Exploring Behavior Discovery Methods for Heterogeneous Swarms of Limited-Capability Robots

We study the problem of determining the emergent behaviors that are possible given a functionally heterogeneous swarm of robots with limited capabilities. Prior work has considered behavior search for homogeneous swarms and proposed the use of novelty search over either a hand-specified or learned behavior space followed by clustering to return a taxonomy of emergent behaviors to the user. In this paper, we seek to better understand the role of novelty search and the efficacy of using clustering to discover novel emergent behaviors. Through a large set of experiments and ablations, we analyze the effect of representations, evolutionary search, and various clustering methods in the search for novel behaviors in a heterogeneous swarm. Our results indicate that prior methods fail to discover many interesting behaviors and that an iterative human-in-the-loop discovery process discovers more behaviors than random search, swarm chemistry, and automated behavior discovery. The combined discoveries of our experiments uncover 23 emergent behaviors, 18 of which are novel discoveries. To the best of our knowledge, these are the first known emergent behaviors for heterogeneous swarms of computation-free agents. Videos, code, and appendix are available at the project website: https://sites.google.com/view/heterogeneous-bd-methodsComment: 11 pages, 9 figures, To be published in Proceedings IEEE International Symposium on Multi-Robot & Multi-Agent Systems (MRS 2023

Engineering the indigoidine-synthesising enzyme BpsA for diverse applications in biotechnology

Blue pigment synthase A (BpsA) is a single module non-ribosomal peptide synthetase (NRPS) originally isolated from the bacterium Streptomyces lavendulae. It synthesises an easily detectible blue pigment called indigoidine from two molecules of L-glutamine in an ATP powered reaction. BpsA is readily purified and amenable to in vitro assays that have a variety of useful applications. By spectrophotometrically quantifying indigoidine levels it is possible to accurately measure the amount of L-glutamine in complex biological fluids including urine, blood plasma and cell culture media. This method has several advantages over existing methods for glutamine measurement, including that it directly reports on glutamine levels. Existing commercially available enzymatic kits first convert glutamine into glutamate and then measure the level of glutamate, which requires additional sample processing and introduces complexity if glutamate may also be present in the target sample. Additionally, we have shown that BpsA can also be used to measure ATP concentrations in a similar manner. We have further developed a BpsA based assay to detect inhibitors of 4’-phosphopantetheinyl transferases (PPTases). PPTases are enzymes that attach a phosphopantetheine arm to fatty acid synthases, NRPSs and polyketide synthases, thereby switching them from an inactive apo form to an active holo form. PPTases have been validated as promising drug targets in several pathogenic bacteria including P. aeruginosa and M. tuberculosis. In order to detect PPTase inhibition, we have shown that BpsA can be purified in its inactive apo form and mixed with the target PPTase as well as a candidate inhibitor in vitro. The level of PPTase inhibition can then be calculated by measuring the rate of indigoidine production. The assay has been optimised for high throughput screening and used to identify several compounds from chemical libraries that inhibit essential PPTases of P. aeruginosa and M. tuberculosis

Streptococcus pneumoniae meningitis and the CNS barriers

Streptococcus pneumoniae (SPN) is a globally significant cause of meningitis, the pathophysiology of which involves damage to the brain by both bacterial virulence factors and the host inflammatory response. In most cases of SPN meningitis bacteria translocate from the blood into the central nervous system (CNS). The principal site of SPN translocation into the CNS is not known, with possible portals of entry proposed to be the cerebral or meningeal blood vessels or the choroid plexus. All require SPN to bind to and translocate across the vascular endothelial barrier, and subsequently the basement membrane and perivascular structures, including an additional epithelial barrier in the case of the blood-CSF barrier. The presence of SPN in the CNS is highly inflammatory resulting in marked neutrophilic infiltration. The secretion of toxic inflammatory mediators by activated neutrophils within the CNS damages pathogen and host alike, including the non-replicative neurons which drives morbidity and mortality. As with the translocation of SPN, the recruitment of neutrophils into the CNS in SPN meningitis necessitates the translocation of neutrophils from the circulation across the vascular barrier, a process that is tightly regulated under basal conditions - a feature of the 'immune specialization' of the CNS. The brain barriers are therefore central to SPN meningitis, both through a failure to exclude bacteria and maintain CNS sterility, and subsequently through the active recruitment and/or failure to exclude circulating leukocytes. The interactions of SPN with these barriers, barrier inflammatory responses, along with their therapeutic implications, are explored in this review

Underground mining of aggregates. Main report

This report examines the economic feasibility of underground mining for crushed rock aggregates in the UK, but particularly in the London, South East and East of England regions (the South East area of England). These regions import substantial volumes of crushed rock, primarily from the East Midlands and South West regions, requiring relatively long transport distances to market for this bulk commodity. A key part of the research was to determine whether or not aggregate could be produced and delivered to a local market from an underground aggregates operation at a cost comparable with that for production and transport of the commodity from traditional surface quarries located further afield. In essence the investigation asked – could the reduced transport costs compensate for the higher production costs underground so that underground crushed rock aggregates producers can compete with the established Leicestershire and Somerset surface quarries exporting to the South East? Work Programme The research effort involved establishing and verifying cost models for aggregates production, stone processing (sizing and sorting), haulage of product to market, environmental impact mitigation, health and safety, decommissioning and restoration. Another major element of the work was the re-examination of the BGS exploratory borehole and geophysical databases to identify potential areas of crushed rock aggregates resource at depth in the South East area of England. Land use pressure is typically higher in this area of England than elsewhere so another major part of the research was the identification of potential concurrent uses of land around the surface facilities of underground aggregates mines. The value, development costs for specific developments and determination of yields expected, from these uses were estimated. These were also used to investigate potential economic benefits associated with after uses of remediated surface land above potential underground aggregates mines and also for the new underground space that would be created. Key technical issues such as subsidence within relatively heavily populated areas of the South East area of England were also addressed. Economic Results The discounted cost of aggregate delivered at a discount rate of 10% was the metric used to appraise the options. This is the price of aggregate that leads to a zero net present value of project cash flows realised over the aggregates project life. The results show that the discounted costs of aggregate delivered to a local South East area of England market from an underground mine producing 3.5 million tonnes per annum (MTPA) of crushed rock aggregates, are in the range of £13.03 per tonne to £13.93 per tonne for the top six prospect locations. These are greater than the corresponding cost for a “reference” quarry in Leicestershire producing 3.5 MTPA (£10.95 per tonne), but lower than a “reference” quarry in Leicestershire producing 1.25 MTPA (£16.48 per tonne). These figures indicate that underground crushed rock aggregate mines located within the South East area of England may be able to compete for a share in the overall market by replacing / displacing aggregate imported from the quarries in Leicestershire and Somerset producing around or less than 1.25 MTPA. The surprise in these figures is not really that the more remote surface quarry has a lower discounted cost of aggregate delivered, but that the values for the quarry and underground mine are so close. The capital intensity for the development of underground aggregates mines was found to be higher than that required for surface quarries of comparable scale, by a factor ranging from 1.33 to 1.65 and thus may represent a disincentive for aggregates operators. Carbon Emissions The total carbon emissions of the ‘reference’ 3.5 MTPA quarry in Leicestershire were estimated at 9.28 kg CO2/tonne aggregate delivered and this is to be compared with carbon emissions for the 150 metre deep underground mines serving the local market which were estimated at 9.31 kg CO2/tonne delivered for a Bletchley prospect using an adit to access the sub-surface and 14.25 kg CO2/tonne delivered for a prospect based on the Chitty bore hole using a shaft. Depth of the mine is a key factor in determination of the relative carbon emissions from each of the underground mining operations considered as electricity consumption for ventilation, pumping and winding is proportional to depth. Recommendations The current research generated seven principal recommendations which are discussed in detail in the concluding section of the report. These are: Appraise policy incentives for underground aggregates mining. Conduct an industry-wide consultation on findings from the current research. Obtain public and stakeholder opinion on new uses for underground space. Conduct research to reducing the energy intensity of mine services. Develop a deep level aggregates-specific drilling campaign. Investigate underground aggregates mines developed from existing surface quarries. Investigate underground aggregates as co-products of industrial minerals mining

Infrared Observations During the Secondary Eclipse of HD 209458b: I. 3.6-Micron Occultation Spectroscopy Using the VLT

We search for an infrared signature of the transiting extrasolar planet HD 209458b during secondary eclipse. Our method, which we call `occultation spectroscopy,' searches for the disappearance and reappearance of weak spectral features due to the exoplanet as it passes behind the star and later reappears. We argue that at the longest infrared wavelengths, this technique becomes preferable to conventional `transit spectroscopy'. We observed the system in the wing of the strong nu-3 band of methane near 3.6 microns during two secondary eclipses, using the VLT/ISAAC spectrometer at a spectral resolution of 3300. Our analysis, which utilizes a model template spectrum, achieves sufficient precision to expect detection of the spectral structure predicted by an irradiated, low-opacity (cloudless), low-albedo, thermochemical equilibrium model for the exoplanet atmosphere. However, our observations show no evidence for the presence of this spectrum from the exoplanet, with the statistical significance of the non-detection depending on the timing of the secondary eclipse, which depends on the assumed value for the orbital eccentricity. Our results reject certain specific models of the atmosphere of HD 209458b as inconsistent with our observations at the 3-sigma level, given assumptions about the stellar and planetary parameters.Comment: 26 pages, 8 figures Accepted to Astrophysical Journa

Serum Amyloid P Aids Complement-Mediated Immunity to Streptococcus pneumoniae

The physiological functions of the acute phase protein serum amyloid P (SAP) component are not well defined, although they are likely to be important, as no natural state of SAP deficiency has been reported. We have investigated the role of SAP for innate immunity to the important human pathogen Streptococcus pneumoniae. Using flow cytometry assays, we show that SAP binds to S. pneumoniae, increases classical pathway–dependent deposition of complement on the bacteria, and improves the efficiency of phagocytosis. As a consequence, in mouse models of infection, mice genetically engineered to be SAP-deficient had an impaired early inflammatory response to S. pneumoniae pneumonia and were unable to control bacterial replication, leading to the rapid development of fatal infection. Complement deposition, phagocytosis, and control of S. pneumoniae pneumonia were all improved by complementation with human SAP. These results demonstrate a novel and physiologically significant role for SAP for complement-mediated immunity against an important bacterial pathogen, and provide further evidence for the importance of the classical complement pathway for innate immunity