Using serological diagnostics to characterize remaining high-incidence pockets of malaria in forest-fringe Cambodia

BACKGROUND

Over the last decades, the number of malaria cases has drastically reduced in Cambodia. As the overall prevalence of malaria in Cambodia declines, residual malaria transmission becomes increasingly fragmented over smaller remote regions. The aim of this study was to get an insight into the burden and epidemiological parameters of Plasmodium infections on the forest-fringe of Cambodia.

METHODS

950 participants were recruited in the province of Mondulkiri in Cambodia and followed up from 2018 to 2020. Whole-blood samples were processed for Plasmodium spp. identification by PCR as well as for a serological immunoassay. A risk factor analysis was conducted for Plasmodium vivax PCR-detected infections throughout the study, and for P. vivax seropositivity at baseline. To evaluate the predictive effect of seropositivity at baseline on subsequent PCR-positivity, an analysis of P. vivax infection-free survival time stratified by serological status at baseline was performed.

RESULTS

Living inside the forest significantly increased the odds of P. vivax PCR-positivity by a factor of 18.3 (95% C.I. 7.7-43.5). Being a male adult was also a significant predictor of PCR-positivity. Similar risk profiles were identified for P. vivax seropositivity. The survival analysis showed that serological status at baseline significantly correlated with subsequent infection. Serology is most informative outside of the forest, where 94.0% (95% C.I. 90.7-97.4%) of seronegative individuals survived infection-free, compared to 32.4% (95% C.I.: 22.6-46.6%) of seropositive individuals.

CONCLUSION

This study justifies the need for serological diagnostic assays to target interventions in this region, particularly in demographic groups where a lot of risk heterogeneity persists, such as outside of the forest.

Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites

Challenges in understanding the origin of recurrent Plasmodium vivax infections constrains the surveillance of antimalarial efficacy and transmission of this neglected parasite. Recurrent infections within an individual may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or new inoculations (reinfection). Molecular inference of familial relatedness (identity-by-descent or IBD) based on whole genome sequence data, together with analysis of the intervals between parasitaemic episodes ("time-to-event" analysis), can help resolve the probable origin of recurrences. Whole genome sequencing of predominantly low-density P. vivax infections is challenging, so an accurate and scalable genotyping method to determine the origins of recurrent parasitaemia would be of significant benefit. We have developed a P. vivax genome-wide informatics pipeline to select specific microhaplotype panels that can capture IBD within small, amplifiable segments of the genome. Using a global set of 615 P. vivax genomes, we derived a panel of 100 microhaplotypes, each comprising 3-10 high frequency SNPs within <200 bp sequence windows. This panel exhibits high diversity in regions of the Asia-Pacific, Latin America and the horn of Africa (median HE = 0.70-0.81) and it captured 89% (273/307) of the polyclonal infections detected with genome-wide datasets. Using data simulations, we demonstrate lower error in estimating pairwise IBD using microhaplotypes, relative to traditional biallelic SNP barcodes. Our panel exhibited high accuracy in predicting the country of origin (median Matthew's correlation coefficient >0.9 in 90% countries tested) and it also captured local infection outbreak and bottlenecking events. The informatics pipeline is available open-source and yields microhaplotypes that can be readily transferred to high-throughput amplicon sequencing assays for surveillance in malaria-endemic regions.

Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis

The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most population genetic studies in P. falciparum focus on regions of high transmission where parasite populations are large and genetically diverse, such as sub-Saharan Africa. Understanding population dynamics in low transmission settings, however, is of particular importance as these are often where drug resistance first evolves. Here, we use the Pacific Coast of Colombia and Ecuador as a model for understanding the population structure and evolution of Plasmodium parasites in small populations harboring less genetic diversity. The combination of low transmission and a high proportion of monoclonal infections means there are few outcrossing events and clonal lineages persist for long periods of time. Yet despite this, the population is evolutionarily labile and has successfully adapted to changes in drug regime. Using newly sequenced whole genomes, we measure relatedness between 166 parasites, calculated as identity by descent (IBD), and find 17 distinct but highly related clonal lineages, six of which have persisted in the region for at least a decade. This inbred population structure is captured in more detail with IBD than with other common population structure analyses like PCA, ADMIXTURE, and distance-based trees. We additionally use patterns of intra-chromosomal IBD and an analysis of haplotypic variation to explore past selection events in the region. Two genes associated with chloroquine resistance, crt and aat1, show evidence of hard selective sweeps, while selection appears soft and/or incomplete at three other key resistance loci (dhps, mdr1, and dhfr). Overall, this work highlights the strength of IBD analyses for studying parasite population structure and resistance evolution in regions of low transmission, and emphasizes that drug resistance can evolve and spread in small populations, as will occur in any region nearing malaria elimination.

Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study

Multiplexed PCR amplicon sequencing (AmpSeq) is an increasingly popular application for cost-effective monitoring of threatened species and managed wildlife populations, and shows strong potential for genomic epidemiology of infectious disease. AmpSeq data from infectious microbes can inform disease control in multiple ways, including measuring drug resistance marker prevalence, distinguishing imported from local cases, and determining the effectiveness of therapeutics. We describe the design and comparative evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites: a four-locus panel ('4CAST') composed of highly diverse antigens, and a 129-locus panel ('AMPLseq') composed of drug resistance markers, highly diverse loci for inferring relatedness, and a locus to detect Plasmodium vivax co-infection. We explore the performance of each panel in various public health use cases with in silico simulations as well as empirical experiments. The 4CAST panel appears highly suitable for evaluating the number of distinct parasite strains within samples (complexity of infection), showing strong performance across a wide range of parasitemia levels without a DNA pre-amplification step. For relatedness inference, the larger AMPLseq panel performs similarly to two existing panels of comparable size, despite differences in the data and approach used for designing each panel. Finally, we describe an R package (paneljudge) that facilitates the design and comparative evaluation of genetic panels for relatedness estimation, and we provide general guidance on the design and implementation of AmpSeq panels for genomic epidemiology of infectious disease.

Evaluating the reliability of mobility metrics from aggregated mobile phone data as proxies for SARS-CoV-2 transmission in the USA: a population-based study

BACKGROUND

In early 2020, the response to the SARS-CoV-2 pandemic focused on non-pharmaceutical interventions, some of which aimed to reduce transmission by changing mixing patterns between people. Aggregated location data from mobile phones are an important source of real-time information about human mobility on a population level, but the degree to which these mobility metrics capture the relevant contact patterns of individuals at risk of transmitting SARS-CoV-2 is not clear. In this study we describe changes in the relationship between mobile phone data and SARS-CoV-2 transmission in the USA.

METHODS

In this population-based study, we collected epidemiological data on COVID-19 cases and deaths, as well as human mobility metrics collated by advertisement technology that was derived from global positioning systems, from 1396 counties across the USA that had at least 100 laboratory-confirmed cases of COVID-19. We grouped these counties into six ordinal categories, defined by the National Center for Health Statistics (NCHS) and graded from urban to rural, and quantified the changes in COVID-19 transmission using estimates of the effective reproduction number (Rt) between Jan 22 and July 9, 2020, to investigate the relationship between aggregated mobility metrics and epidemic trajectory. For each county, we model the time series of Rt values with mobility proxies.

FINDINGS

We show that the reproduction number is most strongly associated with mobility proxies for change in the travel into counties (0·757 [95% CI 0·689 to 0·857]), but this relationship primarily holds for counties in the three most urban categories as defined by the NCHS. This relationship weakens considerably after the initial 15 weeks of the epidemic (0·442 [-0·492 to -0·392]), consistent with the emergence of more complex local policies and behaviours, including masking.

INTERPRETATION

Our study shows that the integration of mobility metrics into retrospective modelling efforts can be useful in identifying links between these metrics and Rt. Importantly, we highlight potential issues in the data generation process for transmission indicators derived from mobile phone data, representativeness, and equity of access, which must be addressed to improve the interpretability of these data in public health.

FUNDING

There was no funding source for this study.

Advances and opportunities in malaria population genomics

Almost 20 years have passed since the first reference genome assemblies were published for Plasmodium falciparum, the deadliest malaria parasite, and Anopheles gambiae, the most important mosquito vector of malaria in sub-Saharan Africa. Reference genomes now exist for all human malaria parasites and nearly half of the ~40 important vectors around the world. As a foundation for genetic diversity studies, these reference genomes have helped advance our understanding of basic disease biology and drug and insecticide resistance, and have informed vaccine development efforts. Population genomic data are increasingly being used to guide our understanding of malaria epidemiology, for example by assessing connectivity between populations and the efficacy of parasite and vector interventions. The potential value of these applications to malaria control strategies, together with the increasing diversity of genomic data types and contexts in which data are being generated, raise both opportunities and challenges in the field. This Review discusses advances in malaria genomics and explores how population genomic data could be harnessed to further support global disease control efforts.

Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast

Characterising connectivity between geographically separated biological populations is a common goal in many fields. Recent approaches to understanding connectivity between malaria parasite populations, with implications for disease control efforts, have used estimates of relatedness based on identity-by-descent (IBD). However, uncertainty around estimated relatedness has not been accounted for. IBD-based relatedness estimates with uncertainty were computed for pairs of monoclonal Plasmodium falciparum samples collected from five cities on the Colombian-Pacific coast where long-term clonal propagation of P. falciparum is frequent. The cities include two official ports, Buenaventura and Tumaco, that are separated geographically but connected by frequent marine traffic. Fractions of highly-related sample pairs (whose classification using a threshold accounts for uncertainty) were greater within cities versus between. However, based on both highly-related fractions and on a threshold-free approach (Wasserstein distances between parasite populations) connectivity between Buenaventura and Tumaco was disproportionally high. Buenaventura-Tumaco connectivity was consistent with transmission events involving parasites from five clonal components (groups of statistically indistinguishable parasites identified under a graph theoretic framework). To conclude, P. falciparum population connectivity on the Colombian-Pacific coast abides by accessibility not isolation-by-distance, potentially implicating marine traffic in malaria transmission with opportunities for targeted intervention. Further investigations are required to test this hypothesis. For the first time in malaria epidemiology (and to our knowledge in ecological and epidemiological studies more generally), we account for uncertainty around estimated relatedness (an important consideration for studies that plan to use genotype versus whole genome sequence data to estimate IBD-based relatedness); we also use threshold-free methods to compare parasite populations and identify clonal components. Threshold-free methods are especially important in analyses of malaria parasites and other recombining organisms with mixed mating systems where thresholds do not have clear interpretation (e.g. due to clonal propagation) and thus undermine the cross-comparison of studies.

A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices

Genetic surveillance of malaria parasites supports malaria control programmes, treatment guidelines and elimination strategies. Surveillance studies often pose questions about malaria parasite ancestry (e.g. how antimalarial resistance has spread) and employ statistical methods that characterise parasite population structure. Many of the methods used to characterise structure are unsupervised machine learning algorithms which depend on a genetic distance matrix, notably principal coordinates analysis (PCoA) and hierarchical agglomerative clustering (HAC). PCoA and HAC are sensitive to both the definition of genetic distance and algorithmic specification. Importantly, neither algorithm infers malaria parasite ancestry. As such, PCoA and HAC can inform (e.g. via exploratory data visualisation and hypothesis generation), but not answer comprehensively, key questions about malaria parasite ancestry. We illustrate the sensitivity of PCoA and HAC using 393 Plasmodium falciparum whole genome sequences collected from Cambodia and neighbouring regions (where antimalarial resistance has emerged and spread recently) and we provide tentative guidance for the use and interpretation of PCoA and HAC in malaria parasite genetic epidemiology. This guidance includes a call for fully transparent and reproducible analysis pipelines that feature (i) a clearly outlined scientific question; (ii) a clear justification of analytical methods used to answer the scientific question along with discussion of any inferential limitations; (iii) publicly available genetic distance matrices when downstream analyses depend on them; and (iv) sensitivity analyses. To bridge the inferential disconnect between the output of non-inferential unsupervised learning algorithms and the scientific questions of interest, tailor-made statistical models are needed to infer malaria parasite ancestry. In the absence of such models speculative reasoning should feature only as discussion but not as results.

A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery

Motivation

Artificial intelligence, trained via machine learning (e.g. neural nets, random forests) or computational statistical algorithms (e.g. support vector machines, ridge regression), holds much promise for the improvement of small-molecule drug discovery. However, small-molecule structure-activity data are high dimensional with low signal-to-noise ratios and proper validation of predictive methods is difficult. It is poorly understood which, if any, of the currently available machine learning algorithms will best predict new candidate drugs.

Results

The quantile-activity bootstrap is proposed as a new model validation framework using quantile splits on the activity distribution function to construct training and testing sets. In addition, we propose two novel rank-based loss functions which penalize only the out-of-sample predicted ranks of high-activity molecules. The combination of these methods was used to assess the performance of neural nets, random forests, support vector machines (regression) and ridge regression applied to 25 diverse high-quality structure-activity datasets publicly available on ChEMBL. Model validation based on random partitioning of available data favours models that overfit and ‘memorize’ the training set, namely random forests and deep neural nets. Partitioning based on quantiles of the activity distribution correctly penalizes extrapolation of models onto structurally different molecules outside of the training data. Simpler, traditional statistical methods such as ridge regression can outperform state-of-the-art machine learning methods in this setting. In addition, our new rank-based loss functions give considerably different results from mean squared error highlighting the necessity to define model optimality with respect to the decision task at hand.

Availability and implementation

All software and data are available as Jupyter notebooks found at https://github.com/owatson/QuantileBootstrap.

Supplementary information

Supplementary data are available at Bioinformatics online.

Using observational data to quantify bias of traveller-derived COVID-19 prevalence estimates in Wuhan, China

BACKGROUND

The incidence of coronavirus disease 2019 (COVID-19) in Wuhan, China, has been estimated using imported case counts of international travellers, generally under the assumptions that all cases of the disease in travellers have been ascertained and that infection prevalence in travellers and residents is the same. However, findings indicate variation among locations in the capacity for detection of imported cases. Singapore has had very strong epidemiological surveillance and contact tracing capacity during previous infectious disease outbreaks and has consistently shown high sensitivity of case-detection during the COVID-19 outbreak.

METHODS

We used a Bayesian modelling approach to estimate the relative capacity for detection of imported cases of COVID-19 for 194 locations (excluding China) compared with that for Singapore. We also built a simple mathematical model of the point prevalence of infection in visitors to an epicentre relative to that in residents.

FINDINGS

The weighted global ability to detect Wuhan-to-location imported cases of COVID-19 was estimated to be 38% (95% highest posterior density interval [HPDI] 22-64) of Singapore's capacity. This value is equivalent to 2·8 (95% HPDI 1·5-4·4) times the current number of imported and reported cases that could have been detected if all locations had had the same detection capacity as Singapore. Using the second component of the Global Health Security index to stratify likely case-detection capacities, the ability to detect imported cases relative to Singapore was 40% (95% HPDI 22-67) among locations with high surveillance capacity, 37% (18-68) among locations with medium surveillance capacity, and 11% (0-42) among locations with low surveillance capacity. Treating all travellers as if they were residents (rather than accounting for the brief stay of some of these travellers in Wuhan) contributed modestly to underestimation of prevalence.

INTERPRETATION

Estimates of case counts in Wuhan based on assumptions of 100% detection in travellers could have been underestimated by several fold. Furthermore, severity estimates will be inflated several fold since they also rely on case count estimates. Finally, our model supports evidence that underdetected cases of COVID-19 have probably spread in most locations around the world, with greatest risk in locations of low detection capacity and high connectivity to the epicentre of the outbreak.

FUNDING

US National Institute of General Medical Sciences, and Fellowship Foundation Ramon Areces.

Quantifying bias of COVID-19 prevalence and severity estimates in Wuhan, China that depend on reported cases in international travelers

Risk of COVID-19 infection in Wuhan has been estimated using imported case counts of international travelers, often under the assumption that all cases in travelers are ascertained. Recent work indicates variation among countries in detection capacity for imported cases. Singapore has historically had very strong epidemiological surveillance and contact-tracing capacity and has shown in the COVID-19 epidemic evidence of a high sensitivity of case detection. We therefore used a Bayesian modeling approach to estimate the relative imported case detection capacity for other countries compared to that of Singapore. We estimate that the global ability to detect imported cases is 38% (95% HPDI 22% - 64%) of Singapore's capacity. Equivalently, an estimate of 2.8 (95% HPDI 1.5 - 4.4) times the current number of imported cases, could have been detected, if all countries had had the same detection capacity as Singapore. Using the second component of the Global Health Security index to stratify likely case-detection capacities, we found that the ability to detect imported cases relative to Singapore among high surveillance locations is 40% (95% HPDI 22% - 67%), among intermediate surveillance locations it is 37% (95% HPDI 18% - 68%), and among low surveillance locations it is 11% (95% HPDI 0% - 42%). Using a simple mathematical model, we further find that treating all travelers as if they were residents (rather than accounting for the brief stay of some of these travelers in Wuhan) can modestly contribute to underestimation of prevalence as well. We conclude that estimates of case counts in Wuhan based on assumptions of perfect detection in travelers may be underestimated by several fold, and severity correspondingly overestimated by several fold. Undetected cases are likely in countries around the world, with greater risk in countries of low detection capacity and high connectivity to the epicenter of the outbreak.

Resolving the cause of recurrent Plasmodium vivax malaria probabilistically

Relapses arising from dormant liver-stage Plasmodium vivax parasites (hypnozoites) are a major cause of vivax malaria. However, in endemic areas, a recurrent blood-stage infection following treatment can be hypnozoite-derived (relapse), a blood-stage treatment failure (recrudescence), or a newly acquired infection (reinfection). Each of these requires a different prevention strategy, but it was not previously possible to distinguish between them reliably. We show that individual vivax malaria recurrences can be characterised probabilistically by combined modelling of time-to-event and genetic data within a framework incorporating identity-by-descent. Analysis of pooled patient data on 1441 recurrent P. vivax infections in 1299 patients on the Thailand-Myanmar border observed over 1000 patient follow-up years shows that, without primaquine radical curative treatment, 3 in 4 patients relapse. In contrast, after supervised high-dose primaquine only 1 in 40 relapse. In this region of frequent relapsing P. vivax, failure rates after supervised high-dose primaquine are significantly lower (∼3%) than estimated previously.

Estimating Relatedness Between Malaria Parasites

Understanding the relatedness of individuals within or between populations is a common goal in biology. Increasingly, relatedness features in genetic epidemiology studies of pathogens. These studies are relatively new compared to those in humans and other organisms, but are important for designing interventions and understanding pathogen transmission. Only recently have researchers begun to routinely apply relatedness to apicomplexan eukaryotic malaria parasites, and to date have used a range of different approaches on an ad hoc basis. Therefore, it remains unclear how to compare different studies and which measures to use. Here, we systematically compare measures based on identity-by-state (IBS) and identity-by-descent (IBD) using a globally diverse data set of malaria parasites, Plasmodium falciparum and P. vivax, and provide marker requirements for estimates based on IBD. We formally show that the informativeness of polyallelic markers for relatedness inference is maximized when alleles are equifrequent. Estimates based on IBS are sensitive to allele frequencies, which vary across populations and by experimental design. For portability across studies, we thus recommend estimates based on IBD. To generate estimates with errors below an arbitrary threshold of 0.1, we recommend ∼100 polyallelic or 200 biallelic markers. Marker requirements are immediately applicable to haploid malaria parasites and other haploid eukaryotes. C.I.s facilitate comparison when different marker sets are used. This is the first attempt to provide rigorous analysis of the reliability of, and requirements for, relatedness inference in malaria genetic epidemiology. We hope it will provide a basis for statistically informed prospective study design and surveillance strategies.

Balloon valvuloplasty in a dog with congenital bicuspid aortic valve and supravalvar aortic stenosis (atypical Shone's complex)

An 8-month-old intact female pug was presented for evaluation and possible balloon valvuloplasty (BV) for severe aortic stenosis. A bicuspid, severely stenotic aortic valve of type 3 morphology with a supravalvar stenosis component was diagnosed, consistent with the diagnosis of atypical Shone's complex. There was severe concentric hypertrophy of the left ventricle, with increased echogenicity of the myocardium nearest to the endocardial border. Mild left atrial enlargement was observed. Selective angiography and transesophageal echocardiography revealed an enlarged and relatively tortuous ascending aorta. The changes to the ascending aorta and the anatomy of the lesion made retrograde access to the left ventricle challenging. Ultimately, BV was successful using a pediatric valvuloplasty balloon catheter and rapid right ventricular pacing, and the pressure gradient across the aortic valve was decreased by more than 50% compared with preoperative measurements. Although valvar aortic stenosis is rare in veterinary medicine, this report highlights the potential challenges and feasibility of BV for this disease.

Correction to: Mapping malaria by combining parasite genomic and epidemiologic data

The original article [1] contained an error in the presentation of Figure 1; this error has now been rectified and Figure 1 is now presented correctly.

Mapping malaria by combining parasite genomic and epidemiologic data

BACKGROUND

Recent global progress in scaling up malaria control interventions has revived the goal of complete elimination in many countries. Decreasing transmission intensity generally leads to increasingly patchy spatial patterns of malaria transmission in elimination settings, with control programs having to accurately identify remaining foci in order to efficiently target interventions.

FINDINGS

The role of connectivity between different pockets of local transmission is of increasing importance as programs near elimination since humans are able to transfer parasites beyond the limits of mosquito dispersal, thus re-introducing parasites to previously malaria-free regions. Here, we discuss recent advances in the quantification of spatial epidemiology of malaria, particularly Plasmodium falciparum, in the context of transmission reduction interventions. Further, we highlight the challenges and promising directions for the development of integrated mapping, modeling, and genomic approaches that leverage disparate datasets to measure both connectivity and transmission.

CONCLUSION

A more comprehensive understanding of the spatial transmission of malaria can be gained using a combination of parasite genetics and epidemiological modeling and mapping. However, additional molecular and quantitative methods are necessary to answer these public health-related questions.

hmmIBD: software to infer pairwise identity by descent between haploid genotypes

Background

A number of recent malaria studies have used identity by descent (IBD) to study epidemiological processes relevant to malaria control. In this paper, a software package, hmmIBD, is introduced for estimating pairwise IBD between haploid genomes, such as those of the malaria parasite, sampled from one or two populations. Source code is freely available.

Methods

The performance of hmmIBD was verified using simulated data and benchmarked against an existing method for detecting IBD within populations. Code for all tests is freely available. The utility of hmmIBD for detecting IBD across populations was demonstrated using Plasmodium falciparum data from Cambodia and Ghana.

Results

Alongside an existing method, hmmIBD was highly accurate, sensitive and specific. It is fast, requiring only 70 s on average to analyse 50 whole genome sequences on a laptop computer, and scales linearly in the number of pairwise comparisons. Treatment of different populations under hmmIBD improves detection of IBD across populations.

Conclusion

Fast and accurate software for detecting IBD in malaria parasite genetic data sampled from one or two populations is presented. The latter will likely be a useful feature for malaria elimination efforts, since it could facilitate identification of imported malaria cases. Software is robust to possible misspecification of the genotyping error and the recombination rate. However, exclusion of data in regions whose rates vary greatly from their genome-wide average is recommended.

Electronic supplementary material

The online version of this article (10.1186/s12936-018-2349-7) contains supplementary material, which is available to authorized users.

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent

With the rapidly increasing abundance and accessibility of genomic data, there is a growing interest in using population genetic approaches to characterize fine-scale dispersal of organisms, providing insight into biological processes across a broad range of fields including ecology, evolution and epidemiology. For sexually recombining haploid organisms such as the human malaria parasite P. falciparum, however, there have been no systematic assessments of the type of data and methods required to resolve fine scale connectivity. This analytical gap hinders the use of genomics for understanding local transmission patterns, a crucial goal for policy makers charged with eliminating this important human pathogen. Here we use data collected from four clinics with a catchment area spanning approximately 120 km of the Thai-Myanmar border to compare the ability of divergence (FST) and relatedness based on identity by descent (IBD) to resolve spatial connectivity between malaria parasites collected from proximal clinics. We found no relationship between inter-clinic distance and FST, likely due to sampling of highly related parasites within clinics, but a significant decline in IBD-based relatedness with increasing inter-clinic distance. This association was contingent upon the data set type and size. We estimated that approximately 147 single-infection whole genome sequenced parasite samples or 222 single-infection parasite samples genotyped at 93 single nucleotide polymorphisms (SNPs) were sufficient to recover a robust spatial trend estimate at this scale. In summary, surveillance efforts cannot rely on classical measures of genetic divergence to measure P. falciparum transmission on a local scale. Given adequate sampling, IBD-based relatedness provides a useful alternative, and robust trends can be obtained from parasite samples genotyped at approximately 100 SNPs.

Artemether-Lumefantrine and Dihydroartemisinin-Piperaquine Exert Inverse Selective Pressure on Plasmodium Falciparum Drug Sensitivity-Associated Haplotypes in Uganda

BACKGROUND

Altered sensitivity to multiple antimalarial drugs is mediated by polymorphisms in pfmdr1, which encodes the Plasmodium falciparum multidrug resistance transporter. In Africa the N86Y and D1246Y polymorphisms have been shown to be selected by treatment, with artemether-lumefantrine (AL) and dihydroartemisinin-piperaquine (DP) selecting for wild-type and mutant alleles, respectively. However, there has been little study of pfmdr1 haplotypes, in part because haplotype analyses are complicated by multiclonal infections.

METHODS

We fit a haplotype frequency estimation model, which accounts for multiclonal infections, to the polymorphic pfmdr1 N86Y, Y184F, and D1246Y alleles in samples from a longitudinal trial comparing AL and DP to treat uncomplicated P falciparum malaria in Tororo, Uganda from 2007 to 2012. We regressed estimates onto covariates of trial arm and selective drug pressure.

RESULTS

Yearly trends showed increasing frequency estimates for haplotypes with wild type pfmdr1 N86 and D1246 alleles and decreasing frequency estimates for haplotypes with the mutant pfmdr1 86Y allele. Considering days since prior therapy, we saw evidence suggestive of selection by AL for haplotypes with N86 combined with 184F, D1246, or both, and against all haplotypes with 86Y, and evidence suggestive of selection by DP for 86Y only when combined with Y184 and 1246Y (haplotype YYY) and against haplotypes NFD and NYY.

CONCLUSIONS

Based on our model, AL selected several haplotypes containing N86, whereas DP selection was haplotype specific, demonstrating the importance of haplotype analyses. Inverse selective pressure of AL and DP on the complementary haplotypes NFD and YYY suggests that rotating artemisinin-based antimalarial combination regimens may be the best treatment option to prevent resistance selection.

The influence of maternal energy status during midgestation on beef offspring carcass characteristics and meat quality

Research has suggested that maternal undernutrition may cause the development of a thrifty phenotype in the offspring, potentially resulting in greater adiposity and reduced muscle mass. These alterations in adipose and muscle development could have lasting impacts on offspring growth, carcass characteristics, and meat quality. However, limited research exists evaluating the impact of maternal energy status on these economically important traits of the offspring. Therefore, the objective of this study was to determine the influence of maternal energy status during midgestation on offspring carcass characteristics and meat quality. To alter maternal energy status, cows either grazed dormant, winter range (positive energy status [PES]) or were fed in a drylot at 80% of the energy requirements for BW maintenance (negative energy status [NES]) during a mean period of 102 ± 10.9 to 193 ± 10.9 d of gestation. Changes in BCS, BW, LM area (LMA), and 12th rib backfat were measured throughout midgestation. At the end of midgestation, cows in the NES group had a reduction (P ≤ 0.05) in BCS, BW, LMA, and 12th rib backfat when compared with PES dams. Cows and calves were managed similarly after midgestation through weaning and calves were managed and fed a common diet through the receiving, backgrounding, and finishing phases in the feedlot. Calves were harvested after 208 d in the feedlot, carcass characteristics were recorded, and strip loins were recovered for analysis of objective color and Warner-Bratzler shear force (WBSF). Maternal energy status had no influence on offspring HCW, dressing percent, LMA, percent KPH, marbling score, percent intramuscular fat, objective color, or WBSF (P > 0.10). Progeny of NES cows tended to have improvements in 12th rib backfat and USDA yield grade (P < 0.10). Greater ratio of marbling score to 12th rib fat thickness and ratio of percent intramuscular fat to 12th rib fat thickness (P < 0.05) were discovered in progeny from cows experiencing a NES during midgestation. These results suggest that maternal energy status during midgestation may impact fat deposition in intramuscular and subcutaneous fat depots without impacting muscle mass.

Clinical Features and Magnetic Resonance Imaging Findings in 7 Dogs with Central Nervous System Aspergillosis

Background

Systemic aspergillosis is a manifestation of Aspergillus sp. infection that can result in central nervous system (CNS) involvement with marked alterations in CNS function. Information regarding the clinical presentation and magnetic resonance imaging (MRI) findings in cases of aspergillosis with CNS involvement is lacking, resulting in a need for better understanding of this disease.

Hypothesis/Objectives

The primary objectives were to describe the clinical features and MRI findings in dogs with CNS aspergillosis. The secondary objectives were to describe clinicopathologic findings and case outcome.

Animals

Seven dogs with CNS aspergillosis.

Methods

Archived records from 6 institutions were reviewed to identify cases with MRI of CNS aspergillosis confirmed with serum galactomannan enzyme immunoassay (EIA) testing, culture, or supported by histopathology. Signalment, clinical, MRI, clinicopathologic, histopathologic, and microbiologic findings were recorded and evaluated.

Results

Aspergillosis of the CNS was identified in 7 dogs from 3 institutions. The median age was 3 years and six were German Shepherd dogs. Five dogs had signs of vestibular dysfunction as a component of multifocal neurological abnormalities. The MRI findings ranged from normal to abnormal, including hemorrhagic infarction and mass lesions.

Conclusions and Clinical Importance

Until now, all reported MRI findings in dogs with CNS aspergillosis have been abnormal. We document that CNS aspergillosis in dogs, particularly German Shepherd dogs, can be suspected based on neurologic signs, whether MRI findings are normal or abnormal. Confirmatory testing with galactomannan EIA, urine, cerebrospinal fluid (CSF) or tissue culture should be performed in cases where aspergillosis is a differential diagnosis.

Submarine groundwater discharge from the South Australian Limestone Coast region estimated using radium and salinity

The Tertiary Limestone Aquifer (TLA) is one of the major regional hydrogeological systems of southern Australia. Submarine groundwater discharge (SGD) of freshwater from the TLA occurs through spring creeks, beach springs and diffusively through beach sands, but the magnitude of the total flux is not known. Here, a range of potential environmental tracers (including temperature, salinity, (222)Rn, (223)Ra, (224)Ra, (226)Ra, (228)Ra, and (4)He) were measured in potential sources of SGD and in seawater along a 45 km transect off the coastline to evaluate SGD from the TLA. Whilst most tracers had a distinct signature in the sources of water to the coastline, salinity and the radium quartet had the most distinct SGD signal in seawater. A one-dimensional advection-dispersion model was used to estimate the terrestrial freshwater component of SGD (Qfw) using salinity and the recirculated seawater component (Qrsw) using radium activity in seawater. Qfw was estimated at 1.2-4.6 m(3) s(-1), similar in magnitude to previously measured spring creek discharge (∼3 m(3) s(-1)) for the area. This suggests that other terrestrial groundwater discharge processes (beach springs and diffuse discharge through beach sands) were no more than 50% of spring creek discharge. The largest component of total SGD was Qrsw, estimated at 500-1000 m(3) s(-1) and possibly greater. The potential for wave, storm, or buoyancy-driven porewater displacement from the seafloor could explain the large recirculation flux for this section of the Southern Ocean Continental Shelf.

Estimation of malaria haplotype and genotype frequencies: a statistical approach to overcome the challenge associated with multiclonal infections

Background

Reliable measures of anti-malarial resistance are crucial for malaria control. Resistance is typically a complex trait: multiple mutations in a single parasite (a haplotype or genotype) are necessary for elaboration of the resistant phenotype. The frequency of a genetic motif (proportion of parasite clones in the parasite population that carry a given allele, haplotype or genotype) is a useful measure of resistance. In areas of high endemicity, malaria patients generally harbour multiple parasite clones; they have multiplicities of infection (MOIs) greater than one. However, most standard experimental procedures only allow measurement of marker prevalence (proportion of patient blood samples that test positive for a given mutation or combination of mutations), not frequency. It is misleading to compare marker prevalence between sites that have different mean MOIs; frequencies are required instead.

Methods

A Bayesian statistical model was developed to estimate Plasmodium falciparum genetic motif frequencies from prevalence data collected in the field. To assess model performance and computational speed, a detailed simulation study was implemented. Application of the model was tested using datasets from five sites in Uganda. The datasets included prevalence data on markers of resistance to sulphadoxine-pyrimethamine and an average MOI estimate for each study site.

Results

The simulation study revealed that the genetic motif frequencies that were estimated using the model were more accurate and precise than conventional estimates based on direct counting. Importantly, the model did not require measurements of the MOI in each patient; it used the average MOI in the patient population. Furthermore, if a dataset included partially genotyped patient blood samples, the model imputed the data that were missing. Using the model and the Ugandan data, genotype frequencies were estimated and four biologically relevant genotypes were identified.

Conclusions

The model allows fast, accurate, reliable estimation of the frequency of genetic motifs associated with resistance to anti-malarials using prevalence data collected from malaria patients. The model does not require per-patient MOI measurements and can easily analyse data from five markers. The model will be a valuable tool for monitoring markers of anti-malarial drug resistance, including markers of resistance to artemisinin derivatives and partner drugs.

The interaction of disrupted type II neuregulin 1 and chronic adolescent stress on adult anxiety- and fear-related behaviors

The incidence of anxiety, mood, substance abuse disorders and schizophrenia increases during adolescence. Epidemiological evidence confirms that exposure to stress during sensitive periods of development can create vulnerabilities that put genetically predisposed individuals at increased risk for psychiatric disorders. Neuregulin 1 (NRG1) is a frequently identified schizophrenia susceptibility gene that has also been associated with the psychotic features of bipolar disorder. Previously, we established that Type II NRG1 is expressed in the hypothalamic-pituitary-adrenal (HPA) axis neurocircuitry. We also found, using a line of Nrg1 hypomorphic rats (Nrg1(Tn)), that genetic disruption of Type II NRG1 results in altered HPA axis function and environmental reactivity. The present studies used the Nrg1(Tn) rats to test whether Type II NRG1 gene disruption and chronic stress exposure during adolescence interact to alter adult anxiety- and fear-related behaviors. Male and female Nrg1(Tn) and wild-type rats were exposed to chronic variable stress (CVS) during mid-adolescence and then tested for anxiety-like behavior, cued fear conditioning and basal corticosterone secretion in adulthood. The disruption of Type II NRG1 alone significantly impacts rat anxiety-related behavior by reversing normal sex-related differences and impairs the ability to acquire cued fear conditioning. Sex-specific interactions between genotype and adolescent stress also were identified such that CVS-treated wild-type females exhibited a slight reduction in anxiety-like behavior and basal corticosterone, while CVS-treated Nrg1(Tn) females exhibited a significant increase in cued fear extinction. These studies confirm the importance of Type II NRG1 in anxiety and fear behaviors and point to adolescence as a time when stressful experiences can shape adult behavior and HPA axis function.

Motoneuron programmed cell death in response to proBDNF

Motoneurons (MN) as well as most neuronal populations undergo a temporally and spatially specific period of programmed cell death (PCD). Several factors have been considered to regulate the survival of MNs during this period, including availability of muscle-derived trophic support and activity. The possibility that target-derived factors may also negatively regulate MN survival has been considered, but not pursued. Neurotrophin precursors, through their interaction with p75(NTR) and sortilin receptors have been shown to induce cell death during development and following injury in the CNS. In this study, we find that muscle cells produce and secrete proBDNF. ProBDNF through its interaction with p75(NTR) and sortilin, promotes a caspase-dependent death of MNs in culture. We also provide data to suggest that proBDNF regulates MN PCD during development in vivo.

Disruption of the neuregulin 1 gene in the rat alters HPA axis activity and behavioral responses to environmental stimuli

Exposure to stress can result in an increased risk for psychiatric disorders, especially among genetically predisposed individuals. Neuregulin 1 (NRG1) is a susceptibility gene for schizophrenia and is also associated with psychotic bipolar disorder. In the rat, the neurons of the hypothalamic paraventricular nucleus show strong expression of Nrg1 mRNA. In patients with schizophrenia, a single nucleotide polymorphism in the 5' region of NRG1 interacts with psychosocial stress to affect reactivity to expressed emotion. However, there is virtually no information on the role of NRG1 in hypothalamic-pituitary-adrenal axis function, and whether the protein is expressed in the paraventricular nucleus is unknown. The present studies utilize a unique line of Nrg1 hypomorphic rats (Nrg1(Tn)) generated by gene trapping with the Sleeping Beauty transposon. We first established that the Nrg1(Tn) rats displayed reduced expression of both the mRNA and protein corresponding to the Type II NRG1 isoform. After confirming, using wild type animals, that Type II NRG1 is expressed in the neurocircuitry involved in regulating hypothalamic-pituitary-adrenal axis responses to environmental stimuli, the Nrg1(Tn) rats were then used to test the hypothesis that altered expression of Type II NRG1 disrupts stress regulation and reactivity. In support of this hypothesis, Nrg1(Tn) rats have disrupted basal and acute stress recovery corticosterone secretion, differential changes in expression of glucocorticoid receptors in the pituitary, paraventricular nucleus and hippocampus, and a failure to habituate to an open field. Together, these findings point to NRG1 as a potential novel regulator of neuroendocrine responses to stress as well as behavioral reactivity.

Membrane recycling and calcium dynamics during settlement and adhesion of zoospores of the green alga Ulva linza

Recruitment of individuals of the marine alga Ulva linza on to a suitable habitat involves the settlement of motile zoospores on to a substratum during which a preformed adhesive is secreted by vesicular exocytosis. The fluorescent styryl dye FM 1-43 and fluorescent Ca(2+) indicators were used to follow membrane cycling and changes in cytosolic Ca(2+) ([Ca(2+)](cyt)) associated with settlement. When swimming zoospores were exposed continuously to FM 1-43, the plasma membrane was preferentially labelled. During settlement, FM 1-43-labelled plasma membrane was rapidly internalized reflecting high membrane turnover. The internalized membrane was focused into a discrete region indicating targeting of membrane to an endosome-like compartment. Acetoxymethyl (AM)-ester derivatives were found to be unsuitable for monitoring [Ca(2+)](cyt) because the dyes were rapidly sequestered from the cytoplasm into sub-cellular compartments. [Ca(2+)](cyt) was, however, reliably measured using dextran-conjugated calcium indicators delivered into cells using a biolistic technique. Cells loaded with Oregon Green BAPTA-1 dextran (Invitrogen, Paisley, UK) showed diffuse cytosolic loading and reliably responded to imposed changes in [Ca(2+)](cyt). During settlement, zoospores exhibited both localized and diffuse increases in [Ca(2+)](cyt) implying a role for [Ca(2+)](cyt) in exocytosis of the adhesive.

Male breast cancer in World War II aviation: a case report and review

Increased incidence of malignancies within aviators is well documented. Commercial female flyers have been found to have a higher risk of developing breast cancer. However, there has not been any report of male breast cancer related to flying either alone or where malignant melanoma and other primary cancers are also associated. We report two male World War II, British Royal Air Force pilots with primary breast carcinoma associated with two other primary cancer sites.

Apparent absence of a redox requirement for blue light activation of pump current in broad bean guard cells

In guard cells, membrane hyperpolarization in response to a blue light (BL) stimulus is achieved by the activation of a plasma membrane H(+)-ATPase. Using the patch clamp technique on broad bean (Vicia faba) guard cells we demonstrate that both steady-state- and BL-induced pump currents require ATP and are blocked by vanadate perfused into the guard cell during patch clamp recording. Background-pump current and BL-activated currents are voltage independent over a wide range of membrane potentials. During BL-activated responses significant hyperpolarization is achieved that is sufficient to promote K(+) uptake. BL activation of pump current becomes desensitized by three or four pulses of 30 s x 100 micromol m(-2) s(-1) BL. This desensitization is not a result of pump inhibition as maximal responses to fusicoccin are observed after full BL desensitization. BL treatments prior to whole cell recording show that BL desensitization is not due to washout of a secondary messenger by whole cell perfusion, but appears to be an important feature of the BL-stimulated pump response. We found no evidence for an electrogenic BL-stimulated redox chain in the plasma membrane of guard cells as no steady-state- or BL-activated currents are detected with NADH or NADPH added to the cytosol in the absence of ATP. Steady-state- nor BL-activated currents are affected by the inclusion along with ATP of 1 mM NADH in the pipette under saturating red light or by including NADPH in the pipette under darkness or saturating red light. These data suggest that reduced products of photosynthesis do not significantly modulate plasma membrane pump currents and are unlikely to be critical regulators in BL-stimulation of the plasma membrane H(+)-ATPase in guard cells.

The Galactic Worm GW 123.4-1.5: A Mushroom-shaped H i Cloud

The Dominion Radio Astrophysical Observatory's Synthesis Telescope provides the highest resolution data (1&arcmin; and 0.82 km s-1) to date of an H i worm candidate. Observed as part of the Canadian Galactic Plane Survey, mushroom-shaped GW 123.4-1.5 extends only a few hundred parsecs, contains approximately 105 M middle dot in circle of neutral hydrogen, and appears unrelated to a conventional shell or chimney structure. Our preliminary Zeus two-dimensional models use a single off-plane explosion with a modest ( approximately 1051 ergs) energy input. These generic simulations generate, interior to an expanding outer blast wave, a buoyant cloud whose structure resembles the morphology of the observed feature. Unlike typical model superbubbles, the stem can be narrow because its width is not governed by the pressure behind the blast wave or the disk scale height. Using this type of approach, it should be possible to more accurately model the thin stem and other details of GW 123.4-1.5 in the future.

The use of the latissimus dorsi musculocutaneous flap for immediate correction of the deformity resulting from breast conservation surgery

Breast conservation surgery is now widely accepted as the treatment of choice in early breast cancer. Randomised controlled trials have shown comparable recurrence and survival rates following breast conservation when compared to mastectomy, with the perceived advantage that it should leave a cosmetically acceptable result without reconstruction. It is our experience that an adequate local excision may result in a poor cosmetic result with distortion of the nipple position, especially in women with small breasts. Between January 1994 and July 1996, we have performed 30 procedures, combining a wide local excision and axillary lymph node clearance for breast cancer with immediate reconstruction of the defect with a latissimus dorsi musculocutaneous flap. All patients had postoperative radiotherapy to the residual breast and, where appropriate, to the axilla. Adjuvant hormonal therapy or chemotherapy was prescribed where indicated. Patient's ages ranged from 36 to 72 years. All tumours were in the lateral, superior or inferior quadrants. The mean combined operating time was 120 min. Two patients required postoperative blood transfusion. Mean hospital stay was 8 days. Histology confirmed tumour clearance in all cases and six patients had axillary lymph node metastases. There were two cases of minor wound infection and six cases of seroma at the donor site. We conclude that breast cancers are ideally treated by a multidisciplinary team and that an immediate latissimus dorsi musculocutaneous flap may correct the deformities often seen after breast conservation surgery.

Overview and initial results of the very long baseline interferometry space observatory programme

High angular resolution images of extragalactic radio sources are being made with the Highly Advanced Laboratory for Communications and Astronomy (HALCA) satellite and ground-based radio telescopes as part of the Very Long Baseline Interferometry (VLBI) Space Observatory Programme (VSOP). VSOP observations at 1.6 and 5 gigahertz of the milli-arc-second-scale structure of radio quasars enable the quasar core size and the corresponding brightness temperature to be determined, and they enable the motions of jet components that are close to the core to be studied. Here, VSOP images of the gamma-ray source 1156+295, the quasar 1548+056, the ultraluminous quasar 0014+813, and the superluminal quasar 0212+735 are presented and discussed.

Seal-promoting solutions and pipette perfusion for patch clamping plant cells

Patch-clamp technology has greatly increased our knowledge of plant membrane transport. However, the success of patch clamping crucially relies on establishing a high resistance (G omega) seal between the membrane and the patch-clamp pipette. This can prove problematic in many plant-cell preparations. It is therefore of great importance to develop protocols for protoplast isolation, maintenance and seal formation that improve seal rate. This study investigated whether the pH and the K+ and the Cl(-)concentration of the pipette solution had an effect on the seal formation. High pH and absence of K+ significantly promoted membrane sealing, whereas the concentration of Cl- had no effect. To reap the benefit of seal-promoting pipette solutions and yet retain the option to adjust this solution to experimental requirements, a pipette perfusion apparatus was implemented. The perfusion system was successfully applied in cell-attached patch, excised-patch and whole-cell configurations, using plasma membrane and tonoplast of three different species. The system enables complete solution exchange within minutes and is potentially of great benefit in the study of channel selectivity, the application of (cytoplasmic) channel blockers and the study of primary and secondary transport.

A randomised phase III cross-over study of tamoxifen versus megestrol acetate in advanced and recurrent breast cancer

139 peri- and postmenopausal women with advanced or recurrent breast cancer who had not received prior hormonal therapy were randomised in an open, cross-over study comparing the synthetic progestogen megestrol acetate with tamoxifen. The response rate (CR/PR) to megestrol acetate (25%; 95% confidence interval (CI) 15-35%) was not significantly different from that produced by tamoxifen (33%, CI 22-44%). Time-to-treatment failure was also similar in the two groups. Cross-over treatment was given on progression in 76 cases. Cross-over response (CR/PR) was seen in 3 of 35 patients (9%) receiving megestrol acetate as second-line therapy and in 6 of 41 patients (15%) receiving tamoxifen second-line. There was no significant difference in survival between the groups (P = 0.17) with median survival times of 24 and 32 months for the megestrol acetate and tamoxifen groups, respectively. The toxicity profile of the two drugs was different, although significant toxicity was rare with either agent. Megestrol acetate is an effective treatment for advanced breast cancer in older women when used either as first- or second-line treatment. Cross-over response is seen following both treatments. Given that most patients now receive tamoxifen as adjuvant treatment, megestrol acetate would appear to be one of the logical choices for patients who find the side-effects of tamoxifen unacceptable and for those who relapse on tamoxifen with further hormone therapy being clinically indicated.

A galactic chimney in the Perseus arm of the Milky Way

Galaxies are surrounded by large haloes of hot gas which must be replenished as the gas cools. This has led to the concept of galactic 'chimneys'--cavities in the interstellar medium, created by multiple supernova explosions, that can act as conduits for the efficient transport of hot gas from a galaxy's disk to its halo. Here we present a high-resolution map of atomic hydrogen in the Perseus arm of our galaxy, which shows clear evidence for the existence of such a chimney. This chimney appears to have been formed by the energetic winds from a cluster of young massive stars, and may currently have reached the stage of bowing out into the halo.

Identification of trimetazidine metabolites in human urine and plasma

1. The objective was to use modern mass spectrometric techniques to update current information on the metabolism of trimetazidine in human subjects found by previous studies. 2. Urine and plasma samples were taken from four healthy human volunteers taking part in a larger kinetic study. Each subject received an oral dose of 80-mg trimetazidine daily for 4 days. 3. Identification and quantitation of trimetazidine and its metabolites in urine and plasma were achieved using modern liquid chromatography-mass spectrometric methods. 4. The major drug-related component observed in urine and plasma was unchanged trimetazidine. In addition to the parent drug, 10 metabolites were detected in urine in concentrations ranging from 0.008 (0.01% dose) to 1.094 micrograms.ml-1 (1.4% dose). Metabolic profiles following acute and chronic doses of trimetazidine were qualitatively similar.

Laser microsurgery of higher plant cell walls permits patch-clamp access

Plasma membranes of guard cells in epidermal peels of Vicia faba and Commelina communis can be made accessible to a patch-clamp pipet by removing a small portion (1-3 micrometers in diameter) of the guard cell wall using a microbeam of ultraviolet light generated by a nitrogen laser. Using this laser microsurgical technique, we have measured channel activity across plasma membranes of V. faba guard cells in both cell-attached and isolated patch configurations. Measurements made in the inside-out patch configuration revealed two distinct K(+)-selective channels. Major advantages of the laser microsurgical technique include the avoidance of enzymatic protoplast isolation, the ability to study cell types that have been difficult to isolate as protoplasts or for which enzymatic isolation protocols result in protoplasts not amenable to patch-clamp studies, the maintenance of positional information in single-channel measurements, reduced disruption of cell-wall-mediated signaling pathways, and the ability to investigate intercellular signaling through studies of cells remaining situated within tissue.