Towards Real-Time Crowd Simulation Under Uncertainty Using an Agent-Based Model and an Unscented Kalman Filter

Agent-based modelling (ABM) is ideally suited to simulating crowds of people as it captures the complex behaviours and interactions between individuals that lead to the emergence of crowding. Currently, it is not possible to use ABM for real-time simulation due to the absence of established mechanisms for dynamically incorporating real-time data. This means that, although models are able to perform useful offline crowd simulations, they are unable to simulate the behaviours of crowds in real time. This paper begins to address this drawback by demonstrating how a data assimilation algorithm, the Unscented Kalman Filter (UKF), can be used to incorporate pseudo-real data into an agent-based model at run time. Experiments are conducted to test how well the algorithm works when a proportion of agents are tracked directly under varying levels of uncertainty. Notably, the experiments show that the behaviour of unobserved agents can be inferred from the behaviours of those that are observed. This has implications for modelling real crowds where full knowledge of all individuals will never be known. In presenting a new approach for creating real-time simulations of crowds, this paper has important implications for the management of various environments in global cities, from single buildings to larger structures such as transportation hubs, sports stadiums, through to entire city regions

Surveillance of malaria vector population density and biting behaviour in western Kenya

BACKGROUND: Malaria is a great public health burden and Africa suffers the largest share of malaria-attributed deaths. Despite control efforts targeting indoor malaria transmission, such as insecticide-treated bed nets (ITNs) and deployment of indoor residual spraying, transmission of the parasite in western Kenya is still maintained. This study was carried out to determine the impact of ITNs on indoor vector densities and biting behaviour in western Kenya. METHODS: Indoor collection of adult mosquitoes was done monthly in six study sites in western Kenya using pyrethrum spray collections from 2012 to 2014. The rotator trap collections were done in July–August in 2013 and May–June in 2014. Mosquitoes were collected every 2 h between 18.00 and 08.00 h. Human behaviour study was conducted via questionnaire surveys. Species within Anopheles gambiae complex was differentiated by PCR and sporozoite infectivity was determined by ELISA. Species distribution was determined and bed net coverage in the study sites was recorded. RESULTS: During the study a total of 5,469 mosquito vectors were collected from both PSC and Rotator traps comprising 3,181 (58.2%) Anopheles gambiae and 2,288 (41.8%) Anopheles funestus. Compared to all the study sites, Rae had the highest density of An. gambiae with a mean of 1.2 (P < 0.001) while Kombewa had the highest density of An. funestus with a mean of 1.08 (P < 0.001). Marani had the lowest density of vectors with 0.06 An. gambiae and 0.17 An. funestus (P < 0.001). Among the 700 PCR confirmed An. gambiaes.l. individuals, An. gambiaes.s. accounted for 49% and An. arabiensis 51%. Over 50% of the study population stayed outdoors between 18.00 and 20.00 and 06.00 and 08.00 which was the time when highest densities of blood fed vectors were collected. Anopheles gambies.s. was the main malaria parasite vector in the highland sites and An. arabiensis in the lowland sites. Bed net ownership in 2012 averaged 87% across the study sites. CONCLUSIONS: This study suggests that mass distribution of ITNs has had a significant impact on vector densities, species distribution and sporozoite rate. However, shift of biting time poses significant threats to the current malaria vector control strategies which heavily rely on indoor controls

Asymmetric Switching in a Homodimeric ABC Transporter: A Simulation Study

ABC transporters are a large family of membrane proteins involved in a variety of cellular processes, including multidrug and tumor resistance and ion channel regulation. Advances in the structural and functional understanding of ABC transporters have revealed that hydrolysis at the two canonical nucleotide-binding sites (NBSs) is co-operative and non-simultaneous. A conserved core architecture of bacterial and eukaryotic ABC exporters has been established, as exemplified by the crystal structure of the homodimeric multidrug exporter Sav1866. Currently, it is unclear how sequential ATP hydrolysis arises in a symmetric homodimeric transporter, since it implies at least transient asymmetry at the NBSs. We show by molecular dynamics simulation that the initially symmetric structure of Sav1866 readily undergoes asymmetric transitions at its NBSs in a pre-hydrolytic nucleotide configuration. MgATP-binding residues and a network of charged residues at the dimer interface are shown to form a sequence of putative molecular switches that allow ATP hydrolysis only at one NBS. We extend our findings to eukaryotic ABC exporters which often consist of two non-identical half-transporters, frequently with degeneracy substitutions at one of their two NBSs. Interestingly, many residues involved in asymmetric conformational switching in Sav1866 are substituted in degenerate eukaryotic NBS. This finding strengthens recent suggestions that the interplay of a consensus and a degenerate NBS in eukaroytic ABC proteins pre-determines the sequence of hydrolysis at the two NBSs

Controlled Human Malaria Infection in Semi-Immune Kenyan Adults (CHMI-SIKA): a study protocol to investigate in vivo Plasmodium falciparum malaria parasite growth in the context of pre-existing immunity [version 2; peer review: 2 approved]

Malaria remains a major public health burden despite approval for implementation of a partially effective pre-erythrocytic malaria vaccine. There is an urgent need to accelerate development of a more effective multi-stage vaccine. Adults in malaria endemic areas may have substantial immunity provided by responses to the blood stages of malaria parasites, but field trials conducted on several blood-stage vaccines have not shown high levels of efficacy. We will use the controlled human malaria infection (CHMI) models with malaria-exposed volunteers to identify correlations between immune responses and parasite growth rates in vivo. Immune responses more strongly associated with control of parasite growth should be prioritized to accelerate malaria vaccine development. We aim to recruit up to 200 healthy adult volunteers from areas of differing malaria transmission in Kenya, and after confirming their health status through clinical examination and routine haematology and biochemistry, we will comprehensively characterize immunity to malaria using >100 blood-stage antigens. We will administer 3,200 aseptic, purified, cryopreserved Plasmodium falciparum sporozoites (PfSPZ Challenge) by direct venous inoculation. Serial quantitative polymerase chain reaction to measure parasite growth rate in vivo will be undertaken. Clinical and laboratory monitoring will be undertaken to ensure volunteer safety. In addition, we will also explore the perceptions and experiences of volunteers and other stakeholders in participating in a malaria volunteer infection study. Serum, plasma, peripheral blood mononuclear cells and whole blood will be stored to allow a comprehensive assessment of adaptive and innate host immunity. We will use CHMI in semi-immune adult volunteers to relate parasite growth outcomes with antibody responses and other markers of host immunity. / Registration: ClinicalTrials.gov identifier NCT02739763

Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK2E Complex

ATP-Binding Cassette transporters are ubiquitous membrane proteins that convert the energy from ATP-binding and hydrolysis into conformational changes of the transmembrane region to allow the translocation of substrates against their concentration gradient. Despite the large amount of structural and biochemical data available for this family, it is still not clear how the energy obtained from ATP hydrolysis in the ATPase domains is “transmitted” to the transmembrane domains. In this work, we focus our attention on the consequences of hydrolysis and inorganic phosphate exit in the maltose uptake system (MalFGK2E) from Escherichia coli. The prime goal is to identify and map the structural changes occurring during an ATP-hydrolytic cycle. For that, we use extensive molecular dynamics simulations to study three potential intermediate states (with 10 replicates each): an ATP-bound, an ADP plus inorganic phosphate-bound and an ADP-bound state. Our results show that the residues presenting major rearrangements are located in the A-loop, in the helical sub-domain, and in the “EAA motif” (especially in the “coupling helices” region). Additionally, in one of the simulations with ADP we were able to observe the opening of the NBD dimer accompanied by the dissociation of ADP from the ABC signature motif, but not from its corresponding P-loop motif. This work, together with several other MD studies, suggests a common communication mechanism both for importers and exporters, in which ATP-hydrolysis induces conformational changes in the helical sub-domain region, in turn transferred to the transmembrane domains via the “coupling helices”

Water Flow Behavior and Storage Potential of the Semi-Arid Ephemeral River System in the Mara Basin of Kenya

Alluvial corridors of ephemeral river systems provide viable opportunities for natural water storage in dry lands. Whilst alluvial corridors are widely recognized as water buffers, particularly for areas experiencing constant water scarcity, little research has been undertaken in Sub-Saharan Africa to explore their hydrological variability and water resource potential as alternative water sources for nearby communities. This study investigated the water flow behavior and storage potential of an ephemeral river system in the Mara Basin of Kenya for purposes of supporting water resources development and ecological sustainability. The water flow processes – including the recharge rates and water loss processes – from existing sand storage systems were established through monitoring of ground and surface water levels. Water samples along the alluvial corridor were collected and analyzed for major ions and isotopic signatures required to establish the water storage dynamics. The storage potential was estimated through Probing and Electrical Resistivity Tomography techniques, augmented with in-situ measurements of hydraulic conductivities and channel bed porosities. The mean annual storage volume in the alluvium of the study reach was estimated at 1.1 Mm3, potentially capable of providing for the annual domestic and livestock water demands of the area. Transmission losses into the alluvium beneath the ephemeral channel-bed were noted to attenuate the flood peak discharges, depending on the level of saturation of the alluvial bed. However, water storage in the alluvium was subject to losses through evapotranspiration and seepage through fractured bedrocks. The study demonstrated the potential of alluvial corridors as water storage buffers providing alternative water sources to communities within the dry land regions with water scarcity, thereby to supporting ecosystem sustainability

Preparation, characterization, and optimization of primaquine-loaded solid lipid nanoparticles

Wesley Nyaigoti Omwoyo,1,2 Bernhards Ogutu,3,4 Florence Oloo,3,5 Hulda Swai,6 Lonji Kalombo,6 Paula Melariri,6 Geoffrey Maroa Mahanga,2 Jeremiah Waweru Gathirwa3,4 1Department of Chemistry, Maasai Mara University, Narok, Kenya; 2Department of Chemistry, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya; 3Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya; 4Kenya Medical Research Institute, Nairobi, Kenya; 5Department of Chemical Sciences and Technology, Technical University of Kenya, Nairobi, Kenya; 6Department of Polymers and Composites, Council for Scientific and Industrial Research, Pretoria, South Africa Abstract: Primaquine (PQ) is one of the most widely used antimalarial drugs and is the only available drug that combats the relapsing form of malaria. PQ use in higher doses is limited by severe tissue toxicity including hematological- and gastrointestinal-related side effects. Nanoformulation of drugs in an appropriate drug carrier system has been extensively studied and shown to have the potential to improve bioavailability, thereby enhancing activity, reducing dose frequency, and subsequently reducing toxicity. The aim of this work was to design, synthesize, and characterize PQ-loaded solid lipid nanoparticles (SLNs) (PQ-SLNs) as a potential drug-delivery system. SLNs were prepared by a modified solvent emulsification evaporation method based on a water-in-oil-in-water (w/o/w) double emulsion. The mean particle size, zeta potential, drug loading, and encapsulation efficiency of the PQ-SLNs were 236 nm, +23 mV, 14%, and 75%, respectively. The zeta potential of the SLNs changed dramatically, from -6.54 mV to +23.0 mV, by binding positively charged chitosan as surface modifier. A spherical morphology of PQ-SLNs was seen by scanning electron microscope. In vitro, release profile depicted a steady drug release over 72 hours. Differential scanning calorimeter thermograms demonstrated presence of drug in drug-loaded nanoparticles along with disappearance of decomposition exotherms, suggesting increased physical stability of drug in prepared formulations. Negligible changes in characteristic peaks of drug in Fourier transform infrared spectra indicated absence of any interaction among the various components entrapped in the nanoparticle formulation. The nanoformulated PQ was 20% more effective as compared with conventional oral dose when tested in Plasmodium berghei-infected Swiss albino mice. This study demonstrated an efficient method of forming a nanomedicine delivery system for antimalarial drugs. Keywords: double emulsion, nanomedicine drug-delivery system, antimalarial, nanotechnolog