Tight Bounds for MIS in Multichannel Radio Networks

Daum et al. [PODC'13] presented an algorithm that computes a maximal independent set (MIS) within $O(\log^2 n/F+\log n \mathrm{polyloglog} n)$ rounds in an $n$-node multichannel radio network with $F$ communication channels. The paper uses a multichannel variant of the standard graph-based radio network model without collision detection and it assumes that the network graph is a polynomially bounded independence graph (BIG), a natural combinatorial generalization of well-known geographic families. The upper bound of that paper is known to be optimal up to a polyloglog factor. In this paper, we adapt algorithm and analysis to improve the result in two ways. Mainly, we get rid of the polyloglog factor in the runtime and we thus obtain an asymptotically optimal multichannel radio network MIS algorithm. In addition, our new analysis allows to generalize the class of graphs from those with polynomially bounded local independence to graphs where the local independence is bounded by an arbitrary function of the neighborhood radius.Comment: 37 pages, to be published in DISC 201

Modelling environmental factors correlated with podoconiosis: a geospatial study of non-filarial elephantiasis

Introduction The precise trigger of podoconiosis — endemic non-filarial elephantiasis of the lower legs — is unknown. Epidemiological and ecological studies have linked the disease with barefoot exposure to red clay soils of volcanic origin. Histopathology investigations have demonstrated that silicon, aluminium, magnesium and iron are present in the lower limb lymph node macrophages of both patients and non-patients living barefoot on these clays. We studied the spatial variation (variations across an area) in podoconiosis prevalence and the associated environmental factors with a goal to better understanding the pathogenesis of podoconiosis. Methods Fieldwork was conducted from June 2011 to February 2013 in 12 kebeles (administrative units) in northern Ethiopia. Geo-located prevalence data and soil samples were collected and analysed along with secondary geological, topographic, meteorological and elevation data. Soil data were analysed for chemical composition, mineralogy and particle size, and were interpolated to provide spatially continuous information. Exploratory, spatial, univariate and multivariate regression analyses of podoconiosis prevalence were conducted in relation to primary (soil) and secondary (elevation, precipitation, and geology) covariates. Results Podoconiosis distribution showed spatial correlation with variation in elevation and precipitation. Exploratory analysis identified that phyllosilicate minerals, particularly clay (smectite and kaolinite) and mica groups, quartz (crystalline silica), iron oxide, and zirconium were associated with podoconiosis prevalence. The final multivariate model showed that the quantities of smectite (RR = 2.76, 95% CI: 1.35, 5.73; p = 0.007), quartz (RR = 1.16, 95% CI: 1.06, 1.26; p = 0.001) and mica (RR = 1.09, 95% CI: 1.05, 1.13; p < 0.001) in the soil had positive associations with podoconiosis prevalence. Conclusions More quantities of smectite, mica and quartz within the soil were associated with podoconiosis prevalence. Together with previous work indicating that these minerals may influence water absorption, potentiate infection and be toxic to human cells, the present findings suggest that these particles may play a role in the pathogenesis of podoconiosis and acute adenolymphangitis, a common cause of morbidity in podoconiosis patients

The MemProtMD database : a resource for membrane-embedded protein structures and their lipid interactions

Integral membrane proteins fulfil important roles in many crucial biological processes, including cell signalling, molecular transport and bioenergetic processes. Advancements in experimental techniques are revealing high resolution structures for an increasing number of membrane proteins. Yet, these structures are rarely resolved in complex with membrane lipids. In 2015, the MemProtMD pipeline was developed to allow the automated lipid bilayer assembly around new membrane protein structures, released from the Protein Data Bank (PDB). To make these data available to the scientific community, a web database (http://memprotmd.bioch.ox.ac.uk) has been developed. Simulations and the results of subsequent analysis can be viewed using a web browser, including interactive 3D visualizations of the assembled bilayer and 2D visualizations of lipid contact data and membrane protein topology. In addition, ensemble analyses are performed to detail conserved lipid interaction information across proteins, families and for the entire database of 3506 PDB entries. Proteins may be searched using keywords, PDB or Uniprot identifier, or browsed using classification systems, such as Pfam, Gene Ontology annotation, mpstruc or the Transporter Classification Database. All files required to run further molecular simulations of proteins in the database are provided

Using trait-based filtering as a predictive framework for conservation: A case study of bats on farms in southeastern Australia

1.With world-wide changes in human land use, an important challenge for conservation biologists is to develop frameworks to predict how species will respond to landscape change. Environmental filtering, where different environments favour different species' traits, has the potential to be a useful predictive framework. Therefore, it is important to advance our understanding of how species with different traits respond to environmental variables. 2.We investigated the distribution of microbats in a 1000000ha agricultural region in southeastern Australia, with specific emphasis on the effects of tree density on bat species characterized by different sizes, wing shapes and echolocation frequencies. The study area is substantially cleared, and trees are continuing to decline because grazing inhibits tree regeneration. We monitored bat activity acoustically at 80 sites spanning a wide range of tree densities. We used regression modelling to quantify the response of bats to tree density and other ecological covariates, and RLQ analysis to assess how different traits correlated with various environmental gradients. 3.Total bat activity and species richness peaked at intermediate tree densities. Species composition was explained by tree density and the traits of individual species. Sites with low tree cover were dominated by large, fast-flying species, whereas sites with dense tree cover were dominated by smaller, highly manoeuvrable species. These findings are consistent with recent findings from other locations around the world. 4.Synthesis and applications. Trait-based predictive frameworks enable landscape managers to assess how different management strategies and landscape modifications are likely to affect different species. Here, we propose a framework to derive general predictions of how bats respond to landscape modification, based on tree density and species traits. We apply this framework to a current conservation issue of tree decline in our study area and derive management priorities including: (i) maintaining a range of tree densities throughout the region; (ii) ensuring the persistence of locations with intermediate tree densities; and (iii) using environmentally sensitive grazing practices, for example, by incorporating long rest periods. Trait-based predictive frameworks enable landscape managers to assess how different management strategies and landscape modifications are likely to affect different species. Here, we propose a framework to derive general predictions of how bats respond to landscape modification, based on tree density and species traits. We apply this framework to a current conservation issue of tree decline in our study area and derive management priorities including: (i) maintaining a range of tree densities throughout the region; (ii) ensuring the persistence of locations with intermediate tree densities; and (iii) using environmentally sensitive grazing practices, for example, by incorporating long rest periods

Experimental Evaluation of Wireless Simulation Assumptions

All analytical and simulation research on ad hoc wireless networks must necessarily model radio propagation using simplifying assumptions. We provide a comprehensive review of six assumptions that are still part of many ad hoc network simulation studies, despite increasing awareness of the need to represent more realistic features, including hills, obstacles, link asymmetries, and unpredictable fading. We use an extensive set of measurements from a large outdoor routing experiment to demonstrate the weakness of these assumptions, and show how these assumptions cause simulation results to differ significantly from experimental results. We close with a series of recommendations for researchers, whether they develop protocols, analytic models, or simulators for ad hoc wireless networks

Natural variation in immune responses to neonatal mycobacterium bovis bacillus calmette-guerin (BCG) vaccination in a cohort of Gambian infants

Background There is a need for new vaccines for tuberculosis (TB) that protect against adult pulmonary disease in regions where BCG is not effective. However, BCG could remain integral to TB control programmes because neonatal BCG protects against disseminated forms of childhood TB and many new vaccines rely on BCG to prime immunity or are recombinant strains of BCG. Interferon-gamma (IFN-) is required for immunity to mycobacteria and used as a marker of immunity when new vaccines are tested. Although BCG is widely given to neonates IFN- responses to BCG in this age group are poorly described. Characterisation of IFN- responses to BCG is required for interpretation of vaccine immunogenicity study data where BCG is part of the vaccination strategy. Methodology/Principal Findings 236 healthy Gambian babies were vaccinated with M. bovis BCG at birth. IFN-, interleukin (IL)-5 and IL-13 responses to purified protein derivative (PPD), killed Mycobacterium tuberculosis (KMTB), M. tuberculosis short term culture filtrate (STCF) and M. bovis BCG antigen 85 complex (Ag85) were measured in a whole blood assay two months after vaccination. Cytokine responses varied up to 10 log-fold within this population. The majority of infants (89-98% depending on the antigen) made IFN- responses and there was significant correlation between IFN- responses to the different mycobacterial antigens (Spearman’s coefficient ranged from 0.340 to 0.675, p=10-6-10-22). IL-13 and IL-5 responses were generally low and there were more non-responders (33-75%) for these cytokines. Nonetheless, significant correlations were observed for IL-13 and IL-5 responses to different mycobacterial antigens Conclusions/Significance Cytokine responses to mycobacterial antigens in BCG-vaccinated infants are heterogeneous and there is significant inter-individual variation. Further studies in large populations of infants are required to identify the factors that determine variation in IFN- responses

Of Malicious Motes and Suspicious Sensors

How efficiently can a malicious device disrupt communication in a wireless network? Imagine a basic game involving two honest players, Alice and Bob, who want to exchange information, and an adversary, Collin, who can disrupt communication using a limited budget of B broadcasts. How long can Collin delay Alice and Bob from communicating? In fact, the trials and tribulations of Alice and Bob capture the fundamental difficulty shared by several n-player problems, including reliable broadcast, leader election, static k-selection, and t-resilient consensus. We provide round complexity lower bounds—and (nearly) tight upper bounds—for each of those problems. These results imply bounds on adversarial efficiency, which we analyze in terms of jamming gain and disruption-free complexity

Host genetic susceptibility to mycetoma

Mycetoma is one of the badly neglected tropical diseases characterised by subcutaneous painless swelling, multiple sinuses and discharge containing aggregates of the infecting organism known as grains. Risk factors conferring susceptibility to mycetoma include environmental factors, pathogen factors such as virulence and the infecting dose in addition to host factors such as immunological and genetic predisposition. Epidemiological evidence suggests that host genetic factors may regulate susceptibility to mycetoma and other fungal infections but they are likely to be complex genetic traits where multiple genes interact with each other and environmental factors, as well as the pathogen, to cause disease. This paper reviews what is known about genetic predisposition to fungal infections that might be relevant to mycetoma as well as all studies carried out to explore host genetic susceptibility to mycetoma. Most studies were investigating polymorphisms in candidate genes related to the host immune response. A total of 13 genes had allelic variants found to be associated with mycetoma and these genes lie in different pathways and systems such as innate and adaptive immune systems, sex hormones biosynthesis and some genes coding for host enzymes. None of these studies have been replicated. Advances in genomic science and the supporting technology have paved the way for large-scale genome-wide association and next generation sequencing (NGS) studies, underpinning a new strategy to systematically interrogate the genome for variants associated with mycetoma. Dissecting the contribution of host genetic variation to susceptibility to mycetoma will enable the identification of pathways that are potential targets for new treatments for mycetoma and will also enhance the ability to stratify “at-risk” individuals allowing the possibility to develop preventive and personalised clinical care strategies in the future