Outbreak detection algorithms for seasonal disease data: a case study using ross river virus disease

<p>Abstract</p> <p>Background</p> <p>Detection of outbreaks is an important part of disease surveillance. Although many algorithms have been designed for detecting outbreaks, few have been specifically assessed against diseases that have distinct seasonal incidence patterns, such as those caused by vector-borne pathogens.</p> <p>Methods</p> <p>We applied five previously reported outbreak detection algorithms to Ross River virus (RRV) disease data (1991-2007) for the four local government areas (LGAs) of Brisbane, Emerald, Redland and Townsville in Queensland, Australia. The methods used were the Early Aberration Reporting System (EARS) C1, C2 and C3 methods, negative binomial cusum (NBC), historical limits method (HLM), Poisson outbreak detection (POD) method and the purely temporal SaTScan analysis. Seasonally-adjusted variants of the NBC and SaTScan methods were developed. Some of the algorithms were applied using a range of parameter values, resulting in 17 variants of the five algorithms.</p> <p>Results</p> <p>The 9,188 RRV disease notifications that occurred in the four selected regions over the study period showed marked seasonality, which adversely affected the performance of some of the outbreak detection algorithms. Most of the methods examined were able to detect the same major events. The exception was the seasonally-adjusted NBC methods that detected an excess of short signals. The NBC, POD and temporal SaTScan algorithms were the only methods that consistently had high true positive rates and low false positive and false negative rates across the four study areas. The timeliness of outbreak signals generated by each method was also compared but there was no consistency across outbreaks and LGAs.</p> <p>Conclusions</p> <p>This study has highlighted several issues associated with applying outbreak detection algorithms to seasonal disease data. In lieu of a true gold standard, a quantitative comparison is difficult and caution should be taken when interpreting the true positives, false positives, sensitivity and specificity.</p

Malaria burden and costs of intensifi ed control in Bhutan, 2006–14: an observational study and situation analysis

Introduction The number of malaria cases has fallen in Bhutan in the past two decades, and the country has a goal of complete elimination of malaria by 2016. The aims of this study are to ascertain the trends and burden of malaria, the costs of intensifi ed control activities, the main donors of funding for the control activities, and the costs of diff erent preventive measures in the pre-elimination phase (2006–14) in Bhutan. Methods We undertook a descriptive analysis of malaria surveillance data from 2006 to 2014, using data from the Vector-borne Disease Control Programme (VDCP) run by the Department of Public Health of Bhutan’s Ministry of Health. Malaria morbidity and mortality in local Bhutanese people and foreign nationals were analysed. The cost of diff erent control and preventive measures were calculated, and the average numbers of long-lasting insecticidal nests per person were estimated. Findings A total of 5491 confi rmed malaria cases occurred in Bhutan between 2006 and 2014. By 2013, there was an average of one long-lasting insecticidal net for every 1·51 individuals. The cost of procuring long-lasting insecticidal nets accounted for more than 90% of the total cost of prevention measures. The Global Fund to Fight AIDS, Tuberculosis and Malaria was the main international donor, accounting for more than 80% of the total funds. Interpretation The malaria burden in Bhutan decreased signifi cantly during the study period with high coverage of long-lasting insecticidal nets. The foreseeable challenges that require national attention to maintain a malaria-free status after elimination are importation of malaria, especially from India; continued protection of the population in endemic districts through complete coverage with long-lasting insecticidal nets and indoor residual spraying; and exploration of local funding modalities post-elimination in the event of a reduction in international funding

Suppression of mRNAs Encoding Tegument Tetraspanins from Schistosoma mansoni Results in Impaired Tegument Turnover

Schistosomes express a family of integral membrane proteins, called tetraspanins (TSPs), in the outer surface membranes of the tegument. Two of these tetraspanins, Sm-TSP-1 and Sm-TSP-2, confer protection as vaccines in mice, and individuals who are naturally resistant to S. mansoni infection mount a strong IgG response to Sm-TSP-2. To determine their functions in the tegument of S. mansoni we used RNA interference to silence expression of Sm-tsp-1 and Sm-tsp-2 mRNAs. Soaking of parasites in Sm-tsp dsRNAs resulted in 61% (p = 0.009) and 74% (p = 0.009) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in adult worms, and 67%–75% (p = 0.011) and 69%–89% (p = 0.004) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in schistosomula compared to worms treated with irrelevant control (luciferase) dsRNA. Ultrastructural morphology of adult worms treated in vitro with Sm-tsp-2 dsRNA displayed a distinctly vacuolated and thinner tegument compared with controls. Schistosomula exposed in vitro to Sm-tsp-2 dsRNA had a significantly thinner and more vacuolated tegument, and morphology consistent with a failure of tegumentary invaginations to close. Injection of mice with schistosomula that had been electroporated with Sm-tsp-1 and Sm-tsp-2 dsRNAs resulted in 61% (p = 0.005) and 83% (p = 0.002) reductions in the numbers of parasites recovered from the mesenteries four weeks later when compared to dsRNA-treated controls. These results imply that tetraspanins play important structural roles impacting tegument development, maturation or stability

Bond-rearrangement and ionization mechanisms in the photo-double-ionization of simple hydrocarbons (C2H4, C2H3F, and 1,1-C2H2F2) near and above threshold

Citation: Gaire, B., Gatton, A., Wiegandt, F., Neff, J., Janke, C., Zeller, S., . . . Weber, T. (2016). Bond-rearrangement and ionization mechanisms in the photo-double-ionization of simple hydrocarbons (C2H4, C2H3F, and 1,1-C2H2F2) near and above threshold. Physical Review A, 94(3), 8. doi:10.1103/PhysRevA.94.033412We investigate bond-rearrangement driven by photo-double-ionization (PDI) near and above the double-ionization threshold in a sequence of carbon-carbon double-bonded hydrocarbon molecules: ethylene, fluoroethylene, and 1,1-difluoroethylene. We employ the kinematically complete cold target recoil ion momentum spectroscopy method to resolve all photo-double-ionization events leading to two-ion fragments. We observe changes in the branching ratios of different dissociative ionization channels depending on the presence of no, one, or two fluorine atoms. The role of the fluorine atom in the bond-rearrangement channels is intriguing, as evident by the reordering of the threshold energies of the PDI in the fluorinated molecules. These effects offer a compelling argument that the electronegativity of the fluorine (or the polarity of the molecule) strongly influences the potential energy surfaces of the molecules and drives bond rearrangement during the dissociation process. The energy sharing and the relative angle between the three-dimensional momentum vectors of the two electrons enable us to distinguish between knockout and other ionization mechanisms of the PDI processes

Comparative effectiveness of malaria prevention measures: a systematic review and network meta-analysis.

Malaria causes significant morbidity and mortality worldwide. There are several preventive measures that are currently employed, including insecticide-treated nets (ITNs, including long-lasting insecticidal nets and insecticidal-treated bed nets), indoor residual spraying (IRS), prophylactic drugs (PD), and untreated nets (UN). However, it is unclear which measure is the most effective for malaria prevention. We therefore undertook a network meta-analysis to compare the efficacy of different preventive measures on incidence of malaria infection. A systematic literature review was undertaken across four medical and life sciences databases (PubMed, Cochrane Central, Embase, and Web of Science) from their inception to July 2016 to compare the effectiveness of different preventive measures on malaria incidence. Data from the included studies were analysed for the effectiveness of several measures against no intervention (NI). This was carried out using an automated generalized pairwise modeling (GPM) framework for network meta-analysis to generate mixed treatment effects against a common comparator of no intervention (NI). There were 30 studies that met the inclusion criteria from 1998-2016. The GPM framework led to a final ranking of effectiveness of measures in the following order from best to worst: PD, ITN, IRS and UN, in comparison with NI. However, only ITN (RR: 0.49, 95% CI: 0.32-0.74) showed precision while other methods [PD (RR: 0.24, 95% CI: 0.004-15.43), IRS (RR: 0.55, 95% CI: 0.20-1.56) and UN (RR: 0.73, 95% CI: 0.28-1.90)] demonstrating considerable uncertainty associated with their point estimates. Current evidence is strong for the protective effect of ITN interventions in malaria prevention. Even though ITNs were found to be the only preventive measure with statistical support for their effectiveness, the role of other malaria control measures may be important adjuncts in the global drive to eliminate malaria

Interrupting Malaria Transmission: Quantifying the Impact of Interventions in Regions of Low to Moderate Transmission

Malaria has been eliminated from over 40 countries with an additional 39 currently planning for, or committed to, elimination. Information on the likely impact of available interventions, and the required time, is urgently needed to help plan resource allocation. Mathematical modelling has been used to investigate the impact of various interventions; the strength of the conclusions is boosted when several models with differing formulation produce similar data. Here we predict by using an individual-based stochastic simulation model of seasonal Plasmodium falciparum transmission that transmission can be interrupted and parasite reintroductions controlled in villages of 1,000 individuals where the entomological inoculation rate is <7 infectious bites per person per year using chemotherapy and bed net strategies. Above this transmission intensity bed nets and symptomatic treatment alone were not sufficient to interrupt transmission and control the importation of malaria for at least 150 days. Our model results suggest that 1) stochastic events impact the likelihood of successfully interrupting transmission with large variability in the times required, 2) the relative reduction in morbidity caused by the interventions were age-group specific, changing over time, and 3) the post-intervention changes in morbidity were larger than the corresponding impact on transmission. These results generally agree with the conclusions from previously published models. However the model also predicted changes in parasite population structure as a result of improved treatment of symptomatic individuals; the survival probability of introduced parasites reduced leading to an increase in the prevalence of sub-patent infections in semi-immune individuals. This novel finding requires further investigation in the field because, if confirmed, such a change would have a negative impact on attempts to eliminate the disease from areas of moderate transmission

Identification of optimal epitopes for Plasmodium falciparum rapid diagnostic tests that target histidine-rich proteins 2 and 3

Rapid diagnostic tests (RDTs) represent important tools to diagnose malaria infection. To improve understanding of the variable performance of RDTs that detect the major target in Plasmodium falciparum, namely, histidine-rich protein 2 (HRP2), and to inform the design of better tests, we undertook detailed mapping of the epitopes recognized by eight HRP-specific monoclonal antibodies (MAbs). To investigate the geographic skewing of this polymorphic protein, we analyzed the distribution of these epitopes in parasites from geographically diverse areas. To identify an ideal amino acid motif for a MAb to target in HRP2 and in the related protein HRP3, we used a purpose-designed script to perform bioinformatic analysis of 448 distinct gene sequences from pfhrp2 and from 99 sequences from the closely related gene pfhrp3. The frequency and distribution of these motifs were also compared to the MAb epitopes. Heat stability testing of MAbs immobilized on nitrocellulose membranes was also performed. Results of these experiments enabled the identification of MAbs with the most desirable characteristics for inclusion in RDTs, including copy number and coverage of target epitopes, geographic skewing, heat stability, and match with the most abundant amino acid motifs identified. This study therefore informs the selection of MAbs to include in malaria RDTs as well as in the generation of improved MAbs that should improve the performance of HRP-detecting malaria RDTs. Copyright © 2012, American Society for Microbiology

Ultrafast temporal evolution of interatomic Coulombic decay in NeKr dimers

We investigate interatomic Coulombic decay in NeKr dimers after neon inner-valence photoionization [Ne+(2s-1)] using a synchrotron light source. We measure with high energy resolution the two singly charged ions of the Coulomb-exploding dimer dication and the photoelectron in coincidence. By carefully tracing the post-collision interaction between the photoelectron and the emitted ICD electron we are able to probe the temporal evolution of the state as it decays. Although the ionizing light pulses are 80 picoseconds long, we determine the lifetime of the intermediate dimer cation state and visualize the contraction of the nuclear structure on the femtosecond time scale

HRP2 and pLDH-Based Rapid Diagnostic Tests, Expert Microscopy, and PCR for Detection of Malaria Infection during Pregnancy and at Delivery in Areas of Varied Transmission: A Prospective Cohort Study in Burkina Faso and Uganda.

BACKGROUND: Intermittent screening and treatment (IST) of malaria during pregnancy has been proposed as an alternative to intermittent preventive treatment in pregnancy (IPTp), where IPTp is failing due to drug resistance. However, the antenatal parasitaemias are frequently very low, and the most appropriate screening test for IST has not been defined. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a multi-center prospective study of 990 HIV-uninfected women attending ANC in two different malaria transmission settings at Tororo District Hospital, eastern Uganda and Colsama Health Center in western Burkina Faso. Women were enrolled in the study in the second or third trimester of pregnancy and followed to delivery, generating 2,597 blood samples for analysis. Screening tests included rapid diagnostic tests (RDTs) targeting histidine-rich protein 2 (HRP2) and parasite lactate dehydrogenase (pLDH) and microscopy, compared to nPCR as a reference standard. At enrolment, the proportion of pregnant women who were positive for P. falciparum by HRP2/pan pLDH RDT, Pf pLDH/pan pLDH RDT, microscopy and PCR was 38%, 29%, 36% and 44% in Uganda and 21%, 16%, 15% and 35% in Burkina Faso, respectively. All test positivity rates declined during follow-up. In comparison to PCR, the sensitivity of the HRP2/pan pLDH RDT, Pf pLDH/pan pLDH RDT and microscopy was 75.7%, 60.1% and 69.7% in Uganda, 55.8%, 42.6% and 55.8% in Burkina Faso respectively for all antenatal visits. Specificity was greater than 96% for all three tests. Comparison of accuracy using generalized estimating equation revealed that the HRP2- detecting RDT was the most accurate test in both settings. CONCLUSIONS/SIGNIFICANCE: The study suggests that HRP2-based RDTs are the most appropriate point-of-care test currently available for use during pregnancy especially for symptomatic women, but will still miss some PCR-positive women. The clinical significance of these very low density infections needs to be better defined

Mechanisms and dynamics of the NH⁺₂ + H⁺ and NH⁺ + H⁺ + H fragmentation channels upon single-photon double ionization of NH₃

We present state-selective measurements on the NH$_2^{+}$ + H$^{+}$ and NH$^{+}$ + H$^{+}$ + H dissociation channels following single-photon double ionization at 61.5 eV of neutral NH$_{3}$, where the two photoelectrons and two cations are measured in coincidence using 3-D momentum imaging. Three dication electronic states are identified to contribute to the NH$_2^{+}$ + H$^{+}$ dissociation channel, where the excitation in one of the three states undergoes intersystem crossing prior to dissociation, producing a cold NH$_2^+$ fragment. In contrast, the other two states directly dissociate, producing a ro-vibrationally excited NH$_2^+$ fragment with roughly 1 eV of internal energy. The NH$^{+}$ + H$^{+}$ + H channel is fed by direct dissociation from three intermediate dication states, one of which is shared with the NH$_2^{+}$ + H$^{+}$ channel. We find evidence of autoionization contributing to each of the double ionization channels. The distributions of the relative emission angle between the two photoelectrons, as well as the relative angle between the recoil axis of the molecular breakup and the polarization vector of the ionizing field, are also presented to provide insight on both the photoionization and photodissociation mechanisms for the different dication states