PICTUREE-Aedes: A Web Application for Dengue Data Visualization and Case Prediction

Dengue fever remains a significant public health concern in many tropical and subtropical countries, and there is still a need for a system that can effectively combine global risk assessment with timely incidence forecasting. This research describes an integrated application called PICTUREE-Aedes, which can collect and analyze dengue-related data, display simulation results, and forecast outbreak incidence. PICTUREE-Aedes automatically updates global temperature and precipitation data and contains historical records of dengue incidence (1960-2012) and Aedes mosquito occurrences (1960-2014) in its database. The application utilizes a mosquito population model to estimate mosquito abundance, dengue reproduction number, and dengue risk. To predict future dengue outbreak incidence, PICTUREE-Aedes applies various forecasting techniques, including the ensemble Kalman filter, recurrent neural network, particle filter, and super ensemble forecast, which are all based on user-entered case data. The PICTUREE-Aedes' risk estimation identifies favorable conditions for potential dengue outbreaks, and its forecasting accuracy is validated by available outbreak data from Cambodia.

Generation of swine movement network and analysis of efficient mitigation strategies for African swine fever virus

Animal movement networks are essential in understanding and containing the spread of infectious diseases in farming industries. Due to its confidential nature, movement data for the US swine farming population is not readily available. Hence, we propose a method to generate such networks from limited data available in the public domain. As a potentially devastating candidate, we simulate the spread of African swine fever virus (ASFV) in our generated network and analyze how the network structure affects the disease spread. We find that high in-degree farm operations (i.e., markets) play critical roles in the disease spread. We also find that high in-degree based targeted isolation and hypothetical vaccinations are more effective for disease control compared to other centrality-based mitigation strategies. The generated networks can be made more robust by validation with more data whenever more movement data will be available.

Understanding the survival of Zika virus in a vector interconnected sexual contact network

The recent outbreaks of the insect-vectored Zika virus have demonstrated its potential to be sexually transmitted, which complicates modeling and our understanding of disease dynamics. Autochthonous outbreaks in the US mainland may be a consequence of both modes of transmission, which affect the outbreak size, duration, and virus persistence. We propose a novel individual-based interconnected network model that incorporates both insect-vectored and sexual transmission of this pathogen. This model interconnects a homogeneous mosquito vector population with a heterogeneous human host contact network. The model incorporates the seasonal variation of mosquito abundance and characterizes host dynamics based on age group and gender in order to produce realistic projections. We use a sexual contact network which is generated on the basis of real world sexual behavior data. Our findings suggest that for a high relative transmissibility of asymptomatic hosts, Zika virus shows a high probability of sustaining in the human population for up to 3 months without the presence of mosquito vectors. Zika outbreaks are strongly affected by the large proportion of asymptomatic individuals and their relative transmissibility. The outbreak size is also affected by the time of the year when the pathogen is introduced. Although sexual transmission has a relatively low contribution in determining the epidemic size, it plays a role in sustaining the epidemic and creating potential endemic scenarios.

Estimation of swine movement network at farm level in the US from the Census of Agriculture data

Swine movement networks among farms/operations are an important source of information to understand and prevent the spread of diseases, nearly nonexistent in the United States. An understanding of the movement networks can help the policymakers in planning effective disease control measures. The objectives of this work are: (1) estimate swine movement probabilities at the county level from comprehensive anonymous inventory and sales data published by the United States Department of Agriculture - National Agriculture Statistics Service database, (2) develop a network based on those estimated probabilities, and (3) analyze that network using network science metrics. First, we use a probabilistic approach based on the maximum information entropy method to estimate the movement probabilities among different swine populations. Then, we create a swine movement network using the estimated probabilities for the counties of the central agricultural district of Iowa. The analysis of this network has found evidence of the small-world phenomenon. Our study suggests that the US swine industry may be vulnerable to infectious disease outbreaks because of the small-world structure of its movement network. Our system is easily adaptable to estimate movement networks for other sets of data, farm animal production systems, and geographic regions.

Quantifying the impact of early-stage contact tracing on controlling Ebola diffusion

Recent experience of the Ebola outbreak in 2014 highlighted the importance of immediate response measure to impede transmission in the early stage. To this aim, efficient and effective allocation of limited resources is crucial. Among the standard interventions is the practice of following up with the recent physical contacts of the infected individuals -- known as contact tracing. In an effort to understand the effects of contact tracing protocols objectively, we explicitly develop a model of Ebola transmission incorporating contact tracing. Our modeling framework is individual-based, patient-centric, stochastic and parameterizable to suit early-stage Ebola transmission. Notably, we propose an activity driven network approach to contact tracing, and estimate the basic reproductive ratio of the epidemic growth in different scenarios. Exhaustive simulation experiments suggest that early contact tracing paired with rapid hospitalization can effectively impede the epidemic growth. Resource allocation needs to be carefully planned to enable early detection of the contacts and rapid hospitalization of the infected people.

Flow measurements via two-particle azimuthal correlations in Au + Au collisions at sqrt [s(NN)]=130 GeV

Two-particle azimuthal correlation functions are presented for charged hadrons produced in Au+Au collisions at the Relativistic Heavy Ion Collider (sqrt [s(NN)]=130 GeV). The measurements permit determination of elliptic flow without event-by-event estimation of the reaction plane. The extracted elliptic flow values (v2) show significant sensitivity to both the collision centrality and the transverse momenta of emitted hadrons, suggesting rapid thermalization and relatively strong velocity fields. When scaled by the eccentricity of the collision zone epsilon, the scaled elliptic flow shows little or no dependence on centrality for charged hadrons with relatively low p(T). A breakdown of this epsilon scaling is observed for charged hadrons with pT >1.0 GeV/c.

Measurement of Lambda and Lambda(macro) particles in Au+Au collisions at the square root of S(NN) = 130 GeV

We present results on the measurement of Lambda and Lambda(macro) production in Au+Au collisions at square root of (S (NN) = 130 GeV with the PHENIX detector at the Relativistic Heavy Ion Collider. The transverse momentum spectra were measured for minimum bias and for the 5% most central events. The Lambda;/Lambda ratios are constant as a function of p(T) and the number of participants. The measured net Lambda density is significantly larger than predicted by models based on hadronic strings (e.g., HIJING) but in approximate agreement with models which include the gluon-junction mechanism.

Net charge fluctuations in Au + Au interactions at sqrt[s(NN)]=130 GeV

Data from Au + Au interactions at sqrt[s(NN)]=130 GeV, obtained with the PHENIX detector at the Relativistic Heavy-Ion Collider, are used to investigate local net charge fluctuations among particles produced near midrapidity. According to recent suggestions, such fluctuations may carry information from the quark-gluon plasma. This analysis shows that the fluctuations are dominated by a stochastic distribution of particles, but are also sensitive to other effects, like global charge conservation and resonance decays.

Centrality dependence of pi(+/-), K(+/-), p, and (-)p production from sqrt[s(NN)] = 130 GeV Au + Au collisions at RHIC

Identified pi(+/-), K(+/-), p, and (-)p transverse momentum spectra at midrapidity in sqrt[s(NN)] = 130 GeV Au+Au collisions were measured by the PHENIX experiment at RHIC as a function of collision centrality. Average transverse momenta increase with the number of participating nucleons in a similar way for all particle species. Within errors, all midrapidity particle yields per participant are found to be increasing with the number of participating nucleons. There is an indication that K(+/-), p, and (-)p yields per participant increase faster than the pi(+/-) yields. In central collisions at high transverse momenta (p(T) > or =2 GeV/c), (-)p and p yields are comparable to the pi(+/-) yields.

Transverse-mass dependence of two-pion correlations in Au+Au collisions at square root[s(NN)] = 130 GeV

Two-pion correlations in square root[s(NN)] = 130 GeV Au+Au collisions at RHIC have been measured over a broad range of pair transverse momentum k(T) by the PHENIX experiment at RHIC. The k(T) dependent transverse radii are similar to results from heavy-ion collisions at square root[s(NN)] = 4.1, 4.9, and 17.3 GeV, whereas the longitudinal radius increases monotonically with beam energy. The ratio of the outwards to sidewards transverse radii (R(out)/R(side)) is consistent with unity and independent of k(T).

Measurement of single electrons and implications for charm production in Au+Au collisions at square root[s(NN)] = 130 GeV

Transverse momentum spectra of electrons from Au+Au collisions at square root[s(NN)] = 130 GeV have been measured at midrapidity by the PHENIX experiment at the Relativistic Heavy Ion Collider. The spectra show an excess above the background from photon conversions and light hadron decays. The electron signal is consistent with that expected from semileptonic decays of charm. The yield of the electron signal dN(e)/dy for p(T) > 0.8 GeV/c is 0.025+/-0.004(stat)+/-0.010(syst) in central collisions, and the corresponding charm cross section is 380+/-60(stat)+/-200(syst) microb per binary nucleon-nucleon collision.

Suppression of hadrons with large transverse momentum in central Au+Au collisions at root square[s(NN)] = 130 GeV

Transverse momentum spectra for charged hadrons and for neutral pions in the range 1 GeV/c<p(T)<5 GeV/c have been measured by the PHENIX experiment at RHIC in Au+Au collisions at root square[s(NN)] = 130 GeV. At high p(T) the spectra from peripheral nuclear collisions are consistent with scaling the spectra from p+p collisions by the average number of binary nucleon-nucleon collisions. The spectra from central collisions are significantly suppressed when compared to the binary-scaled p+p expectation, and also when compared to similarly binary-scaled peripheral collisions, indicating a novel nuclear-medium effect in central nuclear collisions at RHIC energies.

Measurement of the midrapidity transverse energy distribution from square root of [(s)NN] = 130 GeV Au + Au collisions at RHIC

The first measurement of energy produced transverse to the beam direction at the Relativistic Heavy-Ion Collider at Brookhaven National Laboratory is presented. The midrapidity transverse energy density per participating nucleon rises steadily with the number of participants, closely paralleling the rise in charged-particle density, such that <E(T)>/<N(ch)> remains relatively constant as a function of centrality. The energy density calculated via Bjorken's prescription for the 2% most central Au+Au collisions at square root[s(NN)] = 130 GeV is at least epsilon(Bj) = 4.6 GeV/fm(3), which is a factor of 1.6 larger than found at sqrt[s(NN)] = 17.2 GeV ( Pb+Pb at CERN).

Centrality dependence of charged particle multiplicity in Au-Au collisions at square root of (s)NN = 130 GeV

We present results for the charged-particle multiplicity distribution at midrapidity in Au-Au collisions at square root of [s(NN)] = 130 GeV measured with the PHENIX detector at RHIC. For the 5% most central collisions we find dN(ch)/d eta(vertical line eta = 0) = 622+/-1(stat)+/-41(syst). The results, analyzed as a function of centrality, show a steady rise of the particle density per participating nucleon with centrality.