Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis

Flux balance analysis (FBA) is an increasingly useful approach for modeling the behavior of metabolic systems. However, standard FBA modeling of genetic knockouts cannot predict drug combination synergies observed between serial metabolic targets, even though such synergies give rise to some of the most widely used antibiotic treatments. Here we extend FBA modeling to simulate responses to chemical inhibitors at varying concentrations, by diverting enzymatic flux to a waste reaction. This flux diversion yields very similar qualitative predictions to prior methods for single target activity. However, we find very different predictions for combinations, where flux diversion, which mimics the kinetics of competitive metabolic inhibitors, can explain serial target synergies between metabolic enzyme inhibitors that we confirmed in Escherichia coli cultures. FBA flux diversion opens the possibility for more accurate genome-scale predictions of drug synergies, which can be used to suggest treatments for infections and other diseases.     

Can Community Health Workers Report Accurately on Births and Deaths? Results of Field Assessments in Ethiopia,Malawi and Mali

Introduction

Most low-income countries lack complete and accurate vital registration systems. As a result, measures of under-five mortality rates rely mostly on household surveys. In collaboration with partners in Ethiopia, Ghana, Malawi, and Mali, we assessed the completeness and accuracy of reporting of births and deaths by community-based health workers, and the accuracy of annualized under-five mortality rate estimates derived from these data. Here we report on results from Ethiopia, Malawi and Mali.

Method

In all three countries, community health workers (CHWs) were trained, equipped and supported to report pregnancies, births and deaths within defined geographic areas over a period of at least fifteen months. In-country institutions collected these data every month. At each study site, we administered a full birth history (FBH) or full pregnancy history (FPH), to women of reproductive age via a census of households in Mali and via household surveys in Ethiopia and Malawi. Using these FBHs/FPHs as a validation data source, we assessed the completeness of the counts of births and deaths and the accuracy of under-five, infant, and neonatal mortality rates from the community-based method against the retrospective FBH/FPH for rolling twelve-month periods. For each method we calculated total cost, average annual cost per 1,000 population, and average cost per vital event reported.

Results

On average, CHWs submitted monthly vital event reports for over 95 percent of catchment areas in Ethiopia and Malawi, and for 100 percent of catchment areas in Mali. The completeness of vital events reporting by CHWs varied: we estimated that 30%-90% of annualized expected births (i.e. the number of births estimated using a FPH) were documented by CHWs and 22%-91% of annualized expected under-five deaths were documented by CHWs. Resulting annualized under-five mortality rates based on the CHW vital events reporting were, on average, under-estimated by 28% in Ethiopia, 32% in Malawi, and 9% in Mali relative to comparable FPHs. Costs per vital event reported ranged from $21 in Malawi to $149 in Mali.

Discussion

Our findings in Mali suggest that CHWs can collect complete and high-quality vital events data useful for monitoring annual changes in under-five mortality rates. Both the supervision of CHWs in Mali and the rigor of the associated field-based data quality checks were of a high standard, and the size of the pilot area in Mali was small (comprising of approximately 53,205 residents in 4,200 households). Hence, there are remaining questions about whether this level of vital events reporting completeness and data quality could be maintained if the approach was implemented at scale. Our experience in Malawi and Ethiopia suggests that, in some settings, establishing and maintaining the completeness and quality of vital events reporting by CHWs over time is challenging. In this sense, our evaluation in Mali falls closer to that of an efficacy study, whereas our evaluations in Ethiopia and Malawi are more akin to an effectiveness study. Our overall findings suggest that no one-size-fits-all approach will be successful in guaranteeing complete and accurate reporting of vital events by CHWs.     

Screening of the Open Source Malaria Box Reveals an Early Lead Compound for the Treatment of Alveolar Echinococcosis

The metacestode (larval) stage of the tapeworm Echinococcus multilocularis causes alveolar echinococcosis (AE), a very severe and in many cases incurable disease. To date, benzimidazoles such as albendazole and mebendazole are the only approved chemotherapeutical treatment options. Benzimidazoles inhibit metacestode proliferation, but do not act parasiticidal. Thus, benzimidazoles have to be taken a lifelong, can cause adverse side effects such as hepatotoxicity, and are ineffective in some patients. We here describe a newly developed screening cascade for the evaluation of the in vitro efficacy of new compounds that includes assessment of parasiticidal activity. The Malaria Box from Medicines for Malaria Venture (MMV), comprised of 400 commercially available chemicals that show in vitro activity against Plasmodium falciparum, was repurposed. Primary screening was carried out at 10 μM by employing the previously described PGI assay, and resulted in the identification of 24 compounds that caused physical damage in metacestodes. Seven out of these 24 drugs were also active at 1 μM. Dose-response assays revealed that only 2 compounds, namely MMV665807 and MMV665794, exhibited an EC₅₀ value below 5 μM. Assessments using human foreskin fibroblasts and Reuber rat hepatoma cells showed that the salicylanilide MMV665807 was less toxic for these two mammalian cell lines than for metacestodes. The parasiticidal activity of MMV665807 was then confirmed using isolated germinal layer cell cultures as well as metacestode vesicles by employing viability assays, and its effect on metacestodes was morphologically evaluated by electron microscopy. However, both oral and intraperitoneal application of MMV665807 to mice experimentally infected with E. multilocularis metacestodes did not result in any reduction of the parasite load.     

Species Determination and Quantitation in Mixtures Using MRM Mass Spectrometry of Peptides Applied to Meat Authentication

We describe a simple protocol for identifying and quantifying the two components in binary mixtures of species possessing one or more similar proteins. Central to the method is the identification of ''corresponding proteins'' in the species of interest, in other words proteins that are nominally the same but possess species-specific sequence differences. When subject to proteolysis, corresponding proteins will give rise to some peptides which are likewise similar but with species-specific variants. These are ''corresponding peptides''. Species-specific peptides can be used as markers for species determination, while pairs of corresponding peptides permit relative quantitation of two species in a mixture. The peptides are detected using multiple reaction monitoring (MRM) mass spectrometry, a highly specific technique that enables peptide-based species determination even in complex systems. In addition, the ratio of MRM peak areas deriving from corresponding peptides supports relative quantitation. Since corresponding proteins and peptides will, in the main, behave similarly in both processing and in experimental extraction and sample preparation, the relative quantitation should remain comparatively robust. In addition, this approach does not need the standards and calibrations required by absolute quantitation methods. The protocol is described in the context of red meats, which have convenient corresponding proteins in the form of their respective myoglobins. This application is relevant to food fraud detection: the method can detect 1% weight for weight of horse meat in beef. The corresponding protein, corresponding peptide (CPCP) relative quantitation using MRM peak area ratios gives good estimates of the weight for weight composition of a horse plus beef mixture.     

Synthesis,Characterization, and Functionalization of Hybrid Au/CdS and Au/ZnS Core/Shell Nanoparticles

Plasmonic nanoparticles are an attractive material for light harvesting applications due to their easily modified surface, high surface area and large extinction coefficients which can be tuned across the visible spectrum. Research into the plasmonic enhancement of optical transitions has become popular, due to the possibility of altering and in some cases improving photo-absorption or emission properties of nearby chromophores such as molecular dyes or quantum dots. The electric field of the plasmon can couple with the excitation dipole of a chromophore, perturbing the electronic states involved in the transition and leading to increased absorption and emission rates. These enhancements can also be negated at close distances by energy transfer mechanism, making the spatial arrangement of the two species critical. Ultimately, enhancement of light harvesting efficiency in plasmonic solar cells could lead to thinner and, therefore, lower cost devices. The development of hybrid core/shell particles could offer a solution to this issue. The addition of a dielectric spacer between a gold nanoparticles and a chromophore is the proposed method to control the exciton plasmon coupling strength and thereby balance losses with the plasmonic gains. A detailed procedure for the coating of gold nanoparticles with CdS and ZnS semiconductor shells is presented. The nanoparticles show high uniformity with size control in both the core gold particles and shell species allowing for a more accurate investigation into the plasmonic enhancement of external chromophores.     

Equity in Health Care Financing in Low- and Middle-Income Countries: A Systematic Review of Evidence from Studies Using Benefit and Financing Incidence Analyses

IntroductionHealth financing reforms in low- and middle- income countries (LMICs) over the past decades have focused on achieving equity in financing of health care delivery through universal health coverage. Benefit and financing incidence analyses are two analytical methods for comprehensively evaluating how well health systems perform on these objectives. This systematic review assesses progress towards equity in health care financing in LMICs through the use of BIA and FIA.ConclusionStudies evaluated in this systematic review indicate that health care financing in LMICs benefits the rich more than the poor but the burden of financing also falls more on the rich. There is some evidence that primary health care is pro-poor suggesting a greater investment in such services and removal of barriers to care can enhance equity. The results overall suggest that there are impediments to making health care more accessible to the poor and this must be addressed if universal health coverage is to be a reality.     

Selection of the Maximum Spatial Cluster Size of the Spatial Scan Statistic by Using the Maximum Clustering Set-Proportion Statistic

Spatial scan statistics are widely used in various fields. The performance of these statistics is influenced by parameters, such as maximum spatial cluster size, and can be improved by parameter selection using performance measures. Current performance measures are based on the presence of clusters and are thus inapplicable to data sets without known clusters. In this work, we propose a novel overall performance measure called maximum clustering set–proportion (MCS-P), which is based on the likelihood of the union of detected clusters and the applied dataset. MCS-P was compared with existing performance measures in a simulation study to select the maximum spatial cluster size. Results of other performance measures, such as sensitivity and misclassification, suggest that the spatial scan statistic achieves accurate results in most scenarios with the maximum spatial cluster sizes selected using MCS-P. Given that previously known clusters are not required in the proposed strategy, selection of the optimal maximum cluster size with MCS-P can improve the performance of the scan statistic in applications without identified clusters.     

The Point Count Transect Method for Estimates of Biodiversity on Coral Reefs: Improving the Sampling of Rare Species

Understanding patterns in species richness and diversity over environmental gradients (such as altitude and depth) is an enduring component of ecology. As most biological communities feature few common and many rare species, quantifying the presence and abundance of rare species is a crucial requirement for analysis of these patterns. Coral reefs present specific challenges for data collection, with limitations on time and site accessibility making efficiency crucial. Many commonly used methods, such as line intercept transects (LIT), are poorly suited to questions requiring the detection of rare events or species. Here, an alternative method for surveying reef-building corals is presented; the point count transect (PCT). The PCT consists of a count of coral colonies at a series of sample stations, located at regular intervals along a transect. In contrast the LIT records the proportion of each species occurring under a transect tape of a given length. The same site was surveyed using PCT and LIT to compare species richness estimates between the methods. The total number of species increased faster per individual sampled and unit of time invested using PCT. Furthermore, 41 of the 44 additional species recorded by the PCT occurred ≤ 3 times, demonstrating the increased capacity of PCT to detect rare species. PCT provides a more accurate estimate of local-scale species richness than the LIT, and is an efficient alternative method for surveying reef corals to address questions associated with alpha-diversity, and rare or incidental events.