Hierarchical Bayesian geostatistics for C stock prediction in disturbed plantation forest in Zimbabwe

We develop and present a novel Bayesian hierarchical geostatistical model for the prediction of plantation forest carbon stock (C stock) in the eastern highlands of Zimbabwe using multispectral Landsat-8 and Sentinel-2 remotely sensed data. Specifically, we adopt a Bayesian hierarchical methodology encompassing a model-based inferential framework making use of efficient Markov Chain Monte Carlo (MCMC) techniques for assessing model input parameters. Our proposed hierarchical modelling framework evaluates the influence of two but related covariate information sources in C stock prediction in order to build sustainable capacity on carbon reporting and monitoring. The perceived improvements in the spectral and spatial properties of Landsat-8 and Sentinel-2 data and their potential to predict C stock with shorter uncertainty bounds is tested in the developed hierarchical Bayesian models. We utilized the Mean Squared Shortest Distance (MSSD) as the objective function for optimization of sampling locations for equal area coverage. Specifically, we evaluated the models using four selected remotely sensed vegetation indices namely, the normalised difference vegetation index (NDVI), soil adjusted vegetation index (SAVI), enhanced vegetation index (EVI) and an additional distance to settlements anthropogenic variable that justifies from the history of the studied plantation forest in the eastern highlands of Zimbabwe. We evaluated two models making use of Landsat-8 and Sentinel-2 derived predictors using the Root Mean Squared Error (RMSE), Mean Absolute Error (MAE), Coverage (CVG) and Deviance Information Criteria (DIC). The Sentinel-2 based C stock model resulted in RMSE of 1.16 MgCha⁻¹, MAE of 1.11 MgCha⁻¹, CVG of 94.7% and a DIC of −554.7 whilst its Landsat-8 based C stock counterpart yielded a RMSE, MAE, CVG and DIC of 2.69 MgCha⁻¹, 1.77 MgCha⁻¹, 85.4% and 43.1 respectively. Although predictive models from both sensors show great improvement in predictive accuracy when modelling the spatial random effects, the Sentinel-2 based C stock predictive model substantially outperforms its Landsat-8 based C stock counterpart. The Sentinel-2 based C stock predictive hierarchical model therefore adequately addresses multiple sources of uncertainty inherent in the spatial prediction of C stock in disturbed plantation ecosystems. It is evident from the results of this study that carbon reporting and monitoring can always be improved by scouting for improved and easily accessible remote sensing data and allow forest practitioners to keep track of error across space in resource environments of interest.     

Bayesian latent class models in malaria diagnosis

Aims

The main focus of this study is to illustrate the importance of the statistical analysis in the evaluation of the accuracy of malaria diagnostic tests, without admitting a reference test, exploring a dataset (3317) collected in São Tomé and Príncipe.

Methods

Bayesian Latent Class Models (without and with constraints) are used to estimate the malaria infection prevalence, together with sensitivities, specificities, and predictive values of three diagnostic tests (RDT, Microscopy and PCR), in four subpopulations simultaneously based on a stratified analysis by age groups (, 5 years old) and fever status (febrile, afebrile).

Results

In the afebrile individuals with at least five years old, the posterior mean of the malaria infection prevalence is 3.2% with a highest posterior density interval of [2.3–4.1]. The other three subpopulations (febrile 5 years, afebrile or febrile children less than 5 years) present a higher prevalence around 10.3% [8.8–11.7]. In afebrile children under-five years old, the sensitivity of microscopy is 50.5% [37.7–63.2]. In children under-five, the estimated sensitivities/specificities of RDT are 95.4% [90.3–99.5]/93.8% [91.6–96.0] – afebrile – and 94.1% [87.5–99.4]/97.5% [95.5–99.3] – febrile. In individuals with at least five years old are 96.0% [91.5–99.7]/98.7% [98.1–99.2] – afebrile – and 97.9% [95.3–99.8]/97.7% [96.6–98.6] – febrile. The PCR yields the most reliable results in four subpopulations.

Conclusions

The utility of this RDT in the field seems to be relevant. However, in all subpopulations, data provide enough evidence to suggest caution with the positive predictive values of the RDT. Microscopy has poor sensitivity compared to the other tests, particularly, in the afebrile children less than 5 years. This type of findings reveals the danger of statistical analysis based on microscopy as a reference test. Bayesian Latent Class Models provide a powerful tool to evaluate malaria diagnostic tests, taking into account different groups of interest.     

True versus apparent malaria infection prevalence: the contribution of a Bayesian approach

Aims

To present a new approach for estimating the “true prevalence” of malaria and apply it to datasets from Peru, Vietnam, and Cambodia.

Methods

Bayesian models were developed for estimating both the malaria prevalence using different diagnostic tests (microscopy, PCR & ELISA), without the need of a gold standard, and the tests'' characteristics. Several sources of information, i.e. data, expert opinions and other sources of knowledge can be integrated into the model. This approach resulting in an optimal and harmonized estimate of malaria infection prevalence, with no conflict between the different sources of information, was tested on data from Peru, Vietnam and Cambodia.

Results

Malaria sero-prevalence was relatively low in all sites, with ELISA showing the highest estimates. The sensitivity of microscopy and ELISA were statistically lower in Vietnam than in the other sites. Similarly, the specificities of microscopy, ELISA and PCR were significantly lower in Vietnam than in the other sites. In Vietnam and Peru, microscopy was closer to the “true” estimate than the other 2 tests while as expected ELISA, with its lower specificity, usually overestimated the prevalence.

Conclusions

Bayesian methods are useful for analyzing prevalence results when no gold standard diagnostic test is available. Though some results are expected, e.g. PCR more sensitive than microscopy, a standardized and context-independent quantification of the diagnostic tests'' characteristics (sensitivity and specificity) and the underlying malaria prevalence may be useful for comparing different sites. Indeed, the use of a single diagnostic technique could strongly bias the prevalence estimation. This limitation can be circumvented by using a Bayesian framework taking into account the imperfect characteristics of the currently available diagnostic tests. As discussed in the paper, this approach may further support global malaria burden estimation initiatives.     

Severe malaria in children and pregnancy: an update and perspective

This review summarizes progress in preventing and treating severe malaria, which has been accompanied by advances in our understanding of the pathogenesis of severe malaria complications. New drugs such as intravenous artesunate and oral artemisinin combinations, with increased access to insecticide-treated bed nets, are improving outcomes and decreasing malaria deaths. Several groups are beginning to identify characteristics of parasite var genes associated with cerebral malaria. Understanding of the interactions between malaria and other diseases in causing severe anaemia and cerebral malaria has increased substantially, and at the cellular level, the disturbances leading to coma or other complications are becoming clearer.     

An evolutionary perspective on the kinome of malaria parasites

Malaria parasites belong to an ancient lineage that diverged very early from the main branch of eukaryotes. The approximately 90-member plasmodial kinome includes a majority of eukaryotic protein kinases that clearly cluster within the AGC, CMGC, TKL, CaMK and CK1 groups found in yeast, plants and mammals, testifying to the ancient ancestry of these families. However, several hundred millions years of independent evolution, and the specific pressures brought about by first a photosynthetic and then a parasitic lifestyle, led to the emergence of unique features in the plasmodial kinome. These include taxon-restricted kinase families, and unique peculiarities of individual enzymes even when they have homologues in other eukaryotes. Here, we merge essential aspects of all three malaria-related communications that were presented at the Evolution of Protein Phosphorylation meeting, and propose an integrated discussion of the specific features of the parasite's kinome and phosphoproteome.     

Proteases in malaria parasites - a phylogenomic perspective

Malaria continues to be one of the most devastating global health problems due to the high morbidity and mortality it causes in endemic regions. The search for new antimalarial targets is of high priority because of the increasing prevalence of drug resistance in malaria parasites. Malarial proteases constitute a class of promising therapeutic targets as they play important roles in the parasite life cycle and it is possible to design and screen for specific protease inhibitors. In this mini-review, we provide a phylogenomic overview of malarial proteases. An evolutionary perspective on the origin and divergence of these proteases will provide insights into the adaptive mechanisms of parasite growth, development, infection, and pathogenesis.B.     

A historical perspective on malaria control in Brazil

Malaria has always been an important public health problem in Brazil. The earlyhistory of Brazilian malaria and its control was powered by colonisation by Europeansand the forced relocation of Africans as slaves. Internal migration brought malariato many regions in Brazil where, given suitableAnopheles mosquitovectors, it thrived. Almost from the start, officials recognised the problem malariapresented to economic development, but early control efforts were hampered by stilldeveloping public health control and ignorance of the underlying biology and ecologyof malaria. Multiple regional and national malaria control efforts have beenattempted with varying success. At present, the Amazon Basin accounts for 99% ofBrazil’s reported malaria cases with regional increases in incidence often associatedwith large scale public works or migration. Here, we provide an exhaustive summary ofprimary literature in English, Spanish and Portuguese regarding Brazilian malariacontrol. Our goal was not to interpret the history of Brazilian malaria control froma particular political or theoretical perspective, but rather to provide astraightforward, chronological narrative of the events that have transpired in Brazilover the past 200 years and identify common themes.     

Ajuga remota Benth.: from ethnopharmacology to phytomedical perspective in the treatment of malaria

Treatment and control of malaria have become more difficult with the spread of drug-resistant parasites and insecticide-resistant mosquito vectors. In the search for new antimalarial drugs, ethnopharmacological sources should merit more attention. Establishing the safety of traditional herbal medicines, along with identifying their active principles, are essential steps in the production of a properly standardized and accessible herbal medicine. Phytochemical characterization could also serve as a base for the development of new chemical compounds. The genus of Ajuga belongs to the family Lamiaceae and contains at least 301 species. Many of these plants have been used in traditional medicine. Ajuga remota in particular is traditionally used as a herbal remedy for fever and infections, and is prescribed for malaria by 66% of the Kenyan herbalists. A large number of compounds have already been isolated from A. remota, including ergosterol-5,8-endoperoxide (6), ajugarin-I (1), 8-O-acetylharpagide (5) and several phytoecdysteroids. In vitro pharmacological studies have been conducted on constituents of A. remota of which some of them displayed a concentration-dependent inhibition of chloroquine-sensitive and -resistant Plasmodium falciparum and Mycobacterium tuberculosis. Inhibition of parasitaemia was demonstrated in mouse models with P. berghei, supporting the traditional use of the plant against malaria. In this state-of-the-art review, A. remota as a possible therapeutic tool for malaria is discussed.     

Estimating the burden of malaria in Senegal: Bayesian zero-inflated binomial geostatistical modeling of the MIS 2008 data

The Research Center for Human Development in Dakar (CRDH) with the technical assistance of ICF Macro and the National Malaria Control Programme (NMCP) conducted in 2008/2009 the Senegal Malaria Indicator Survey (SMIS), the first nationally representative household survey collecting parasitological data and malaria-related indicators. In this paper, we present spatially explicit parasitaemia risk estimates and number of infected children below 5 years. Geostatistical Zero-Inflated Binomial models (ZIB) were developed to take into account the large number of zero-prevalence survey locations (70%) in the data. Bayesian variable selection methods were incorporated within a geostatistical framework in order to choose the best set of environmental and climatic covariates associated with the parasitaemia risk. Model validation confirmed that the ZIB model had a better predictive ability than the standard Binomial analogue. Markov chain Monte Carlo (MCMC) methods were used for inference. Several insecticide treated nets (ITN) coverage indicators were calculated to assess the effectiveness of interventions. After adjusting for climatic and socio-economic factors, the presence of at least one ITN per every two household members and living in urban areas reduced the odds of parasitaemia by 86% and 81% respectively. Posterior estimates of the ORs related to the wealth index show a decreasing trend with the quintiles. Infection odds appear to be increasing with age. The population-adjusted prevalence ranges from 0.12% in Thillé-Boubacar to 13.1% in Dabo. Tambacounda has the highest population-adjusted predicted prevalence (8.08%) whereas the region with the highest estimated number of infected children under the age of 5 years is Kolda (13940). The contemporary map and estimates of malaria burden identify the priority areas for future control interventions and provide baseline information for monitoring and evaluation. Zero-Inflated formulations are more appropriate in modeling sparse geostatistical survey data, expected to arise more frequently as malaria research is focused on elimination.     

Resurgence of malaria in Bombay (Mumbai) in the 1990s: a historical perspective

Bombay has achieved extraordinary success in controlling its malaria problem for nearly six decades by relying primarily on legislative measures and non-insecticidal methods of mosquito abatement. In 1992, however, malaria reemerged in Bombay with a vengeance. During 1992-1997, the city witnessed a manifold increase in the number of malaria cases diagnosed and treated by the public health system. The large number of malaria patients treated by private practitioners was not recorded by the municipal malaria surveillance system during this period. In 1995, at the peak of the resurgence, public health officials of the Municipal Corporation of Greater Bombay (MCGB) confirmed that 170 persons in the city had died due to malaria. The crisis was unprecedented in Bombay's modern public health history. In response to intense criticism from the media, the city's public health officials attributed the resurgence to the global phenomenon of mosquito-vector resistance to insecticides, and Plasmodium resistance to antimalarial chemoprophylaxis and treatment. Local scientists who investigated the problem offered no support to this explanation. So what might explain the resurgence? What factors led the problem to reach an epidemic level in a matter of two or three years? In addressing the above principal questions, this paper adopts a historical perspective and argues that in the resurgence of malaria in Bombay in the 1990s, there is an element of the 'presence of the past'. In many ways the present public health crisis in Bombay resembles the health scenario that characterized the city at the turn of the 19th century. It is possible to draw parallels between the early public health history of malaria control in Bombay, which was punctuated by events that followed the bubonic plague epidemic of 1896, and the present-day malaria epidemic punctuated by the threat of a plague epidemic in 1994. As such, the paper covers a long period, of almost 100 years. This time-depth is used to illustrate how malaria control programs in Bombay and in other parts of India have evolved through a combination of local historical forces and political expediencies in the context of technological developments. The boom in construction activities in Bombay following the liberalization of the Indian economy in 1991, and the local politics affecting administrative practices of the MCGB, are discussed as crucial factors in the crystallization of the present-day malaria resurgence in Bombay. The paper concludes by arguing that malaria in urban India is a serious problem that cannot be neglected. In the case of Bombay, the solution to the crisis can be found, in part, by reexamining the historical and political issues that have determined the nature and magnitude of the problem over the last century.     

High variation in developmental instability under non-normal developmental error: a Bayesian perspective

The developmental mechanisms behind developmental instability (DI) are only poorly understood. Nevertheless, fluctuating asymmetry (FA) is often used a surrogate for DI. Based on statistical arguments it is often assumed that individual levels of FA are only weakly associated with the underlying DI. Patterns in FA therefore need to be interpreted with caution, and should ideally be transformed into patterns in DI. In order to be able to achieve that, assumptions about the distribution of developmental errors must be made. Current models assume that errors during development are additive and independent such that they yield a normal distribution. The observation that the distribution of FA is often leptokurtic has been interpreted as evidence for between-individual variation in DI. This approach has led to unrealistically high estimates of between-individual variation in DI, and potentially incorrect interpretations of patterns in FA, especially at the individual level. Recently, it has been suggested that the high estimates of variation in DI may be biased upward because either developmental errors are log-normal or gamma distributed and/or low measurement resolution of FA. A proper estimation of the amount (and shape) of heterogeneity in DI is crucial for the interpretation of patterns in FA and their transformation into patterns in DI. Yet, incorrect model assumptions may render misleading inferences. We therefore develop a statistical model to evaluate the sensitivity of results under the normal error model against the two alternative distributions as well as to investigate the importance of low measurement resolution. An analysis of simulated and empirical data sets indicated that bias due to misspecification of the developmental error distribution can be substantial, yet, did not appear to reduce estimates of variation in DI in empirical data sets to a large extent. Effects of low measurement resolution were neglectable. The importance of these results are discussed in the context of the interpretation of patterns in FA.     

School-based participatory health education for malaria control in Ghana: engaging children as health messengers

Background

Infected humans make protective antibody responses to the PfEMP1 adhesion antigens exported by Plasmodium falciparum parasites to the erythrocyte membrane, but little is known about the kinetics of this antibody-receptor binding reaction or how the topology of PfEMP1 on the parasitized erythrocyte membrane influences antibody association with, and dissociation from, its antigenic target.

Methods

A Quartz Crystal Microbalance biosensor was used to measure the association and dissociation kinetics of VAR2CSA PfEMP1 binding to human monoclonal antibodies. Immuno-fluorescence microscopy was used to visualize antibody-mediated adhesion between the surfaces of live infected erythrocytes and atomic force microscopy was used to obtain higher resolution images of the membrane knobs on the infected erythrocyte to estimate knob surface areas and model VAR2CSA packing density on the knob.

Results

Kinetic analysis indicates that antibody dissociation from the VAR2CSA PfEMP1 antigen is extremely slow when there is a high avidity interaction. High avidity binding to PfEMP1 antigens on the surface of P. falciparum-infected erythrocytes in turn requires bivalent cross-linking of epitopes positioned within the distance that can be bridged by antibody. Calculations of the surface area of the knobs and the possible densities of PfEMP1 packing on the knobs indicate that high-avidity cross-linking antibody reactions are constrained by the architecture of the knobs and the large size of PfEMP1 molecules.

Conclusions

High avidity is required to achieve the strongest binding to VAR2CSA PfEMP1, but the structures that display PfEMP1 also tend to inhibit cross-linking between PfEMP1 antigens, by holding many binding epitopes at distances beyond the 15-18 nm sweep radius of an antibody. The large size of PfEMP1 will also constrain intra-knob cross-linking interactions. This analysis indicates that effective vaccines targeting the parasite's vulnerable adhesion receptors should primarily induce strongly adhering, high avidity antibodies whose association rate constant is less important than their dissociation rate constant.     

Impact of placental Plasmodium falciparum malaria on pregnancy and perinatal outcome in sub-Saharan Africa: part III: placental malaria, maternal health, and public health

Plasmodium falciparum infections of the placenta remain a major medical challenge among pregnant women in sub-Saharan Africa. A number of factors influence the prevalence of placental malaria in pregnant women, including maternal age, gravidity, use of prophylaxis, nutrition, host genetics, and level of anti-parasite immunity, as well as parasite genetics and transmission rates [1]. Maternal anemia has been shown to be one of the major complications of placental malaria in sub-Saharan Africa. The mechanisms by which malaria causes anemia are fairly well understood. The pathophysiology of malaria-associated anemia is multifactorial. The most likely mechanisms include (i) hemolysis or the direct destruction of parasitized red blood cells that occurs both intravascularly and by sequestration in the microcirculation, mainly in the spleen; (ii) specific/nonspecific immune responses, whereby red cell survival is shortened; (iii) nonspecific, defective, red cell production, which depresses erythropoiesis, inhibits reticulocyte release, and prematurely destructs red cells during maturation in the bone marrow; and (iv) hypersplenism associated with a reduction in all three blood cell series, that is, causing not only anemia but also thrombocytopenia and leucopenia [2,3]. The relationship between maternal anemia with obstetric factors, however, is not fully understood, and, thus, evaluating the link between malaria, obstetric disorders, and maternal death has been recommended [4]. There have been efforts to quantify the contribution of malaria to maternal morbidity and mortality with the expectation that this would provide the evidence necessary to improve the effectiveness of advocacy to incorporate malaria prevention strategies in Safe Motherhood Programs [5,6]. The effects of placental malaria on maternal health can better be understood when considered in relation with various maternal parameters, including maternal age, parity, peripheral malaria infection, anemia, and HIV infection.