Multi-objective optimization based engineering decision tool

Prior to the acceptance of computer aided engineering (CAE) software in the product development process (PDP), product development was characterized by a design-test-redesign-test cycle. This activity was time consuming and resource intensive. As CAE software tools have been integrated into the PDP, the PDP can be characterized by a design-simulate-redesign-test cycle. The addition of CAE tools to the PDP has reduced the time to market and resource consumption. In the last decade, CAE software has become easier to use and computer power has increased such that CAE software is more widely used in the PDP. In parallel, there has been a desire, in the last decade, to further reduce product development times and resource consumption. To achieve this next step in reduction of PDP time and resource consumption, the need for increased integration of CAE software earlier in the PDP is needed. This will provide the design engineer with increased design problem knowledge earlier in the PDP, which is when increased knowledge about the design problem is most valuable in the PDP timeline and can impact the product design the most. Design problems are characterized by having multiple solutions. The implication of this is that there are multiple acceptable solutions but there are few global optimum solutions. It is the design engineer\u27s chief aim to find the most optimum solution to the design problem at hand. Simply put, the aim of the method presented in this thesis is to integrate computational fluid dynamics (CFD) models earlier in the PDP to facilitate engineering decision making early in the PDP. In this thesis, a simulation workflow is demonstrated that connects computer aided design (CAD) software with CFD software, which is a CAE software, with both connected to a multi-objective optimization algorithm. This simulation workflow is used to generate a Pareto-optimal set of designs, sometimes called non-dominant, set of designs. The design problem is represented in the CAD software with the geometric design variables explicitly defined in the CAD representation of the design problem. The CFD software is used to calculate the performance objectives of the design solution. The multi-objective optimization algorithm evaluates the performance of the design solution and chooses new design variable values for use in the CAD representation. This process continues until the Pareto-optimal set of designs is identified. This is the Level-1 optimization of the overall framework presented in this thesis. The Level-2 optimization consists of an algorithm that operates on the Pareto-optimal set of designs identified in the Level-1 optimization. The algorithm presents the user with a number of designs from the Pareto-optimal set. The user chooses the best design solution from the design solutions shown based on higher-level, qualitative information. This continues until all of the Pareto-optimal designs have been evaluated or the user terminates the process. This simulation flow facilitates using CAE software, specifically CFD, earlier in the PDP which leads to simulation based design. This maximizes design problem knowledge earlier in the PDP, reduces the PDP time, and reduces the resources required to develop a new product

Ecology and evolution of the specialized hemipepsis-wasp (Hymenoptera : Pompilidae) pollination guild in South Africa.

Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.Pollinators are believed to have played a key role in the radiation of flowering plants. The Grant-Stebbins model of pollinator-mediated speciation, in which evolutionary shifts between pollinators result in phenotypic diversification and enforce reproductive isolation, is one of the most compelling hypotheses for the rapid diversification of angiosperms. A key principle in this model is that plant pollination systems tend towards specialization, resulting in convergent suites of floral traits (syndromes) associated with particular types of pollinators. However, the expectation of pollination system specialization is not always supported by ecological data and has also been questioned on theoretical grounds. In this thesis, I examine pollination by Hemipepsis spider-hunting wasps (Hymenoptera, Pompilidae, Pepsinae) and use this system to address questions about levels and proximal mechanisms of floral specialization, floral shifts and convergent evolution of floral traits. Specialized pollination by Hemipepsis wasps is a newly described pollination system within the angiosperms. I document pollination by these wasps for the first time in 15 South African grassland plant species, including two species of Eucomis (Hyacinthaceae) and 13 asclepiads (Apocynaceae: Asclepiadoideae). In one of the asclepiads, Xysmalobium undulatum, I describe a bimodal pollination system involving both Hemipepsis wasps and a cetoniine beetle. I also describe an unusual and potentially antagonistic pollination mechanism whereby wasps are systematically dismembered during the insertion of pollinia in the two asclepiads Pachycarpus asperifolius and P. appendiculatus. I have used these and previous case studies to establish the existence of a new pollination guild, consisting of at least 21 plant species (across 10 genera and three families), that are reliant on four functionally similar species of Hemipepsis wasp for pollination. Plants in the guild are distributed throughout the moist grasslands of eastern South Africa and flower from September through until early May, peaking in December/January. The Hemipepsis-wasp pollination guild is characterized by high levels of functional specialization (17 of the 21 known guild members are pollinated exclusively by Hemipepsis wasps), despite the absence of morphological adaptations to prevent non-pollinating insects from accessing nectar. I used field and laboratory based experiments to explore the function of floral traits in enforcing specialization. These showed that Hemipepsis wasps primarily use scent, rather than visual cues, to locate flowers, but I was unable to firmly identify specific compounds responsible for the attraction of these wasps (compounds that elicited antennal responses in preliminary GC-EAD experiments did not attract wasps in bioassays). The chemical composition of the floral scents of guild members was examined for 71 individuals representing 14 species in addition to previous studies, and found to comprise complex blends of volatiles (usually containing between 30 and 50 compounds), typically dominated by aliphatics and monoterpenes with small amounts of aromatics. I also showed that the floral colours of guild members are similar to background vegetation, suggesting that floral colours are adapted for crypsis to avoid detection by non-pollinating insects. Palatability choice experiments with honeybees showed that non-pollinating insects find the nectars of at least three of the asclepiad guild members distasteful. Plants in this guild thus appear to achieve specialization through biochemical filters (scent as an attractant and differentially palatable nectar) and cryptic coloration. Pollinator-mediated convergence in floral traits is the fundamental basis for pollination syndromes, but has seldom been rigorously analyzed. Flowers in the Hemipepsis-wasp pollination guild share several qualitative traits, including dull greenish- or brownish-white colour, often with purple blotches, exposed sucrose dominant nectar with a relatively high sugar concentration (typically over 50% sugar by weight) and a sweet/spicy fragrance to the human nose. To test for convergent evolution in guild members, I compared scent, nectar and colour traits of guild members to those of congeners with different pollinators. Although traits often differed between guild members and their congeners, I found little evidence for overall convergence in floral scent profiles and nectar properties, but floral colours in the guild were significantly closer to the colour of background vegetation than those of congeners. At this stage, the lack of knowledge about specific floral volatiles that influence Hemipepsis-wasp behaviour and secondary nectar constituents that limit non-pollinator visits makes it difficult to identify the extent of biochemical convergent evolution within the guild. The directions and functional traits involved in evolutionary transitions between pollination by Hemipepsis wasps and other vectors are currently difficult to ascertain as there is limited phylogenetic data for the plant families concerned. In the genus Eucomis, fly and Hemipepsis-wasp pollinated species are very similar in floral morphology and colour, but differ strongly in floral scent. Using manipulative field experiments in conjunction with detailed analyses of colour, scent and morphology, I was able to show that a shift between wasp and fly pollination could be induced simply by manipulating oligosulphides in the scent emission from inflorescences. When considered in combination with other experiments highlighting the importance of scent as a pollinator attractant for all guild members, this suggests that scent properties may have played a key role in the evolutionary transitions between pollination by Hemipepsis wasps and other vectors. This research has established that pollination by Hemipepsis spider-hunting wasps is more geographically and phylogenetically widespread than was previously known, and has confirmed that these wasps are important and consistent pollinators in southern African grassland ecosystems. I have shown that a distinct guild of plants is specialized for pollination by these wasps. The high levels of specialization within this guild highlight the effectiveness of biochemical filters and cryptic coloration in limiting the spectrum of flower visitors. The major challenge ahead will be to identify the floral volatiles that attract Hemipepsis wasps and the non-sugar constituents that make the nectars of some guild members differentially palatable. These would both contribute greatly to our understanding of floral specialization and the mechanisms involved in the radiation of the angiosperms

Survey-based pilot study into the chosen therapy and prophylaxis used by UK primary care veterinary surgeons against canine angiostrongylosis

Canine Angiostrongylosis (CA), a gastropod-borne parasitic infection caused by the metastrongyloid nematode Angiostrongylus vasorum, is an important cause of significant morbidity to domestic dogs across the UK as well as in other European countries. This study aimed to ascertain the frequency at which particular drugs were used by primary care practitioners in the UK for therapy against and prophylaxis for CA. Primary care veterinary clinicians were surveyed using an online questionnaire and face-to-face or telephone interviews. Eighty-six veterinary surgeons responded. The majority of practices (n = 52) included lungworm in their standard anthelmintic protocols; moxidectin was the most common drug used for prophylaxis (n = 71). Fenbendazole was the most frequently selected drug, by 45% of vets, for treatment of confirmed cases of CA despite it being unlicensed for this purpose in the UK and the absence of a clear treatment protocol. The results of this pilot study provide an initial insight into the approach taken by primary care practitioners in their approach to CA. This provides an important starting point for future studies investigating the decision-making for CA amongst UK veterinary surgeons, particularly to clarify whether in a larger cohort an unlicensed drug remains the treatment of choice. The absence of a clear protocol for fenbendazole means that treatment of dogs affected by CA may be suboptimal, increasing the risk of morbidity and mortality

GC-MS/FID/EAD: A method for combining mass spectrometry with gas chromatography-electroantennographic detection

Gas chromatography-electroantennographic detection (GC-EAD), typically combined with a flame ionization detector (FID), is a widely used technique for studying insect semiochemicals. Combining mass spectrometry (MS) with GC-EAD is extremely beneficial, but has seldom been adopted, possibly due to the practical challenges associated with incorporating an MS (under vacuum) into a GC-EAD system. We describe a novel method of incorporating MS into a GC-EAD system, where the FID is maintained in the system rather than being replaced by an MS. With this method, effluent is still split between EAD and FID, with the FID being used to assign components that elicit antennal responses, as in a normal GC-FID/EAD system. The MS is introduced via a second effluent splitter inserted before the split between the EAD and the FID. This method allows for EAD, FID, and MS data to be obtained from a single injection, which is especially useful for analysis of thermally desorbed and solid-phase microextraction (SPME) samples. This configuration is also relatively simple to implement and resolves some of the practical challenges associated with dividing effluent between a detector at atmospheric pressure (a live antenna) and a detector under vacuum (the MS). We present test runs with hawkmoth antennae and floral volatiles to demonstrate the effectiveness of this system, and discuss the challenges and practical solutions to incorporating MS into a GC-EAD system that retains an FID detector

Plant volatiles are a salient cue for foraging mammals : elephants target preferred plants despite background plant odour

To forage nonrandomly, animals must discriminate among food items. Foods differ in look, smell and taste, providing cues for foragers with appropriate senses. Irrespective of the sensory modality, however, foragers can only use cues effectively if they can detect sensory signals above background noise. Recent evidence shows that foraging mammalian herbivores can detect plant odours, but their capacity to select preferred plants in a noisy olfactory background is unknown. Using choice trials, we tested whether the African elephant, Loxodonta africana, uses plant odour as a salient cue despite increasingly complex and challenging background odours. We first established their preference for familiar plant species. We then tested their capacity to discriminate and select preferred plants based on odour alone. We found that elephants successfully chose preferred species even when presented with complex background odours from nonpreferred plants mimicking multispecies vegetation patches. Elephants also succeeded despite our attempt to mask distinguishing odours with large amounts of a synthetic green leaf volatile. GC–MS analysis confirmed that volatile organic compound profiles differed between plant species. In demonstrating that elephants exploit plant odours even when the signal from preferred plants is embedded in sensory noise of background odours, we provide crucial behavioural evidence that olfaction provides an efficient mechanism for selective, nonrandom foraging. Whether mammalian herbivores recognize novel odours, for example from newly invading plant species, or when air pollution degrades odours of familiar plants, needs investigating. Accounting for the capacity of mammalian herbivores to use plant odour cues will improve models of both their foraging behaviour and the ecosystem impacts of their foraging.A.S. and M.H.S. were supported by the South African National Research Foundation (Grants #: 90691, 90448 & 97262).http://www.elsevier.com/locate/anbehav2020-09-01hj2019Mammal Research InstituteZoology and Entomolog

Empirical Quantification of Predictive Uncertainty Due to Model Discrepancy by Training with an Ensemble of Experimental Designs: An Application to Ion Channel Kinetics

When using mathematical models to make quantitative predictions for clinical or industrial use, it is important that predictions come with a reliable estimate of their accuracy (uncertainty quantification). Because models of complex biological systems are always large simplifications, model discrepancy arises—models fail to perfectly recapitulate the true data generating process. This presents a particular challenge for making accurate predictions, and especially for accurately quantifying uncertainty in these predictions. Experimentalists and modellers must choose which experimental procedures (protocols) are used to produce data used to train models. We propose to characterise uncertainty owing to model discrepancy with an ensemble of parameter sets, each of which results from training to data from a different protocol. The variability in predictions from this ensemble provides an empirical estimate of predictive uncertainty owing to model discrepancy, even for unseen protocols. We use the example of electrophysiology experiments that investigate the properties of hERG potassium channels. Here, ‘information-rich’ protocols allow mathematical models to be trained using numerous short experiments performed on the same cell. In this case, we simulate data with one model and fit it with a different (discrepant) one. For any individual experimental protocol, parameter estimates vary little under repeated samples from the assumed additive independent Gaussian noise model. Yet parameter sets arising from the same model applied to different experiments conflict—highlighting model discrepancy. Our methods will help select more suitable ion channel models for future studies, and will be widely applicable to a range of biological modelling problems

The diversity and evolution of pollination systems in large plant clades: Apocynaceae as a case study

Large clades of angiosperms are often characterized by diverse interactions with pollinators, but how these pollination systems are structured phylogenetically and biogeographically is still uncertain for most families. Apocynaceae is a clade of >5300 species with a worldwide distribution. A database representing >10 % of species in the family was used to explore the diversity of pollinators and evolutionary shifts in pollination systems across major clades and regions.The database was compiled from published and unpublished reports. Plants were categorized into broad pollination systems and then subdivided to include bimodal systems. These were mapped against the five major divisions of the family, and against the smaller clades. Finally, pollination systems were mapped onto a phylogenetic reconstruction that included those species for which sequence data are available, and transition rates between pollination systems were calculated.Most Apocynaceae are insect pollinated with few records of bird pollination. Almost three-quarters of species are pollinated by a single higher taxon (e.g. flies or moths); 7 % have bimodal pollination systems, whilst the remaining approx. 20 % are insect generalists. The less phenotypically specialized flowers of the Rauvolfioids are pollinated by a more restricted set of pollinators than are more complex flowers within the Apocynoids + Periplocoideae + Secamonoideae + Asclepiadoideae (APSA) clade. Certain combinations of bimodal pollination systems are more common than others. Some pollination systems are missing from particular regions, whilst others are over-represented.Within Apocynaceae, interactions with pollinators are highly structured both phylogenetically and biogeographically. Variation in transition rates between pollination systems suggest constraints on their evolution, whereas regional differences point to environmental effects such as filtering of certain pollinators from habitats. This is the most extensive analysis of its type so far attempted and gives important insights into the diversity and evolution of pollination systems in large clades

Geographic variation in genetic composition, sexual communication and mating compatibility of the False Codling Moth, Thaumatotibia leucotreta for optimisation of area-wide control

Intraspecific variation in sex pheromones is a driver of reproductive isolation and speciation in insects. The False Codling Moth (FCM) Thaumatotibia leucotreta (Lepidoptera: Tortricidae) is a quarantine pest endemic to sub-Saharan Africa (SSA). The currently available precision control measures for FCM use female sex pheromone components to lure males into traps. However, the existing data on the composition of the female sex pheromone, especially the isomer ratios of the main pheromone component (E/Z)-8-dodecenyl acetate, are inconsistent for populations in SSA. This inconsistency led to speculation about possible reproductive isolation between geographically separated FCM populations and the potential need for local adjustment of pheromone-based FCM control tools. This, however, requires a comparative evaluation of geographic variation in FCM sexual communication and inter-population mating compatibility. We therefore investigated genetic isolation and mating compatibility between five geographically isolated FCM populations in South Africa and analysed the ratio of (E)- and (Z)-8-dodecenyl acetate in females from these populations. The five studied populations were found to form three genetically distinct groups with high genetic distances between each other. Mating compatibility tests showed that mating is possible across these groups, however, males preferred females of their own population when given choices; without a choice, males successfully mated with and transferred spermatophores to females from all other populations. The ratio of (E)- and (Z)-8-dodecenyl acetate was similar (c. 4:1) across the populations, indicating that this main female pheromone component does not cause the observed intra-population mating preferences. It remains to be investigated if qualitative/quantitative variation in other sex pheromone components influences intra-population recognition in South African FCM, providing a base for the development of regionally-specific lures for area-wide control programmes

Assessing a potential non-invasive method for viral diagnostic purposes in European squirrels.

Viral infections globally threaten wild and captive mammal populations, with surveillance options limited by a lack of non-invasive diagnostics; especially when infection is asymptomatic in nature. We explored the potential for hair samples collected from red (Sciurus vulgaris) and grey (Sciurus carolinensis) squirrels to provide a means of screening for adenovirus (ADV) and squirrelpox virus (SQPV) using evolving polymerase chain reaction (PCR) assays. An initial pilot study phase utilised samples opportunistically harvested from grey squirrels controlled in Gwynedd, United Kingdom (UK). The screening of 319 grey squirrel carcasses revealed 58% spleen ADV DNA qPCR and 69% SQPV antibody enzyme linked immunosorbent assay (ELISA) positives. We developed new nested ADV and SQPV qPCRs and examined tail hair samples from a sub-set of 80 of these 319 sampled squirrels and these assays amplified ADV and SQPV DNA in a higher proportion of animals than the original qPCR (94% and 21% respectively). Tail hair samples obtained from six Cumbrian red squirrels which had died from squirrelpox disease also revealed 100% SQPV and 50% ADV DNA positive by the nested qPCR assays. These findings indicate enhanced sensitivity for the new platform. The integration of this non-invasive approach in assessing viral infection has wide application in epidemiological studies of wild mammal populations, in particular, during conservation translocations, where asymptomatic infections are of concern

The diversity and evolution of pollination systems in large plant clades: Apocynaceae as a case study

Background and Aims Large clades of angiosperms are often characterized by diverse interactions with pollinators, but how these pollination systems are structured phylogenetically and biogeographically is still uncertain for most families. Apocynaceae is a clade of >5300 species with a worldwide distribution. A database representing >10 % of species in the family was used to explore the diversity of pollinators and evolutionary shifts in pollination systems across major clades and regions. Methods The database was compiled from published and unpublished reports. Plants were categorized into broad pollination systems and then subdivided to include bimodal systems. These were mapped against the five major divisions of the family, and against the smaller clades. Finally, pollination systems were mapped onto a phylogenetic reconstruction that included those species for which sequence data are available, and transition rates between pollination systems were calculated. Key Results Most Apocynaceae are insect pollinated with few records of bird pollination. Almost three-quarters of species are pollinated by a single higher taxon (e.g. flies or moths); 7 % have bimodal pollination systems, whilst the remaining approx. 20 % are insect generalists. The less phenotypically specialized flowers of the Rauvolfioids are pollinated by a more restricted set of pollinators than are more complex flowers within the Apocynoids + Periplocoideae + Secamonoideae + Asclepiadoideae (APSA) clade. Certain combinations of bimodal pollination systems are more common than others. Some pollination systems are missing from particular regions, whilst others are over-represented. Conclusions Within Apocynaceae, interactions with pollinators are highly structured both phylogenetically and biogeographically. Variation in transition rates between pollination systems suggest constraints on their evolution, whereas regional differences point to environmental effects such as filtering of certain pollinators from habitats. This is the most extensive analysis of its type so far attempted and gives important insights into the diversity and evolution of pollination systems in large clades