Towards a method for rigorous development of generic requirements patterns

We present work in progress on a method for the engineering, validation and verification of generic requirements using domain engineering and formal methods. The need to develop a generic requirement set for subsequent system instantiation is complicated by the addition of the high levels of verification demanded by safety-critical domains such as avionics. Our chosen application domain is the failure detection and management function for engine control systems: here generic requirements drive a software product line of target systems. A pilot formal specification and design exercise is undertaken on a small (twosensor) system element. This exercise has a number of aims: to support the domain analysis, to gain a view of appropriate design abstractions, for a B novice to gain experience in the B method and tools, and to evaluate the usability and utility of that method.We also present a prototype method for the production and verification of a generic requirement set in our UML-based formal notation, UML-B, and tooling developed in support. The formal verification both of the structural generic requirement set, and of a particular application, is achieved via translation to the formal specification language, B, using our U2B and ProB tools

New Langevin and Gradient Thermostats for Rigid Body Dynamics

We introduce two new thermostats, one of Langevin type and one of gradient (Brownian) type, for rigid body dynamics. We formulate rotation using the quaternion representation of angular coordinates; both thermostats preserve the unit length of quaternions. The Langevin thermostat also ensures that the conjugate angular momenta stay within the tangent space of the quaternion coordinates, as required by the Hamiltonian dynamics of rigid bodies. We have constructed three geometric numerical integrators for the Langevin thermostat and one for the gradient thermostat. The numerical integrators reflect key properties of the thermostats themselves. Namely, they all preserve the unit length of quaternions, automatically, without the need of a projection onto the unit sphere. The Langevin integrators also ensure that the angular momenta remain within the tangent space of the quaternion coordinates. The Langevin integrators are quasi-symplectic and of weak order two. The numerical method for the gradient thermostat is of weak order one. Its construction exploits ideas of Lie-group type integrators for differential equations on manifolds. We numerically compare the discretization errors of the Langevin integrators, as well as the efficiency of the gradient integrator compared to the Langevin ones when used in the simulation of rigid TIP4P water model with smoothly truncated electrostatic interactions. We observe that the gradient integrator is computationally less efficient than the Langevin integrators. We also compare the relative accuracy of the Langevin integrators in evaluating various static quantities and give recommendations as to the choice of an appropriate integrator.Comment: 16 pages, 4 figure

Nonequilibrium Temperature and Thermometry in Heat-Conducting Phi-4 Models

We analyze temperature and thermometry for simple nonequilibrium heat-conducting models. We show in detail, for both two- and three-dimensional systems, that the ideal gas thermometer corresponds to the concept of a local instantaneous mechanical kinetic temperature. For the Phi-4 models investigated here the mechanical temperature closely approximates the local thermodynamic equilibrium temperature. There is a significant difference between kinetic temperature and the nonlocal configurational temperature. Neither obeys the predictions of extended irreversible thermodynamics. Overall, we find that kinetic temperature, as modeled and imposed by the Nos\'e-Hoover thermostats developed in 1984, provides the simplest means for simulating, analyzing, and understanding nonequilibrium heat flows.Comment: 20 pages with six figures, revised following review at Physical Review

Delayed gastric emptying and reduced postprandial small bowel water content of equicaloric whole meal bread versus rice meals in healthy subjects: novel MRI insights

BACKGROUND/OBJECTIVES: Postprandial bloating is a common symptom in patients with functional gastrointestinal (GI) diseases. Whole meal bread (WMB) often aggravates such symptoms though the mechanisms are unclear. We used magnetic resonance imaging (MRI) to monitor the intragastric fate of a WMB meal (11% bran) compared to a rice pudding (RP) meal. SUBJECTS/METHODS: 12 healthy volunteers completed this randomised crossover study. They fasted overnight and after an initial MRI scan consumed a glass of orange juice with a 2267 kJ WMB or an equicaloric RP meal. Subjects underwent serial MRI scans every 45 min up to 270 min to assess gastric volumes and small bowel water content and completed a GI symptom questionnaire. RESULTS: The MRI intragastric appearance of the two meals was markedly different. The WMB meal formed a homogeneous dark bolus with brighter liquid signal surrounding it. The RP meal separated into an upper, liquid layer and a lower particulate layer allowing more rapid emptying of the liquid compared to solid phase (sieving). The WMB meal had longer gastric half emptying times (132±8 min) compared to the RP meal (104±7 min), P<0.008. The WMB meal was associated with markedly reduced MRI-visible small bowel free mobile water content compared to the RP meal, P<0.0001. CONCLUSIONS: WMB bread forms a homogeneous bolus in the stomach which inhibits gastric sieving and hence empties slower than the equicaloric rice meal. These properties may explain why wheat causes postprandial bloating and could be exploited to design foods which prolong satiation

Destructive harvesting of wild honey in Miombo woodlands affects keystone elements in the ecosystem

Protected areas cover 13% of the world's terrestrial surface. With increasing demands on land and with challenges of land degradation and climate change, conflicts between conservation and use are on the rise, particularly in developing countries. Effective management of these conflicts requires viable livelihood options for local land users which are in line with nature conservation goals. Consolidation of nature conservation guidelines with local land use practices may be particularly challenging where keystone species are affected or where land uses have the potential for leading to ecosystem changes. This can be an issue even in ecosystems like savannahs, where fire largely defines ecosystem structure. The Miombo woodlands, covering around 2.4 million km2 of land, harbour important diversity and are crucial for livelihoods of around 75 million people in southern Africa. As a result of various pressures, cover and biomass of Miombo woodlands are declining throughout their range. Honey harvesting is an important land use in Miombo areas, both economically and culturally. Wild bees use cavities in trees for their colonies. Harvesting practices in some places include felling of trees with honeycombs to collect the honey and setting fire for pacifying bees. This leads to starvation and death of bee colonies. Given that most tree species are bee pollinated, trees with cavities colonised by wild bees can be classified as keystone elements in these ecosystems. Although ecologically far reaching, the effects of this harvesting practice on tree population structures in Miombo woodlands have seldom been studied. We characterised the ecological effects of destructive harvesting of wild honey on tree population structure and tree species distribution in Miombo woodlands in the Niassa wildlife reserve in Mozambique. The results show that forest structure and tree diversity differed along honey harvesting intensity gradients, with the highest number of fire tolerant tree species in areas with high honey harvesting intensity, which also showed the lowest tree regeneration density and Shannon diversity. Options for reconciling livelihoods with ecosystem maintenance do exist and include non-destructive harvesting based on climbing trees with locally produced ropes and leaving larval combs behind so the colony could continue to grow

Relearning traditional knowledge to achieve sustainability: honey gathering in the miombo woodlands of northern Mozambique

Mozambique’s Niassa Reserve contains Africa’s best preserved miombo woodlands. Half of the households there gather wild honey from natural hives for consumption and income. However, most collectors used destructive techniques: setting fire to the grasses under the hive tree to create smoke and then felling the tree. Cutting trees to obtain honey was the principal source of tree mortality. Trees grow very slowly, about 0.25 cm diameter [dbh]/yr, meaning an average hive tree was nearly 200 years old. Furthermore, of the trees > 20 cm dbh of species important for nectar and hives, only about 15% had cavities. Although fire is intrinsic to miombo woodlands, the increased frequency resulting from anthropogenic sources impedes regeneration of some tree species as well as affecting bees, other wildlife and villages. A few people in the reserve had learned from earlier generations how to gather honey in a nondestructive way, using certain plant species to keep bees from stinging and climbing the trees using ropes to take the honey combs out of the hives. Traditional practices included leaving the larval combs behind so the colony continued to grow. Previously, the older men who had this knowledge had not been willing to share it with younger men. The project arranged for one of the traditional honey hunters to participate in an international conference on honey collection with other indigenous collectors from around the world. This helped him recognize the value of his knowledge. The project team then arranged for him to demonstrate these traditional techniques to groups of honey hunters in nine communities within the Reserve. A yearlater, monitoring revealed that many collectors had adopted these nondestructive techniques. They found them less time consuming, and appreciated that they allowed collectors to return to the same trees repeatedly to obtain honey. Sharing traditional knowledge made honey hunting compatible with the conservation of miombo woodlands

Local influence of boundary conditions on a confined supercooled colloidal liquid

We study confined colloidal suspensions as a model system which approximates the behavior of confined small molecule glass-formers. Dense colloidal suspensions become glassier when confined between parallel glass plates. We use confocal microscopy to study the motion of confined colloidal particles. In particular, we examine the influence particles stuck to the glass plates have on nearby free particles. Confinement appears to be the primary influence slowing free particle motion, and proximity to stuck particles causes a secondary reduction in the mobility of free particles. Overall, particle mobility is fairly constant across the width of the sample chamber, but a strong asymmetry in boundary conditions results in a slight gradient of particle mobility.Comment: For conference proceedings, "Dynamics in Confinement", Grenoble, March 201

By hook or by crook? Morphometry, competition and cooperation in rodent sperm

Background Sperm design varies enormously across species and sperm competition is thought to be a major factor influencing this variation. However, the functional significance of many sperm traits is still poorly understood. The sperm of most murid rodents are characterised by an apical hook of the sperm head that varies markedly in extent across species. In the European woodmouse Apodemus sylvaticus (Muridae), the highly reflected apical hook of sperm is used to form sperm groups, or “trains,” which exhibited increased swimming velocity and thrusting force compared to individual sperm. Methodology/Principal Findings Here we use a comparative study of murine rodent sperm and demonstrate that the apical hook and sperm cooperation are likely to be general adaptations to sperm competition in rodents. We found that species with relatively larger testes, and therefore more intense sperm competition, have a longer, more reflected apical sperm hook. In addition, we show that sperm groups also occur in rodents other than the European woodmouse. Conclusions Our results suggest that in rodents sperm cooperation is more widespread than assumed so far and highlight the importance of diploid versus haploid selection in the evolution of sperm design and function

Clinical risk factors for underlying gastrointestinal malignancy in iron deficiency anaemia–prospective validation of the IDIOM score

Objective: Ten percent of adults presenting with iron deficiency anaemia (IDA) have underlying cancer. This study was undertaken to prospectively validate the observation in a previous retrospective study that three simple clinical parameters can usefully predict the likelihood of gastrointestinal (GI) malignancy on investigation of patients with IDA, and to screen for other potential clinical predictors of risk. Method: Observational study of a cohort of 643 subjects attending an IDA clinic at a District General Hospital between 2012 and 2015, with multivariable analysis of the predictive value of a series of clinical variables including sex, age and haemoglobin concentration ([Hb]) for underlying GI malignancy. Results: Analysis of the validation cohort data confirmed the original observation that sex, age, and Hb were associated with the risk of GI malignancy—the parsimonious model including only these variables yielded odds ratios of 1.9 (95% confidence interval (CI): 1.1, 3.3) for males vs. females; 1.6 (95% CI: 0.9, 2.9) for age >70 vs. ≤70 years; and 2.9 (95% CI:1.2, 6.9) for [Hb] 112 g/l. Combining data from the observation and validation cohorts (total n = 1,363) identified sub-groups with cancer risks ranging from 0% to over 20%. No other predictive clinical variables were identified. Conclusions: Three simple and objective clinical parameters can be combined to provide a clinically useful cancer risk stratification model for subjects with IDA. This may assist with patient counselling and the prioritisation of investigational resources