Scalable Bayesian modeling, monitoring and analysis of dynamic network flow data

Traffic flow count data in networks arise in many applications, such as automobile or aviation transportation, certain directed social network contexts, and Internet studies. Using an example of Internet browser traffic flow through site-segments of an international news website, we present Bayesian analyses of two linked classes of models which, in tandem, allow fast, scalable and interpretable Bayesian inference. We first develop flexible state-space models for streaming count data, able to adaptively characterize and quantify network dynamics efficiently in real-time. We then use these models as emulators of more structured, time-varying gravity models that allow formal dissection of network dynamics. This yields interpretable inferences on traffic flow characteristics, and on dynamics in interactions among network nodes. Bayesian monitoring theory defines a strategy for sequential model assessment and adaptation in cases when network flow data deviates from model-based predictions. Exploratory and sequential monitoring analyses of evolving traffic on a network of web site-segments in e-commerce demonstrate the utility of this coupled Bayesian emulation approach to analysis of streaming network count data.Comment: 29 pages, 16 figure

Erica the Rhino: a case study in using Raspberry Pi Single Board Computers for interactive art

Erica the Rhino is an interactive art exhibit created by the University of Southampton, UK. Erica was created as part of a city wide art trail in 2013 called "Go! Rhinos", curated by Marwell Wildlife, to raise awareness of Rhino conservation. Erica arrived as a white fibreglass shell which was then painted and equipped with 5 Raspberry Pi Single Board Computers (SBC). These computers allowed the audience to interact with Erica through a range of sensors and actuators. In particular, the audience could feed and stroke her to prompt reactions, as well as send her Tweets to change her behaviour. Pi SBCs were chosen because of their ready availability and their educational pedigree. During the deployment, 'coding clubs' were run in the shopping centre where Erica was located, these allowed children to experiment with and program the same components used in Erica. The experience gained through numerous deployments around the country has enabled Erica to be upgraded to increase reliability and ease of maintenance, whilst the release of the Pi 2 has allowed her responsiveness to be improved

Testing SOAR Tools in Use

Modern security operation centers (SOCs) rely on operators and a tapestry of logging and alerting tools with large scale collection and query abilities. SOC investigations are tedious as they rely on manual efforts to query diverse data sources, overlay related logs, and correlate the data into information and then document results in a ticketing system. Security orchestration, automation, and response (SOAR) tools are a new technology that promise to collect, filter, and display needed data; automate common tasks that require SOC analysts' time; facilitate SOC collaboration; and, improve both efficiency and consistency of SOCs. SOAR tools have never been tested in practice to evaluate their effect and understand them in use. In this paper, we design and administer the first hands-on user study of SOAR tools, involving 24 participants and 6 commercial SOAR tools. Our contributions include the experimental design, itemizing six characteristics of SOAR tools and a methodology for testing them. We describe configuration of the test environment in a cyber range, including network, user, and threat emulation; a full SOC tool suite; and creation of artifacts allowing multiple representative investigation scenarios to permit testing. We present the first research results on SOAR tools. We found that SOAR configuration is critical, as it involves creative design for data display and automation. We found that SOAR tools increased efficiency and reduced context switching during investigations, although ticket accuracy and completeness (indicating investigation quality) decreased with SOAR use. Our findings indicated that user preferences are slightly negatively correlated with their performance with the tool; overautomation was a concern of senior analysts, and SOAR tools that balanced automation with assisting a user to make decisions were preferred

Digital energy visualisations in the workplace: the e-Genie tool

Building management systems are designed for energy managers; there are few energy feedback systems designed to engage staff. A tool, known as e-Genie, was developed to engage workplace occupants with energy data and support them to take action to reduce energy use. Building on research insights within the field, e-Genie’s novel approach encourages users to make plans to meet energy saving goals, supports discussion, and considers social energy behaviours (e.g. discussing energy issues, taking part in campaigns) as well as individual actions. A field based study of e-Genie indicated that visualisations of energy data were engaging and that the discussion ‘Pinboard’ was particularly popular. Pre- and post survey (N = 77) evaluation of users indicated that people were significantly more concerned about energy issues and reported engaging more in social energy behaviour after ~two weeks of e-Genie being installed. Concurrently, objective measures of electricity use decreased over the same period, and continued decreasing over subsequent weeks. Indications are that occupant facing energy feedback visualisations can be successful in reducing energy use in the workplace; furthermore supporting social energy behaviour in the workplace is likely to be a useful direction for promoting action

Designing programs for eliminating canine rabies from islands: Bali, Indonesia as a case study

<p>Background: Canine rabies is one of the most important and feared zoonotic diseases in the world. In some regions rabies elimination is being successfully coordinated, whereas in others rabies is endemic and continues to spread to uninfected areas. As epidemics emerge, both accepted and contentious control methods are used, as questions remain over the most effective strategy to eliminate rabies. The Indonesian island of Bali was rabies-free until 2008 when an epidemic in domestic dogs began, resulting in the deaths of over 100 people. Here we analyze data from the epidemic and compare the effectiveness of control methods at eliminating rabies.</p> <p>Methodology/Principal Findings: Using data from Bali, we estimated the basic reproductive number, R0, of rabies in dogs, to be ~1·2, almost identical to that obtained in ten–fold less dense dog populations and suggesting rabies will not be effectively controlled by reducing dog density. We then developed a model to compare options for mass dog vaccination. Comprehensive high coverage was the single most important factor for achieving elimination, with omission of even small areas (<0.5% of the dog population) jeopardizing success. Parameterizing the model with data from the 2010 and 2011 vaccination campaigns, we show that a comprehensive high coverage campaign in 2012 would likely result in elimination, saving ~550 human lives and ~$15 million in prophylaxis costs over the next ten years.</p> <p>Conclusions/Significance: The elimination of rabies from Bali will not be achieved through achievable reductions in dog density. To ensure elimination, concerted high coverage, repeated, mass dog vaccination campaigns are necessary and the cooperation of all regions of the island is critical. Momentum is building towards development of a strategy for the global elimination of canine rabies, and this study offers valuable new insights about the dynamics and control of this disease, with immediate practical relevance.</p&gt

Acute Oak Decline and Agrilus biguttatus: The Co-Occurrence of Stem Bleeding and D-Shaped Emergence Holes in Great Britain

Acute Oak Decline (AOD) is a new condition affecting both species of native oak, Quercus robur and Quercus petraea, in Great Britain. The decline is characterised by a distinctive set of externally visible stem symptoms; bark cracks that “weep” dark exudate are found above necrotic lesions in the inner bark. Emergence holes of the buprestid beetle, Agrilus biguttatus are often also seen on the stems of oak within affected woodlands. This investigation assesses the extent to which the external symptoms of these two agents co-occur and reveals the spatial and temporal patterns present in affected woodland. Annual monitoring in eight affected woodlands showed that stem bleeding and emergence holes frequently occur on the same trees, with new emergence holes significantly more likely to occur when trees already have stem bleeds. Trials with coloured prism traps confirm A. biguttatus was present at all experimental sites. Beetle emergence is linked primarily to a few heavily declining trees, indicating that susceptibility may vary between hosts and that those with reduced health may be predisposed to AOD. Stem bleeds occur on trees in close proximity to the locations of trees with exit holes

HMDB: the Human Metabolome Database

The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at

Life, time, and the organism:Temporal registers in the construction of life forms

In this paper, we articulate how time and temporalities are involved in the making of living things. For these purposes, we draw on an instructive episode concerning Norfolk Horn sheep. We attend to historical debates over the nature of the breed, whether it is extinct or not, and whether presently living exemplars are faithful copies of those that came before. We argue that there are features to these debates that are important to understanding contemporary configurations of life, time and the organism, especially as these are articulated within the field of synthetic biology. In particular, we highlight how organisms are configured within different material and semiotic assemblages that are always structured temporally. While we identify three distinct structures, namely the historical, phyletic and molecular registers, we do not regard the list as exhaustive. We also highlight how these structures are related to the care and value invested in the organisms at issue. Finally, because we are interested ultimately in ways of producing time, our subject matter requires us to think about historiographical practice reflexively. This draws us into dialogue with other scholars interested in time, not just historians, but also philosophers and sociologists, and into conversations with them about time as always multiple and never an inert background

Large herbivores may alter vegetation structure of semi-arid savannas through soil nutrient mediation

In savannas, the tree–grass balance is governed by water, nutrients, fire and herbivory, and their interactions. We studied the hypothesis that herbivores indirectly affect vegetation structure by changing the availability of soil nutrients, which, in turn, alters the competition between trees and grasses. Nine abandoned livestock holding-pen areas (kraals), enriched by dung and urine, were contrasted with nearby control sites in a semi-arid savanna. About 40 years after abandonment, kraal sites still showed high soil concentrations of inorganic N, extractable P, K, Ca and Mg compared to controls. Kraals also had a high plant production potential and offered high quality forage. The intense grazing and high herbivore dung and urine deposition rates in kraals fit the accelerated nutrient cycling model described for fertile systems elsewhere. Data of a concurrent experiment also showed that bush-cleared patches resulted in an increase in impala dung deposition, probably because impala preferred open sites to avoid predation. Kraal sites had very low tree densities compared to control sites, thus the high impala dung deposition rates here may be in part driven by the open structure of kraal sites, which may explain the persistence of nutrients in kraals. Experiments indicated that tree seedlings were increasingly constrained when competing with grasses under fertile conditions, which might explain the low tree recruitment observed in kraals. In conclusion, large herbivores may indirectly keep existing nutrient hotspots such as abandoned kraals structurally open by maintaining a high local soil fertility, which, in turn, constrains woody recruitment in a negative feedback loop. The maintenance of nutrient hotspots such as abandoned kraals by herbivores contributes to the structural heterogeneity of nutrient-poor savanna vegetation

Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

OBJECTIVE: Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired β-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology. RESEARCH DESIGN AND METHODS: We have conducted a meta-analysis of genome-wide association tests of ∼2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates. RESULTS: Nine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 × 10(-4)), improved β-cell function (P = 1.1 × 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets. CONCLUSIONS: We have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis