Spud 1.0: generalising and automating the user interfaces of scientific computer models

The interfaces by which users specify the scenarios to be simulated by scientific computer models are frequently primitive, under-documented and ad-hoc text files which make using the model in question difficult and error-prone and significantly increase the development cost of the model. In this paper, we present a model-independent system, Spud, which formalises the specification of model input formats in terms of formal grammars. This is combined with an automated graphical user interface which guides users to create valid model inputs based on the grammar provided, and a generic options reading module, libspud, which minimises the development cost of adding model options. <br><br> Together, this provides a user friendly, well documented, self validating user interface which is applicable to a wide range of scientific models and which minimises the developer input required to maintain and extend the model interface

Life cycle assessment of biofuels from Jatropha curcas in West Africa: a field study

In recent years, liquid biofuels for transport have benefited from significant political support due to their potential role in curbing climate change and reducing our dependence on fossil fuels. They may also participate to rural development by providing new markets for agricultural production. However, the growth of energy crops has raised concerns due to their high consumption of conventional fuels, fertilizers and pesticides, their impacts on ecosystems and their competition for arable land with food crops. Lowinput species such as Jatropha curcas, a perennial, inedible crop well adapted to semiarid regions, has received much interest as a new alternative for biofuel production, minimizing adverse effects on the environment and food supply. Here, we used life-cycle assessment to quantify the benefits of J. curcas biofuel production inWest Africa in terms of greenhouse gas emissions and fossil energy use, compared with fossil diesel fuel and other biofuels. Biodiesel from J. curcas has a much higher performance than current biofuels, relative to oil-derived diesel fuels. Under West Africa conditions, J. curcas biodiesel allows a 72% saving in greenhouse gas emissions compared with conventional diesel fuel, and its energy yield (the ratio of biodiesel energy output to fossil energy input) is 4.7. J. curcas production studied is eco-compatible for the impacts under consideration and fits into the context of sustainable development

The relationship between web enjoyment and student perceptions and learning using a web-based tutorial

Web enjoyment has been regarded as a component of system experience. However, there has been little targeted research considering the role of web enjoyment alone in student learning using web-based systems. To address this gap, this study aims to examine the influence of web enjoyment on learning performance and perceptions by controlling system experience as a variable in the study. 74 students participated in the study, using a web-based tutorial covering subject matter in the area of 'Computation and algorithms'. Their learning performance was assessed with a pre-test and a post-test and their learning perceptions were evaluated with a questionnaire. The results indicated that there are positive relationships between the levels of web enjoyment and perceived usefulness and non-linear navigation for users with similar, significant levels of system experience. The implications of these findings in relation to web-based learning are explored and ways in which the needs of students who report different levels of web enjoyment might be met are discussed

What science can do for democracy – A complexity science approach

Political scientists have conventionally assumed that achieving democracy is a one-way ratchet. Only very recently has the question of ‘democratic backsliding’ attracted any research attention. We argue that democratic instability is best understood with tools from complexity science. The explanatory power of complexity science arises from several features of complex systems. Their relevance in the context of democracy is discussed. Several policy recommendations are offered to help (re)stabilize current systems of representative democracy

Gender- and gamete-specific patterns of X chromosome segregation in a three-gendered nematode

Meiosis is at the core of sexual reproduction and alterations to its program can have dramatic effects. In this study, we investigate the segregation pattern of the X chromosome in Auanema rhodensis, a three-gendered nematode. This species has an atypical pattern of X chromosome segregation during male spermatogenesis that results in the exclusive production of haplo-X sperm. Here we use a combination of genetic and cytological approaches to show that while XX females undergo conventional meiosis to produce mostly haplo-X oocytes, hermaphrodites undergo atypical meiosis to produce nullo-X oocytes and mostly diplo-X sperm. Gender- and gamete-specific alterations of the normal meiotic program include non-pairing of the X homologs and precocious separation of X chromatids. Given these intra-species, intra-individual and intra-gametogenesis variations in meiotic program of A. rhodensis, we argue that it is an ideal model to study the plasticity of meiosis and how it can be modulated

The Web of Connections between Tourism Companies in Elba: Structure and Dynamics

Tourism destination networks are amongst the most complex dynamical systems, involving a myriad of human-made and natural resources. In this work we report a complex network-based systematic analysis of the Elba (Italy) tourism destination network, including the characterization of its structure in terms of a set of several traditional measurements, the investigation of its modularity, as well as its comprehensive study in terms of the recently reported superedges approach. In particular, structural (the number of paths of distinct lengths between pairs of nodes, as well as the number of reachable companies) and dynamical features (transition probabilities and the inward/outward activations and accessibilities) are measured and analyzed, leading to a series of important findings related to the interactions between tourism companies. Among the several reported results, it is shown that the type and size of the companies influence strongly their respective activations and accessibilities, while their geographical position does not seem to matter. It is also shown that the Elba tourism network is largely fragmented and heterogeneous, so that it could benefit from increased integration.Comment: 13 pages, 7 figures, 5 tables. Corrected typos and added reference

Molecular crowding defines a common origin for the Warburg effect in proliferating cells and the lactate threshold in muscle physiology

Aerobic glycolysis is a seemingly wasteful mode of ATP production that is seen both in rapidly proliferating mammalian cells and highly active contracting muscles, but whether there is a common origin for its presence in these widely different systems is unknown. To study this issue, here we develop a model of human central metabolism that incorporates a solvent capacity constraint of metabolic enzymes and mitochondria, accounting for their occupied volume densities, while assuming glucose and/or fatty acid utilization. The model demonstrates that activation of aerobic glycolysis is favored above a threshold metabolic rate in both rapidly proliferating cells and heavily contracting muscles, because it provides higher ATP yield per volume density than mitochondrial oxidative phosphorylation. In the case of muscle physiology, the model also predicts that before the lactate switch, fatty acid oxidation increases, reaches a maximum, and then decreases to zero with concomitant increase in glucose utilization, in agreement with the empirical evidence. These results are further corroborated by a larger scale model, including biosynthesis of major cell biomass components. The larger scale model also predicts that in proliferating cells the lactate switch is accompanied by activation of glutaminolysis, another distinctive feature of the Warburg effect. In conclusion, intracellular molecular crowding is a fundamental constraint for cell metabolism in both rapidly proliferating- and non-proliferating cells with high metabolic demand. Addition of this constraint to metabolic flux balance models can explain several observations of mammalian cell metabolism under steady state conditions

Learning health ‘safety’ within non-technical skills interprofessional simulation education: a qualitative study

Background: Healthcare increasingly recognises and focusses on the phenomena of ‘safe practice’ and ‘patient safety.’ Success with non-technical skills (NTS) training in other industries has led to widespread transposition to healthcare education, with communication and teamwork skills central to NTS frameworks. Objective: This study set out to identify how the context of interprofessional simulation learning influences NTS acquisition and development of ‘safety’ amongst learners. Methods: Participants receiving a non-technical skills (NTS) safety focussed training package were invited to take part in a focus group interview which set out to explore communication, teamwork, and the phenomenon of safety in the context of the learning experiences they had within the training programme. The analysis was aligned with a constructivist paradigm and took an interactive methodological approach. The analysis proceeded through three stages, consisting of open, axial, and selective coding, with constant comparisons taking place throughout each phase. Each stage provided categories that could be used to explore the themes of the data. Additionally, to ensure thematic saturation, transcripts of observed simulated learning encounters were then analysed. Results: Six themes were established at the axial coding level, i.e., analytical skills, personal behaviours, communication, teamwork, context, and pedagogy. Underlying these themes, two principal concepts emerged, namely: intergroup contact anxiety – as both a result of and determinant of communication – and teamwork, both of which must be considered in relation to context. These concepts have subsequently been used to propose a framework for NTS learning. Conclusions: This study highlights the role of intergroup contact anxiety and teamwork as factors in NTS behaviour and its dissipation through interprofessional simulation learning. Therefore, this should be a key consideration in NTS education. Future research is needed to consider the role of the affective non-technical attributes of intergroup contact anxiety and teamwork as focuses for education and determinants of safe behaviour

Owning an overweight or underweight body: distinguishing the physical, experienced and virtual body

Our bodies are the most intimately familiar objects we encounter in our perceptual environment. Virtual reality provides a unique method to allow us to experience having a very different body from our own, thereby providing a valuable method to explore the plasticity of body representation. In this paper, we show that women can experience ownership over a whole virtual body that is considerably smaller or larger than their physical body. In order to gain a better understanding of the mechanisms underlying body ownership, we use an embodiment questionnaire, and introduce two new behavioral response measures: an affordance estimation task (indirect measure of body size) and a body size estimation task (direct measure of body size). Interestingly, after viewing the virtual body from first person perspective, both the affordance and the body size estimation tasks indicate a change in the perception of the size of the participant’s experienced body. The change is biased by the size of the virtual body (overweight or underweight). Another novel aspect of our study is that we distinguish between the physical, experienced and virtual bodies, by asking participants to provide affordance and body size estimations for each of the three bodies separately. This methodological point is important for virtual reality experiments investigating body ownership of a virtual body, because it offers a better understanding of which cues (e.g. visual, proprioceptive, memory, or a combination thereof) influence body perception, and whether the impact of these cues can vary between different setups

Scaling of cardiac morphology is interrupted by birth in the developing sheep Ovis aries.

Scaling of the heart across development can reveal the degree to which variation in cardiac morphology depends on body mass. In this study, we assessed the scaling of heart mass, left and right ventricular masses, and ventricular mass ratio, as a function of eviscerated body mass across fetal and postnatal development in Horro sheep Ovis aries (~50-fold body mass range; N = 21). Whole hearts were extracted from carcasses, cleaned, dissected into chambers and weighed. We found a biphasic relationship when heart mass was scaled against body mass, with a conspicuous 'breakpoint' around the time of birth, manifest not by a change in the scaling exponent (slope), but rather a jump in the elevation. Fetal heart mass (g) increased with eviscerated body mass (Mb , kg) according to the power equation 4.90 Mb0.88 ± 0.26 (± 95%CI) , whereas postnatal heart mass increased according to 10.0 Mb0.88 ± 0.10 . While the fetal and postnatal scaling exponents are identical (0.88) and reveal a clear dependence of heart mass on body mass, only the postnatal exponent is significantly less than 1.0, indicating the postnatal heart becomes a smaller component of body mass as the body grows, which is a pattern found frequently with postnatal cardiac development among mammals. The rapid doubling in heart mass around the time of birth is independent of any increase in body mass and is consistent with the normalization of wall stress in response to abrupt changes in volume loading and pressure loading at parturition. We discuss variation in scaling patterns of heart mass across development among mammals, and suggest that the variation results from a complex interplay between hard-wired genetics and epigenetic influences