Post-genomic science & society : Getting our fangs into omics science and its implications

Genomics and genetic findings have been hailed with promises of unlocked codes and new frontiers of personalized medicine. Despite cautions about gene hype, the strong cultural pull of genes and genomics has allowed consideration of genomic personhood. Populated by the complicated records of mass spectrometer, proteomics, which studies the human protein, has not achieved either the funding or the popular cultural appeal proteomics scientists had hoped it would. While proteomics, being focused on the proteins that actually indicate and create disease states, has a more direct potential for clinical applications than genomic risk predictions, culturally, it has not provided the material for identity creation. In our ethnographic research, we explore how proteomic scientists attempting to shape an appeal to personhood through which legitimacy may be defined.

Robots for environmental monitoring : significant advancements and applications

Robotic systems are increasingly being utilised as fundamental data-gathering tools by scientists, allowing new perspectives and a greater understanding of the planet and its environmental processes. Today's robots are already exploring our deep oceans, tracking harmful algal blooms and pollution spread, monitoring climate variables, and even studying remote volcanoes. This article collates and discusses the significant advancements and applications of marine, terrestrial, and airborne robotic systems developed for environmental monitoring during the last two decades. Emerging research trends for achieving large-scale environmental monitoring are also reviewed, including cooperative robotic teams, robot and wireless sensor network (WSN) interaction, adaptive sampling and model-aided path planning. These trends offer efficient and precise measurement of environmental processes at unprecedented scales that will push the frontiers of robotic and natural sciences.

Literacy Theories for the Digital Age: Social, Critical, Multimodal, Spatial, Material and Sensory Lenses

Literacy Theories for the Digital Age insightfully brings together six essential approaches to literacy research and educational practice. The book provides powerful and accessible theories for readers, including Socio-cultural, Critical, Multimodal, Socio-spatial, Socio-material and Sensory Literacies. The brand new Sensory Literacies approach is an original and visionary contribution to the field, coupled with a provocative foreword from leading sensory anthropologist David Howes. This dynamic collection explores a legacy of literacy research while showing the relationships between each paradigm, highlighting their complementarity and distinctions. This highly relevant compendium will inspire readers to explore new frontiers of thought and practice in times of diversity and technological change.

Towards a model of spray-canopy interactions : interception, shatter, bounce and retention of droplets on horizontal leaves

Pesticides used in agricultural systems must be applied in economically viable and environmentally sensitive ways, and this often requires expensive field trials on spray deposition and retention by plant foliage. Computational models to describe whether a spray droplet sticks (adheres), bounces or shatters on impact, and if any rebounding parent or shatter daughter droplets are recaptured, would provide an estimate of spray retention and thereby act as a useful guide prior to any field trials. Parameter-driven interactive software has been implemented to enable the end-user to study and visualise droplet interception and impaction on a single, horizontal leaf. Living chenopodium, wheat and cotton leaves have been scanned to capture the surface topography and realistic virtual leaf surface models have been generated. Individual leaf models have then been subjected to virtual spray droplets and predictions made of droplet interception with the virtual plant leaf. Thereafter, the impaction behaviour of the droplets and the subsequent behaviour of any daughter droplets, up until re-capture, are simulated to give the predicted total spray retention by the leaf. A series of critical thresholds for the stick, bounce, and shatter elements in the impaction process have been developed for different combinations of formulation, droplet size and velocity, and leaf surface characteristics to provide this output. The results show that droplet properties, spray formulations and leaf surface characteristics all influence the predicted amount of spray retained on a horizontal leaf surface. Overall the predicted spray retention increases as formulation surface tension, static contact angle, droplet size and velocity decreases. Predicted retention on cotton is much higher than on chenopodium. The average predicted retention on a single horizontal leaf across all droplet size, velocity and formulations scenarios tested, is 18, 30 and 85% for chenopodium, wheat and cotton, respectively.

Bayesian indirect inference using a parametric auxiliary model

Indirect inference (II) is a methodology for estimating the parameters of an intractable (generative) model on the basis of an alternative parametric (auxiliary) model that is both analytically and computationally easier to deal with. Such an approach has been well explored in the classical literature but has received substantially less attention in the Bayesian paradigm. The purpose of this paper is to compare and contrast a collection of what we call parametric Bayesian indirect inference (pBII) methods. One class of pBII methods uses approximate Bayesian computation (referred to here as ABC II) where the summary statistic is formed on the basis of the auxiliary model, using ideas from II. Another approach proposed in the literature, referred to here as parametric Bayesian indirect likelihood (pBIL), we show to be a fundamentally different approach to ABC II. We devise new theoretical results for pBIL to give extra insights into its behaviour and also its differences with ABC II. Furthermore, we examine in more detail the assumptions required to use each pBII method. The results, insights and comparisons developed in this paper are illustrated on simple examples and two other substantive applications. The first of the substantive examples involves performing inference for complex quantile distributions based on simulated data while the second is for estimating the parameters of a trivariate stochastic process describing the evolution of macroparasites within a host based on real data. We create a novel framework called Bayesian indirect likelihood (BIL) which encompasses pBII as well as general ABC methods so that the connections between the methods can be established.

The engagement of small to medium enterprises for managing waste in building retrofit projects

The market of building retrofits is increasingly more intensified as existing buildings are aging. The building retrofit projects involve existing buildings which impose constraints on stakeholders throughout the project process. They are also risky, complex, less predictable and difficult to be well planned with on-site waste becoming one of the critical issues. Small and Medium Enterprises (SMEs) carry out most of the work in retrofit projects as subcontractors, but they often do not have adequate resources to deal with the specific technical challenges and project risks related to waste. This paper first discusses the requirements of waste management in building retrofit projects considering specific project characteristics and work natures, and highlights the importance of involving SMEs in waste planning and management through an appropriate way. By utilizing semi-structured interviews, this research develops a process model for SMEs to be applied in waste management. A collaboration scenario is also developed for collaborative waste planning and management by SMEs as subcontractors and large companies as main contractors. Findings from the paper will promote coordination of project delivery and waste management in building retrofit projects, and improve the involvement and performance of SMEs in dealing with waste problems.

Critical factors for sustainable reconstruction of post natural disasters

While scientists are still debating the level of climate change impact to new weather patterns, there have been some devastating natural disasters worldwide in the last decade. From cyclones to earthquakes and from Tsunamis to landslides, these disasters occur with formidable forces and crushing effects. As one of the most important arrangements to erase the negative influence of natural disasters and help with the recovery and redevelopment of the hit area, reconstruction is of utmost importance in light of sustainable objectives. However, current reconstruction practice confronts quite a lot of criticisms for focusing on providing short-term necessities. How to conduct the post disaster reconstruction in a long-term perspective and achieve sustainable development is thereby a highlight for industry practice and research. This paper introduced an on-going research project which is aimed at establishing an operational framework for improving sustainability performance of post disaster reconstruction by identifying critical sustainable factors and exploring their internal relationships. The research reported in this paper is part of the project. After a comprehensive literature review, 17 potential critical sustainability factors for post disaster reconstruction were identified. Preliminary examination and discussion of the factors was conducted.

The importance of reporting housing and husbandry in rat research

In 1963, the National Institutes of Health (NIH) first issued guidelines for animal housing and husbandry. The most recent 2010 revision emphasizes animal care “in ways judged to be scientifically, technically, and humanely appropriate” (National Institutes of Health, 2010, p. XIII). The goal of these guidelines is to ensure humanitarian treatment of animals and to optimize the quality of research. Although these animal care guidelines cover a substantial amount of information regarding animal housing and husbandry, researchers generally do not report all these variables (see Table ​Table1).1). The importance of housing and husbandry conditions with respect to standardization across different research laboratories has been debated previously (Crabbe et al., 1999; Van Der Staay and Steckler, 2002; Wahlsten et al., 2003; Wolfer et al., 2004; Van Der Staay, 2006; Richter et al., 2010, 2011). This paper focuses on several animal husbandry and housing issues that are particularly relevant to stress responses in rats, including transportation, handling, cage changing, housing conditions, light levels and the light–dark cycle. We argue that these key animal housing and husbandry variables should be reported in greater detail in an effort to raise awareness about extraneous experimental variables, especially those that have the potential to interact with the stress response.

Analysis of kinase gene expression in the frontal cortex of suicide victims: Implications of fear and stress

Suicide is a serious public health issue that results from an interaction between multiple risk factors including individual vulnerabilities to complex feelings of hopelessness, fear, and stress. Although kinase genes have been implicated in fear and stress, including the consolidation and extinction of fearful memories, expression profiles of those genes in the brain of suicide victims are less clear. Using gene expression microarray data from the Online Stanley Genomics Database 1 and a quantitative PCR, we investigated the expression profiles of multiple kinase genes including the calcium calmodulin-dependent kinase (CAMK), the cyclin-dependent kinase, the mitogen-activated protein kinase (MAPK), and the protein kinase C (PKC) in the prefrontal cortex (PFC) of mood disorder patients died with suicide (N = 45) and without suicide (N = 38). We also investigated the expression pattern of the same genes in the PFC of developing humans ranging in age from birth to 49 year (N = 46). The expression levels of CAMK2B, CDK5, MAPK9, and PRKCI were increased in the PFC of suicide victims as compared to non-suicide controls (false discovery rate, FDR-adjusted p < 0.05, fold change >1.1). Those genes also showed changes in expression pattern during the postnatal development (FDR-adjusted p < 0.05). These results suggest that multiple kinase genes undergo age-dependent changes in normal brains as well as pathological changes in suicide brains. These findings may provide an important link to protein kinases known to be important for the development of fear memory, stress associated neural plasticity, and up-regulation in the PFC of suicide victims. More research is needed to better understand the functional role of these kinase genes that may be associated with the pathophysiology of suicide

Regulation of the Fear Network by Mediators of Stress: Norepinephrine Alters the Balance between Cortical and Subcortical Afferent Excitation of the Lateral Amygdala

Pavlovian auditory fear conditioning involves the integration of information about an acoustic conditioned stimulus (CS) and an aversive unconditioned stimulus in the lateral nucleus of the amygdala (LA). The auditory CS reaches the LA subcortically via a direct connection from the auditory thalamus and also from the auditory association cortex itself. How neural modulators, especially those activated during stress, such as norepinephrine (NE), regulate synaptic transmission and plasticity in this network is poorly understood. Here we show that NE inhibits synaptic transmission in both the subcortical and cortical input pathway but that sensory processing is biased toward the subcortical pathway. In addition binding of NE to β-adrenergic receptors further dissociates sensory processing in the LA. These findings suggest a network mechanism that shifts sensory balance toward the faster but more primitive subcortical input

Fully Bayesian experimental design for pharmacokinetic studies

Utility functions in Bayesian experimental design are usually based on the posterior distribution. When the posterior is found by simulation, it must be sampled from for each future data set drawn from the prior predictive distribution. Many thousands of posterior distributions are often required. A popular technique in the Bayesian experimental design literature to rapidly obtain samples from the posterior is importance sampling, using the prior as the importance distribution. However, importance sampling will tend to break down if there is a reasonable number of experimental observations and/or the model parameter is high dimensional. In this paper we explore the use of Laplace approximations in the design setting to overcome this drawback. Furthermore, we consider using the Laplace approximation to form the importance distribution to obtain a more efficient importance distribution than the prior. The methodology is motivated by a pharmacokinetic study which investigates the effect of extracorporeal membrane oxygenation on the pharmacokinetics of antibiotics in sheep. The design problem is to find 10 near optimal plasma sampling times which produce precise estimates of pharmacokinetic model parameters/measures of interest. We consider several different utility functions of interest in these studies, which involve the posterior distribution of parameter functions.

What is an expert? A systems perspective on expertise

1. Expert knowledge continues to gain recognition as a valuable source of information in a wide range of research applications. Despite recent advances in defining expert knowledge, comparatively little attention has been given to how to view expertise as a system of interacting contributory factors, and thereby, to quantify an individual’s expertise. 2. We present a systems approach to describing expertise that accounts for many contributing factors and their interrelationships, and allows quantification of an individual’s expertise. A Bayesian network (BN) was chosen for this purpose. For the purpose of illustration, we focused on taxonomic expertise. The model structure was developed in consultation with professional taxonomists. The relative importance of the factors within the network were determined by a second set of senior taxonomists. This second set of experts (i.e. supra-experts) also provided validation of the model structure. Model performance was then assessed by applying the model to hypothetical career states in the discipline of taxonomy. Hypothetical career states were used to incorporate the greatest possible differences in career states and provide an opportunity to test the model against known inputs. 3. The resulting BN model consisted of 18 primary nodes feeding through one to three higher-order nodes before converging on the target node (Taxonomic Expert). There was strong consistency among node weights provided by the supra-experts for some nodes, but not others. The higher order nodes, “Quality of work” and “Total productivity”, had the greatest weights. Sensitivity analysis indicated that although some factors had stronger influence in the outer nodes of the network, there was relatively equal influence of the factors leading directly into the target node. Despite differences in the node weights provided by our supra-experts, there was remarkably good agreement among assessments of our hypothetical experts that accurately reflected differences we had built into them. 4. This systems approach provides a novel way of assessing the overall level of expertise of individuals, accounting for multiple contributory factors, and their interactions. Our approach is adaptable to other situations where it is desirable to understand components of expertise.

Reflections on chemistry sessions at the 2012 Healthy Buildings Conference

Scores of well-researched individual papers and posters specifically or indirectly addressing the occurrence, measurement or exposure impacts of chemicals in buildings were presented at 2012 Healthy Buildings Conference. Many of these presentations offered advances in sampling and characterisation of chemical pollutants while others extended the frontiers of knowledge on the emission, adsorption, risk, fate and compositional levels of chemicals in indoor and outdoor microenvironments. Several modelled or monitored indoor chemistry, including processes that generated secondary pollutants. This article provides an overview of the state of knowledge on healthy buildings based on papers presented in chemistry sessions at Healthy Buildings 2012 (HB2012) Conference. It also suggests future directions in healthy buildings research.

Managing growth in the sunshine states : urbanization and planning in Queensland and Florida

This paper compares the urbanization and planning in the two sunshine states of Florida and Queensland highlighting the similarities and differences, evaluates how effective the growth management programs have been, and examines the recent changes and the challenges they bring to the respective states.