecology of collaborative practice for social justice – a more humane academia

Nondestructive Evaluation of the Condition of Subsurface Drainage in Pavements Using Ground Penetrating Radar (GPR)

Subsurface drainage features are routinely incorporated in the design of pavement systems as they are believed to increase pavement service life provided that they are installed correctly and maintained. Maintenance, however, is challenging in that location and subsequent inspection of these systems can be time consuming and laborious. With this in mind, some departments of transportation have turned to ground penetrating radar as one means to rapidly locate subsurface drainage features in pavements and thus alleviate some of the cost and complexity of maintaining these systems, but with mixed results. In this context, this study pursued a two-pronged approach to improve GPR-based location of sub-pavement drainage systems, involving: (1) software-based signal processing and (2) modifications of hardware test configurations. From a signal processing perspective, two complementary signal processing approaches were developed in this work. Method 1 involved algorithms that are designed to reduce GPR signal background clutter and noise by taking advantage of the somewhat uniform nature of the strata underlying constructed pavements and to systematically remove anomalous signals. Method 2 focused on enhancing 2-D image quality to facilitate recognition of hyperbolic signal returns indicative of drain detection. From a hardware perspective, field experiments were also carried out in this work to validate the signal processing algorithms and assess the potential for alternative antenna configurations to enhance detection success. Five different antenna configurations were tested in total. When employed in field settings, the signal processing algorithms demonstrated an ability to routinely detect X-drains (shallow depth, PVC) with 2-3 false alarms per successful detection. Similarly, all known K-drains (moderate depth, metal/clay) in the studied field test regions were successfully identified, although each successful K-drain detection was accompanied by a significant number of potential false alarms. Beyond these signal conditioning related findings, additional recommendations for field deployed GPR survey line selection, antennae configuration, and frequency selection are also provided

The Shipwrecked Shore and Other Metaphors: what we can learn from occupation of, and representations in, virtual worlds

In cyberspace, one’s body can be represented by one's own description, reality can be disrupted and the plain made beautiful or ‘… the beautiful plain’, (Turkle 1999:643). Our case study (cf Stake 1995) sought to explore the opportunities offered to students when they come to class in a virtual world and a differently created learning space. We consider Bullinghurst and Dünser’s (2012) work on augmenting reality for learners to combine the ‘real and the virtual’ to enable students to deal with the abstract. This paper explores student representations in Second Life, a 3D immersive world (www.secondlife.com), and as we engage, we see that the virtual not only enhances both curriculum and practice, but also an emergent scope for visual hermeneutics as both a digital literacy and analytical research tool. The focus of the case is a first year FoLSC group of students, based in Computing, and a first year module with embedded study and academic skills. Our conclusions suggest that offering learning opportunities in different spaces, can, indeed, disrupt – but in a powerful and positive way

A journey into silence: students, stakeholders and the impact of a strategic Governmental Policy Document in the UK.

For our analysis we draw upon Macherey’s essay ‘The text says what is does not say’ (in Walder 1990) where he argues for the legitimacy of interrogating a text for ‘what it tacitly implies, what it does not say … for in order to say anything there are things which must not be said’ (Ibid 217, his italics). As with society, all works have their margins – the incompleteness that reveals their birth and production … ‘ What is important in the work is what it does not say … what the work cannot say … because there the elaboration of the utterances is acted out in a sort of journey to silence’ (Ibid 218). Our critical analysis of the Government e-learning strategy (2005) reveals that rather than harnessing technology to empower the typically disenfranchised within the educational debate, it is those very stakeholders at the margins who are silenced whilst the interests of those with institutional and economic power are given voice. Our analysis will show that rather than creating a stakeholder society, Government through its policy documents positions the already disempowered as either silent or deficit and our conclusions suggest that rather than a discourse of transformation, ‘regulation not education’ (Lillis 2001), is the real goal of the dominant stakeholders