scholarly journals Evaluating the performance of malaria genomics for inferring changes in transmission intensity using transmission modelling

2019 ◽  
Author(s):  
Oliver J. Watson ◽  
Lucy C. Okell ◽  
Joel Hellewell ◽  
Hannah C. Slater ◽  
H. Juliette T. Unwin ◽  
...  
Keyword(s):  
Absolute Error ◽  
Malaria Prevalence ◽  
Transmission Intensity ◽  
Transmission Model ◽  
Genetic Sequencing ◽  
Complex Interactions ◽  
Host Parasite ◽  
The Impact ◽  
Malaria Interventions ◽  
Complexity Of Infection

AbstractAdvances in genetic sequencing and accompanying methodological approaches have resulted in pathogen genetics being used in the control of infectious diseases. To utilise these methodologies for malaria we first need to extend the methods to capture the complex interactions between parasites, human and vector hosts, and environment. Here we develop an individual-based transmission model to simulate malaria parasite genetics parameterised using estimated relationships between complexity of infection and age from 5 regions in Uganda and Kenya. We predict that cotransmission and superinfection contribute equally to within-host parasite genetic diversity at 11.5% PCR prevalence, above which superinfections dominate. Finally, we characterise the predictive power of six metrics of parasite genetics for detecting changes in transmission intensity, before grouping them in an ensemble statistical model. The best performing model successfully predicted malaria prevalence with mean absolute error of 0.055, suggesting genetic tools could be used for monitoring the impact of malaria interventions.

scholarly journals Evaluating the Performance of Malaria Genetics for Inferring Changes in Transmission Intensity Using Transmission Modeling

2020 ◽  
Vol 38 (1) ◽  
pp. 274-289
Author(s):  
Oliver J Watson ◽  
Lucy C Okell ◽  
Joel Hellewell ◽  
Hannah C Slater ◽  
H Juliette T Unwin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clinical Status ◽  
Absolute Error ◽  
Malaria Prevalence ◽  
Transmission Intensity ◽  
Transmission Model ◽  
Genetic Sequencing ◽  
Complex Interactions ◽  
Substantial Progress ◽  
Host Parasite

Abstract Substantial progress has been made globally to control malaria, however there is a growing need for innovative new tools to ensure continued progress. One approach is to harness genetic sequencing and accompanying methodological approaches as have been used in the control of other infectious diseases. However, to utilize these methodologies for malaria, we first need to extend the methods to capture the complex interactions between parasites, human and vector hosts, and environment, which all impact the level of genetic diversity and relatedness of malaria parasites. We develop an individual-based transmission model to simulate malaria parasite genetics parameterized using estimated relationships between complexity of infection and age from five regions in Uganda and Kenya. We predict that cotransmission and superinfection contribute equally to within-host parasite genetic diversity at 11.5% PCR prevalence, above which superinfections dominate. Finally, we characterize the predictive power of six metrics of parasite genetics for detecting changes in transmission intensity, before grouping them in an ensemble statistical model. The model predicted malaria prevalence with a mean absolute error of 0.055. Different assumptions about the availability of sample metadata were considered, with the most accurate predictions of malaria prevalence made when the clinical status and age of sampled individuals is known. Parasite genetics may provide a novel surveillance tool for estimating the prevalence of malaria in areas in which prevalence surveys are not feasible. However, the findings presented here reinforce the need for patient metadata to be recorded and made available within all future attempts to use parasite genetics for surveillance.

scholarly journals Evaluation of different deployment strategies for larviciding to control malaria: a simulation study

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Manuela Runge ◽  
Salum Mapua ◽  
Ismail Nambunga ◽  
Thomas A. Smith ◽  
Nakul Chitnis ◽  
...  
Keyword(s):  
Malaria Transmission ◽  
Critical Role ◽  
Indoor Residual Spraying ◽  
Malaria Prevalence ◽  
Transmission Model ◽  
Malaria Vectors ◽  
Relative Reduction ◽  
Insecticide Treated Nets ◽  
Host Seeking ◽  
The Impact

Abstract Background Larviciding against malaria vectors in Africa has been limited to indoor residual spraying and insecticide-treated nets, but is increasingly being considered by some countries as a complementary strategy. However, despite progress towards improved larvicides and new tools for mapping or treating mosquito-breeding sites, little is known about the optimal deployment strategies for larviciding in different transmission and seasonality settings. Methods A malaria transmission model, OpenMalaria, was used to simulate varying larviciding strategies and their impact on host-seeking mosquito densities, entomological inoculation rate (EIR) and malaria prevalence. Variations in coverage, duration, frequency, and timing of larviciding were simulated for three transmission intensities and four transmission seasonality profiles. Malaria transmission was assumed to follow rainfall with a lag of one month. Theoretical sub-Saharan African settings with Anopheles gambiae as the dominant vector were chosen to explore impact. Relative reduction compared to no larviciding was predicted for each indicator during the simulated larviciding period. Results Larviciding immediately reduced the predicted host-seeking mosquito densities and EIRs to a maximum that approached or exceeded the simulated coverage. Reduction in prevalence was delayed by approximately one month. The relative reduction in prevalence was up to four times higher at low than high transmission. Reducing larviciding frequency (i.e., from every 5 to 10 days) resulted in substantial loss in effectiveness (54, 45 and 53% loss of impact for host-seeking mosquito densities, EIR and prevalence, respectively). In seasonal settings the most effective timing of larviciding was during or at the beginning of the rainy season and least impactful during the dry season, assuming larviciding deployment for four months. Conclusion The results highlight the critical role of deployment strategies on the impact of larviciding. Overall, larviciding would be more effective in settings with low and seasonal transmission, and at the beginning and during the peak densities of the target species populations. For maximum impact, implementers should consider the practical ranges of coverage, duration, frequency, and timing of larviciding in their respective contexts. More operational data and improved calibration would enable models to become a practical tool to support malaria control programmes in developing larviciding strategies that account for the diversity of contexts.

scholarly journals Model-based evaluation of school- and non-school-related measures to control the COVID-19 pandemic

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ganna Rozhnova ◽  
Christiaan H. van Dorp ◽  
Patricia Bruijning-Verhagen ◽  
Martin C. J. Bootsma ◽  
Janneke H. H. M. van de Wijgert ◽  
...  
Keyword(s):  
Reproduction Number ◽  
Additional Benefit ◽  
Transmission Model ◽  
Time Points ◽  
School Based ◽  
Admission Data ◽  
Age Structured ◽  
The Impact ◽  
Pandemic Wave

AbstractThe role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. We use an age-structured transmission model fitted to age-specific seroprevalence and hospital admission data to assess the effects of school-based measures at different time points during the COVID-19 pandemic in the Netherlands. Our analyses suggest that the impact of measures reducing school-based contacts depends on the remaining opportunities to reduce non-school-based contacts. If opportunities to reduce the effective reproduction number (Re) with non-school-based measures are exhausted or undesired and Re is still close to 1, the additional benefit of school-based measures may be considerable, particularly among older school children. As two examples, we demonstrate that keeping schools closed after the summer holidays in 2020, in the absence of other measures, would not have prevented the second pandemic wave in autumn 2020 but closing schools in November 2020 could have reduced Re below 1, with unchanged non-school-based contacts.

scholarly journals Non-human primate and human malaria: past, present and future

2021 ◽  
Author(s):  
Spinello Antinori ◽  
Cecilia Bonazzetti ◽  
Andrea Giacomelli ◽  
Mario Corbellino ◽  
Massimo Galli ◽  
...  
Keyword(s):  
Plasmodium Knowlesi ◽  
Plasmodium Species ◽  
Molecular Techniques ◽  
Malaria Parasites ◽  
Human Malaria ◽  
Complex Interactions ◽  
Zoonotic Malaria ◽  
The Impact ◽  
Human Plasmodium ◽  
Human Primate

Abstract Background Studies of the malaria parasites infecting various non-human primates (NHPs) have increased our understanding of the origin, biology and pathogenesis of human Plasmodium parasites. This review considers the major discoveries concerning NHP malaria parasites, highlights their relationships with human malaria and considers the impact that this may have on attempts to eradicate the disease. Results The first description of NHP malaria parasites dates back to the early 20th century. Subsequently, experimental and fortuitous findings indicating that some NHP malaria parasites can be transmitted to humans have raised concerns about the possible impact of a zoonotic malaria reservoir on efforts to control human malaria. Advances in molecular techniques over the last 15 years have contributed greatly to our knowledge of the existence and geographical distribution of numerous Plasmodium species infecting NHPs, and extended our understanding of their close phylogenetic relationships with human malaria parasites. The clinical application of such techniques has also made it possible to document ongoing spillovers of NHP malaria parasites (Plasmodium knowlesi, P. cynomolgi, P. simium, P. brasilianum) in humans living in or near the forests of Asia and South America, thus confirming that zoonotic malaria can undermine efforts to eradicate human malaria. Conclusions Increasing molecular research supports the prophetic intuition of the pioneers of modern malariology who saw zoonotic malaria as a potential obstacle to the full success of malaria eradication programmes. It is, therefore, important to continue surveillance and research based on one-health approaches in order to improve our understanding of the complex interactions between NHPs, mosquito vectors and humans during a period of ongoing changes in the climate and the use of land, monitor the evolution of zoonotic malaria, identify the populations most at risk and implement appropriate preventive strategies.

scholarly journals Evolution of disease transmission during the COVID-19 pandemic: patterns and determinants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jie Zhu ◽  
Blanca Gallego
Keyword(s):  
Public Health ◽  
Disease Transmission ◽  
Clustering Algorithm ◽  
Health Interventions ◽  
Transmission Model ◽  
Model Parameters ◽  
Public Health Interventions ◽  
Forecasting Accuracy ◽  
Time Lagged ◽  
The Impact

AbstractEpidemic models are being used by governments to inform public health strategies to reduce the spread of SARS-CoV-2. They simulate potential scenarios by manipulating model parameters that control processes of disease transmission and recovery. However, the validity of these parameters is challenged by the uncertainty of the impact of public health interventions on disease transmission, and the forecasting accuracy of these models is rarely investigated during an outbreak. We fitted a stochastic transmission model on reported cases, recoveries and deaths associated with SARS-CoV-2 infection across 101 countries. The dynamics of disease transmission was represented in terms of the daily effective reproduction number ($$R_t$$ R t ). The relationship between public health interventions and $$R_t$$ R t was explored, firstly using a hierarchical clustering algorithm on initial $$R_t$$ R t patterns, and secondly computing the time-lagged cross correlation among the daily number of policies implemented, $$R_t$$ R t , and daily incidence counts in subsequent months. The impact of updating $$R_t$$ R t every time a prediction is made on the forecasting accuracy of the model was investigated. We identified 5 groups of countries with distinct transmission patterns during the first 6 months of the pandemic. Early adoption of social distancing measures and a shorter gap between interventions were associated with a reduction on the duration of outbreaks. The lagged correlation analysis revealed that increased policy volume was associated with lower future $$R_t$$ R t (75 days lag), while a lower $$R_t$$ R t was associated with lower future policy volume (102 days lag). Lastly, the outbreak prediction accuracy of the model using dynamically updated $$R_t$$ R t produced an average AUROC of 0.72 (0.708, 0.723) compared to 0.56 (0.555, 0.568) when $$R_t$$ R t was kept constant. Monitoring the evolution of $$R_t$$ R t during an epidemic is an important complementary piece of information to reported daily counts, recoveries and deaths, since it provides an early signal of the efficacy of containment measures. Using updated $$R_t$$ R t values produces significantly better predictions of future outbreaks. Our results found variation in the effect of early public health interventions on the evolution of $$R_t$$ R t over time and across countries, which could not be explained solely by the timing and number of the adopted interventions.

scholarly journals The effects of non-pharmaceutical interventions on SARS-CoV-2 transmission in different socioeconomic populations in Kuwait: a modeling study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fatima Khadadah ◽  
Abdullah A. Al-Shammari ◽  
Ahmad Alhashemi ◽  
Dari Alhuwail ◽  
Bader Al-Saif ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Reproduction Number ◽  
Transmission Model ◽  
Socioeconomic Groups ◽  
Before And After ◽  
Cross Transmission ◽  
Community Transmission ◽  
The Impact ◽  
Pharmaceutical Interventions ◽  
The Basic Reproduction Number

Abstract Background Aggressive non-pharmaceutical interventions (NPIs) may reduce transmission of SARS-CoV-2. The extent to which these interventions are successful in stopping the spread have not been characterized in countries with distinct socioeconomic groups. We compared the effects of a partial lockdown on disease transmission among Kuwaitis (P1) and non-Kuwaitis (P2) living in Kuwait. Methods We fit a modified metapopulation SEIR transmission model to reported cases stratified by two groups to estimate the impact of a partial lockdown on the effective reproduction number ($$ {\mathcal{R}}_e $$ R e ). We estimated the basic reproduction number ($$ {\mathcal{R}}_0 $$ R 0 ) for the transmission in each group and simulated the potential trajectories of an outbreak from the first recorded case of community transmission until 12 days after the partial lockdown. We estimated $$ {\mathcal{R}}_e $$ R e values of both groups before and after the partial curfew, simulated the effect of these values on the epidemic curves and explored a range of cross-transmission scenarios. Results We estimate $$ {\mathcal{R}}_e $$ R e at 1·08 (95% CI: 1·00–1·26) for P1 and 2·36 (2·03–2·71) for P2. On March 22nd, $$ {\mathcal{R}}_e $$ R e for P1 and P2 are estimated at 1·19 (1·04–1·34) and 1·75 (1·26–2·11) respectively. After the partial curfew had taken effect, $$ {\mathcal{R}}_e $$ R e for P1 dropped modestly to 1·05 (0·82–1·26) but almost doubled for P2 to 2·89 (2·30–3·70). Our simulated epidemic trajectories show that the partial curfew measure greatly reduced and delayed the height of the peak in P1, yet significantly elevated and hastened the peak in P2. Modest cross-transmission between P1 and P2 greatly elevated the height of the peak in P1 and brought it forward in time closer to the peak of P2. Conclusion Our results indicate and quantify how the same lockdown intervention can accentuate disease transmission in some subpopulations while potentially controlling it in others. Any such control may further become compromised in the presence of cross-transmission between subpopulations. Future interventions and policies need to be sensitive to socioeconomic and health disparities.

scholarly journals Photovoltaic Power Forecasting: Assessment of the Impact of Multiple Sources of Spatio-Temporal Data on Forecast Accuracy

Energies ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 1432
Author(s):  
Xwégnon Ghislain Agoua ◽  
Robin Girard ◽  
Georges Kariniotakis
Keyword(s):  
Satellite Images ◽  
Forecast Accuracy ◽  
Absolute Error ◽  
Data Sources ◽  
Test Case ◽  
Temporal Data ◽  
Multiple Sources ◽  
Forecasting Error ◽  
Spatio Temporal ◽  
The Impact

The efficient integration of photovoltaic (PV) production in energy systems is conditioned by the capacity to anticipate its variability, that is, the capacity to provide accurate forecasts. From the classical forecasting methods in the state of the art dealing with a single power plant, the focus has moved in recent years to spatio-temporal approaches, where geographically dispersed data are used as input to improve forecasts of a site for the horizons up to 6 h ahead. These spatio-temporal approaches provide different performances according to the data sources available but the question of the impact of each source on the actual forecasting performance is still not evaluated. In this paper, we propose a flexible spatio-temporal model to generate PV production forecasts for horizons up to 6 h ahead and we use this model to evaluate the effect of different spatial and temporal data sources on the accuracy of the forecasts. The sources considered are measurements from neighboring PV plants, local meteorological stations, Numerical Weather Predictions, and satellite images. The evaluation of the performance is carried out using a real-world test case featuring a high number of 136 PV plants. The forecasting error has been evaluated for each data source using the Mean Absolute Error and Root Mean Square Error. The results show that neighboring PV plants help to achieve around 10% reduction in forecasting error for the first three hours, followed by satellite images which help to gain an additional 3% all over the horizons up to 6 h ahead. The NWP data show no improvement for horizons up to 6 h but is essential for greater horizons.

scholarly journals Modulation of outer medullary NaCl transport and oxygenation by nitric oxide and superoxide

2011 ◽  
Vol 301 (5) ◽  
pp. F979-F996 ◽  
Author(s):  
Aurélie Edwards ◽  
Anita T. Layton
Keyword(s):  
Nitric Oxide ◽  
Active Transport ◽  
Collecting Duct ◽  
Thick Ascending Limb ◽  
Outer Medulla ◽  
Nacl Transport ◽  
Complex Interactions ◽  
Medullary Thick Ascending Limb ◽  
The Impact ◽  
Stimulation Of

We expanded our region-based model of water and solute exchanges in the rat outer medulla to incorporate the transport of nitric oxide (NO) and superoxide (O2−) and to examine the impact of NO-O2− interactions on medullary thick ascending limb (mTAL) NaCl reabsorption and oxygen (O2) consumption, under both physiological and pathological conditions. Our results suggest that NaCl transport and the concentrating capacity of the outer medulla are substantially modulated by basal levels of NO and O2−. Moreover, the effect of each solute on NaCl reabsorption cannot be considered in isolation, given the feedback loops resulting from three-way interactions between O2, NO, and O2−. Notwithstanding vasoactive effects, our model predicts that in the absence of O2−-mediated stimulation of NaCl active transport, the outer medullary concentrating capacity (evaluated as the collecting duct fluid osmolality at the outer-inner medullary junction) would be ∼40% lower. Conversely, without NO-induced inhibition of NaCl active transport, the outer medullary concentrating capacity would increase by ∼70%, but only if that anaerobic metabolism can provide up to half the maximal energy requirements of the outer medulla. The model suggests that in addition to scavenging NO, O2− modulates NO levels indirectly via its stimulation of mTAL metabolism, leading to reduction of O2 as a substrate for NO. When O2− levels are raised 10-fold, as in hypertensive animals, mTAL NaCl reabsorption is significantly enhanced, even as the inefficient use of O2 exacerbates hypoxia in the outer medulla. Conversely, an increase in tubular and vascular flows is predicted to substantially reduce mTAL NaCl reabsorption. In conclusion, our model suggests that the complex interactions between NO, O2−, and O2 significantly impact the O2 balance and NaCl reabsorption in the outer medulla.

The Potential Applications of Raman Spectroscopy in Unravelling Complex Palaeowildfire Ecosystems

2021 ◽  
Author(s):  
Thomas Theurer ◽  
David Muirhead ◽  
David Jolley ◽  
Dmitri Mauquoy
Keyword(s):  
Raman Spectroscopy ◽  
Carbonaceous Material ◽  
Complex Interactions ◽  
Intensity Changes ◽  
Potential Applications ◽  
Ecosystem Studies ◽  
History Of ◽  
The Impact ◽  
Unique Relationship

<p>Raman spectroscopy represents a novel methodology of characterising plant-fire interactions through geological history, with enormous potential. Applications of Raman spectroscopy to charcoal have shown that this is an effective method of understanding intensity changes across palaeofire regimes. Such analyses have relied on the determination of appropriate Raman parameters, given their relationship with temperature of formation and microstructural changes in reference charcoals. Quantitative assessments of charcoal microstructure have also been successfully applied to the assessment of carbonaceous maturation under alternate thermal regimes, such as pyroclastic volcanism. Palaeowildfire systems in association with volcanism may present a complex history of thermal maturation, given interactions between detrital charcoals and volcanogenic deposition. However, whilst palaeofire and volcanic maturation of carbonaceous material are well understood individually, their interaction has yet to be characterised. Here we present the first analysis of palaeofire charcoals derived from volcanic ignition utilising Raman spectroscopy. Our results indicate that complex interactions between volcanism and palaeofire systems may be better understood by the characterisation of charcoal microstructure, alongside palaeobotanical and ecosystem studies. Understanding the unique relationship between wildfires and volcanism, and the impact that this has on the fossil record, may better assist our understanding of wildfire systems in deep history. Further still, this highlights the potential for better understanding the socioecological impacts of modern and future wildfire systems closely associated with volcanic centres. </p>

Changes in mechanisms and intensity of Western U.S. floods, 1960-2013

2021 ◽  
Author(s):  
Jessica Fayne ◽  
Huilin Huang ◽  
Mike Fischella ◽  
Yufei Liu ◽  
Zhaoxin Ban ◽  
...  
Keyword(s):  
Extreme Precipitation ◽  
Large Scale ◽  
Critical Factor ◽  
Flood Frequency ◽  
Atmospheric Rivers ◽  
Convective Storms ◽  
Noticeable Increase ◽  
Complex Interactions ◽  
Different Types ◽  
The Impact

<p>Extreme precipitation, a critical factor in flooding, has selectively increased with warmer temperatures in the Western U.S. Despite this, the streamflow measurements have captured no noticeable increase in large-scale flood frequency or intensity. As flood studies have mostly focused on specific flood events in particular areas, analyses of large-scale floods and their changes have been scarce. For floods during 1960-2013, we identify six flood generating mechanisms (FGMs) that are prominent across the Western U.S., including atmospheric rivers and non-atmospheric rivers, monsoons, convective storms, radiation-driven snowmelt, and rain-on-snow, in order to identify to what extent different types of floods are changing based on the dominant FGM. The inconsistency between extreme precipitation and lack of flood increase suggests that the impact of climate change on flood risk has been modulated by hydro-meteorological and physiographic processes such as sharp increases in temperature that drive increased evapotranspiration and decreased soil moisture. Our results emphasize the importance of FGMs in understanding the complex interactions of flooding and climatic changes and explain the broad spatiotemporal changes that have occurred across the vast Western U.S. for the past 50 years.</p>

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