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The built environment can be considered a foundation for health and wellness. This structure, whether it be neighborhood layout or safe walking trails, impacts decisions relating to individual and community health outcomes. This review compiled the published research that examined the relationship between built environment and health. Findings from the 23 articles reviewed indicate that neighborhoods that are characterized as more walkable, either leisure-oriented or destination-driven, are associated with increased physical activity, increased social capital, lower overweight, lower reports of depression, and less reported alcohol abuse. [ABSTRACT FROM AUTHOR]

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Copyright of Medical Microbiology & Immunology is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

I compare Bratman’s theory with Gilbert’s. I draw attention to their ­similarities, query Bratman’s claim that his theory is the more parsimonious, and point to one theoretical advantage of Gilbert’s theory.

The AAVSO Photometric All-Sky Survey (APASS) provides calibrated magnitudes in the range 7 < V < 17 for the entire sky, in the BVugriZsY bandpasses. While primarily designed for 0.02 mag calibration, it provides photometry over a many-year baseline, and also has near daily cadence in the standard field regions on the equator. Likewise, the Second Generation Synoptic Survey (2GSS) is a follow-on to APASS, and will provide daily cadence in two passbands for the entire sky.

Abstract Background Past experience and modelling suggest that, in most cases, mass treatment strategies are not likely to succeed in interrupting Plasmodium falciparum malaria transmission. However, this does not preclude their use to reduce disease burden. Mass screening and treatment (MSAT) is preferred to mass drug administration (MDA), as the latter involves massive over-use of drugs. This paper reports simulations of the incremental cost-effectiveness of well-conducted MSAT campaigns as a strategy for P. falciparum malaria disease-burden reduction in settings with varying receptivity (ability of the combined vector population in a setting to transmit disease) and access to case management. Methods MSAT incremental cost-effectiveness ratios (ICERs) were estimated in different sub-Saharan African settings using simulation models of the dynamics of malaria and a literature-based MSAT cost estimate. Imported infections were simulated at a rate of two per 1,000 population per annum. These estimates were compared to the ICERs of scaling up case management or insecticide-treated net (ITN) coverage in each baseline health system, in the absence of MSAT. Results MSAT averted most episodes, and resulted in the lowest ICERs, in settings with a moderate level of disease burden. At a low pre-intervention entomological inoculation rate (EIR) of two infectious bites per adult per annum (IBPAPA) MSAT was never more cost-effective than scaling up ITNs or case management coverage. However, at pre-intervention entomological inoculation rates (EIRs) of 20 and 50 IBPAPA and ITN coverage levels of 40 or 60%, respectively, the ICER of MSAT was similar to that of scaling up ITN coverage further. Conclusions In all the transmission settings considered, achieving a minimal level of ITN coverage is a “best buy”. At low transmission, MSAT probably is not worth considering. Instead, MSAT may be suitable at medium to high levels of transmission and at moderate ITN coverage. If undertaken as a burden-reducing intervention, MSAT should be continued indefinitely and should complement, not replace, case management and vector control interventions.

Abstract Background The ‘overall insecticidal effect’ is a key measure used to evaluate public health pesticides for indoor use in experimental hut trials. It depends on the proportion of mosquitoes that are killed out of those that enter the treated hut, intrinsic mortality in the control hut, and the ratio of mosquitoes entering the treatment hut to those entering the control hut. This paper critically examines the way the effect is defined, and discusses how it can be used to infer effectiveness of intervention programmes. Findings The overall insecticidal effect, as defined by the World Health Organization in 2006, can be negative when deterrence from entering the treated hut is high, even if all mosquitoes that enter are killed, wrongly suggesting that the insecticide enhances mosquito survival. Also in the absence of deterrence, even if the insecticide kills all mosquitoes in the treatment hut, the insecticidal effect is less than 100%, unless intrinsic mortality is nil. A proposed alternative definition for the measurement of the overall insecticidal effect has the desirable range of 0 to 1 (100%), provided mortality among non-repelled mosquitoes in the treated hut is less than the corresponding mortality in the control hut. This definition can be built upon to formulate the coverage-dependent insecticidal effectiveness of an intervention programme. Coverage-dependent population protection against feeding can be formulated similarly. Conclusions This paper shows that the 2006 recommended quantity for measuring the overall insecticidal effect is problematic, and proposes an alternative quantity with more desirable properties.

Abstract Background Models of Plasmodium falciparum malaria epidemiology that provide realistic quantitative predictions of likely epidemiological outcomes of existing vector control strategies have the potential to assist in planning for the control and elimination of malaria. This work investigates the applicability of mathematical modelling of malaria transmission dynamics in Rachuonyo South, a district with low, unstable transmission in the highlands of western Kenya. Methods Individual-based stochastic simulation models of malaria in humans and a deterministic model of malaria in mosquitoes as part of the OpenMalaria platform were parameterized to create a scenario for the study area based on data from ongoing field studies and available literature. The scenario was simulated for a period of two years with a population of 10,000 individuals and validated against malaria survey data from Rachuonyo South. Simulations were repeated with multiple random seeds and an ensemble of 14 model variants to address stochasticity and model uncertainty. A one-dimensional sensitivity analysis was conducted to address parameter uncertainty. Results The scenario was able to reproduce the seasonal pattern of the entomological inoculation rate (EIR) and patent infections observed in an all-age cohort of individuals sampled monthly for one year. Using an EIR estimated from serology to parameterize the scenario resulted in a closer fit to parasite prevalence than an EIR estimated using entomological methods. The scenario parameterization was most sensitive to changes in the timing and effectiveness of indoor residual spraying (IRS) and the method used to detect P. falciparum in humans. It was less sensitive than expected to changes in vector biting behaviour and climatic patterns. Conclusions The OpenMalaria model of P. falciparum transmission can be used to simulate the impact of different combinations of current and potential control interventions to help plan malaria control in this low transmission setting. In this setting and for these scenarios, results were highly sensitive to transmission, vector exophagy, exophily and susceptibility to IRS, and the detection method used for surveillance. The level of accuracy of the results will thus depend upon the precision of estimates for each. New methods for analysing and evaluating uncertainty in simulation results will enhance the usefulness of simulations for malaria control decision-making. Improved measurement tools and increased primary data collection will enhance model parameterization and epidemiological monitoring. Further research is needed on the relationship between malaria indices to identify the best way to quantify transmission in low transmission settings. Measuring EIR through mosquito collection may not be the optimal way to estimate transmission intensity in areas with low, unstable transmission.

Abstract Background The bacterium Acetobacter sp. CCTCC M209061 is a promising whole-cell biocatalyst with exclusive anti-Prelog stereoselectivity for the reduction of prochiral ketones that can be used to make valuable chiral alcohols such as (R)-4-(trimethylsilyl)-3-butyn-2-ol. Although it has promising catalytic properties, its stability and reusability are relatively poor compared to other biocatalysts. Hence, we explored various materials for immobilizing the active cells, in order to improve the operational stability of biocatalyst. Results It was found that Ca-alginate give the best immobilized biocatalyst, which was then coated with chitosan to further improve its mechanical strength and swelling-resistance properties. Conditions were optimized for formation of reusable immobilized beads which can be used for repeated batch asymmetric reduction of 4′-chloroacetophenone. The optimized immobilized biocatalyst was very promising, with a specific activity of 85% that of the free-cell biocatalyst (34.66 μmol/min/g dw of cells for immobilized catalyst vs 40.54 μmol/min/g for free cells in the asymmetric reduction of 4′-chloroacetophenone). The immobilized cells showed better thermal stability, pH stability, solvent tolerance and storability compared with free cells. After 25 cycles reaction, the immobilized beads still retained >50% catalytic activity, which was 3.5 times higher than degree of retention of activity by free cells reused in a similar way. The cells could be recultured in the beads to regain full activity and perform a further 25 cycles of the reduction reaction. The external mass transfer resistances were negligible as deduced from Damkohler modulus Da < η < 1 and Thiele modulus 0.3<∅ Conclusions Ca-alginate coated with chitosan is a highly effective material for immobilization of Acetobacter sp. CCTCC M209061 cells for repeated use in the asymmetric reduction of ketones. Only a small cost in terms of the slightly lower catalytic activity compared to free cells could give highly practicable immobilized biocatalyst.

Abstract Background It is unclear how long it takes for health interventions to transition from research and development (R&D) to being used against diseases prevalent in resource-poor countries. We undertook an analysis of the time required to begin implementation of four vaccines and three malaria interventions. We evaluated five milestones for each intervention, and assessed if the milestones were associated with beginning implementation. Methods The authors screened World Health Organization (WHO) databases to determine the number of years between first regulatory approval of interventions, and countries beginning implementation. Descriptive analyses of temporal patterns and statistical analyses using logistic regression and Cox proportional hazard models were used to evaluate associations between five milestones and the beginning of implementation for each intervention. The milestones were: (A) presence of a coordinating group focused on the intervention; (B) availability of an intervention tailored to developing country health systems; (C) international financing commitment, and; (D) initial and (E) comprehensive WHO recommendations. Countries were categorized by World Bank income criteria. Results Five years after regulatory approval, no low-income countries (LICs) had begun implementing any of the vaccines, increasing to an average of only 4% of LICs after 10 years. Each malaria intervention was used by an average of 7% of LICs after five years and 37% after 10 years. Four of the interventions had similar implementation rates to hepatitis B vaccine (HepB), while one was slower and one was faster than HepB. A financing commitment and initial WHO recommendation appeared to be temporally associated with the beginning of implementation. The initial recommendation from WHO was the only milestone associated in all statistical analyses with countries beginning implementation (relative rate = 1.97, P Conclusions Although possible that four milestones were not associated with countries beginning implementation, we propose an alternative interpretation; that the milestones were not realized early enough in each intervention’s development to shorten the time to beginning implementation. We discuss a framework built upon existing literature for consideration during the development of future interventions. Identifying critical milestones and their timing relative to R&D, promises to help new interventions realize their intended public health impact more rapidly.

Abstract Background Artemisinin-based combination therapy (ACT) for treating malaria has activity against immature gametocytes. In theory, this property may complement the effect of terminating otherwise lengthy malaria infections and reducing the parasite reservoir in the human population that can infect vector mosquitoes. However, this has never been verified at a population level in a setting with intense transmission, where chronically infectious asymptomatic carriers are common and cured patients are rapidly and repeatedly re-infected. Methods From 2001 to 2004, malaria vector densities were monitored using light traps in three Tanzanian districts. Mosquitoes were dissected to determine parous and oocyst rates. Plasmodium falciparum sporozoite rates were determined by ELISA. Sulphadoxine-pyrimethamine (SP) monotherapy was used for treatment of uncomplicated malaria in the contiguous districts of Kilombero and Ulanga throughout this period. In Rufiji district, the standard drug was changed to artesunate co-administered with SP (AS + SP) in March 2003. The effects of this change in case management on malaria parasite infection in the vectors were analysed. Results Plasmodium falciparum entomological inoculation rates exceeded 300 infective bites per person per year at both sites over the whole period. The introduction of AS + SP in Rufiji was associated with increased oocyst prevalence (OR [95%CI] = 3.9 [2.9-5.3], p Conclusions In high perennial transmission settings, only a small proportion of infections in humans are symptomatic or treated, so case management with ACT may have little impact on overall infectiousness of the human population. Variations in infection levels in vectors largely depend on the age distribution of the mosquito population. Benefits of ACT in suppressing transmission are more likely to be evident where transmission is already low or effective vector control is widely implemented.

Abstract Background Understanding the relationship between Plasmodium falciparum malaria transmission and health outcomes requires accurate estimates of exposure to infectious mosquitoes. However, measures of exposure such as mosquito density and entomological inoculation rate (EIR) are generally aggregated over large areas and time periods, biasing the outcome-exposure relationship. There are few studies examining the extent and drivers of local variation in malaria exposure in endemic areas. Methods We describe the spatio-temporal dynamics of malaria transmission intensity measured by mosquito density and EIR in the KEMRI/CDC health and demographic surveillance system using entomological data collected during 2002–2004. Geostatistical zero inflated binomial and negative binomial models were applied to obtain location specific (house) estimates of sporozoite rates and mosquito densities respectively. Model-based predictions were multiplied to estimate the spatial pattern of annual entomological inoculation rate, a measure of the number of infective bites a person receive per unit of time. The models included environmental and climatic predictors extracted from satellite data, harmonic seasonal trends and parameters describing space-time correlation. Results Anopheles gambiae s.l was the main vector species accounting for 86 % (n = 2309) of the total mosquitoes collected with the remainder being Anopheles funestus. Sixty eight percent (757/1110) of the surveyed houses had no mosquitoes. Distance to water bodies, vegetation and day temperature were strongly associated with mosquito density. Overall annual point estimates of EIR were 6.7, 9.3 and 9.6 infectious bites per annum for 2002, 2003 and 2004 respectively. Monthly mosquito density and EIR varied over the study period peaking in May during the wet season each year. The predicted and observed densities of mosquitoes and EIR showed a strong seasonal and spatial pattern over the study area. Conclusions Spatio-temporal maps of malaria transmission intensity obtained in this study are not only useful in understanding variability in malaria epidemiology over small areas but also provide a high resolution exposure surface that can be used to analyse the impact of transmission on malaria related and all-cause morbidity and mortality.

Abstract Background There has recently been a substantial decline in malaria incidence in much of Africa. While the decline can clearly be linked to increasing coverage of mosquito vector control interventions and effective drug treatment in most settings, the ubiquity of reduction raises the possibility that additional ecological and associated evolutionary changes may be reinforcing the effectiveness of current vector control strategies in previously unanticipated ways. Presentation of hypothesis Here it is hypothesized that the increasing coverage of insecticide-treated bed nets and other vector control methods may be driving selection for a shift in mosquito life history that reduces their ability to transmit malaria parasites. Specifically it is hypothesized that by substantially increasing the extrinsic rate of mortality experienced in vector populations, these interventions are creating a fitness incentive for mosquitoes to re-allocate their resources towards greater short-term reproduction at the expense of longer-term survival. As malaria transmission is fundamentally dependent on mosquito survival, a life history shift in this direction would greatly benefit control. Testing the hypothesis At present, direct evaluation of this hypothesis within natural vector populations presents several logistical and methodological challenges. In the meantime, many insights can be gained from research previously conducted on wild Drosophila populations. Long-term selection experiments on these organisms suggest that increasing extrinsic mortality by a magnitude similar to that anticipated from the up-scaling of vector control measures generated an increase in their intrinsic mortality rate. Although this increase was small, a change of similar magnitude in Anopheles vector populations would be predicted to reduce malaria transmission by 80%. Implications of hypothesis The hypothesis presented here provides a reminder that evolutionary processes induced by interventions against disease vectors may not always act to neutralize intervention effectiveness. In the search for new intervention strategies, consideration should be given to both the potential disadvantages and advantages of evolutionary processes resulting from their implementation, and attempts made to exploit those with greatest potential to enhance control.

Abstract Background Long-lasting insecticidal nets (LLINs) reduce malaria transmission by protecting individuals from infectious bites, and by reducing mosquito survival. In recent years, millions of LLINs have been distributed across sub-Saharan Africa (SSA). Over time, LLINs decay physically and chemically and are destroyed, making repeated interventions necessary to prevent a resurgence of malaria. Because its effects on transmission are important (more so than the effects of individual protection), estimates of the lifetime of mass distribution rounds should be based on the effective length of epidemiological protection. Methods Simulation models, parameterised using available field data, were used to analyse how the distribution's effective lifetime depends on the transmission setting and on LLIN characteristics. Factors considered were the pre-intervention transmission level, initial coverage, net attrition, and both physical and chemical decay. An ensemble of 14 stochastic individual-based model variants for malaria in humans was used, combined with a deterministic model for malaria in mosquitoes. Results The effective lifetime was most sensitive to the pre-intervention transmission level, with a lifetime of almost 10 years at an entomological inoculation rate of two infectious bites per adult per annum (ibpapa), but of little more than 2 years at 256 ibpapa. The LLIN attrition rate and the insecticide decay rate were the next most important parameters. The lifetime was surprisingly insensitive to physical decay parameters, but this could change as physical integrity gains importance with the emergence and spread of pyrethroid resistance. Conclusions The strong dependency of the effective lifetime on the pre-intervention transmission level indicated that the required distribution frequency may vary more with the local entomological situation than with LLIN quality or the characteristics of the distribution system. This highlights the need for malaria monitoring both before and during intervention programmes, particularly since there are likely to be strong variations between years and over short distances. The majority of SSA's population falls into exposure categories where the lifetime is relatively long, but because exposure estimates are highly uncertain, it is necessary to consider subsequent interventions before the end of the expected effective lifetime based on an imprecise transmission measure.

Abstract Background Chiral alcohols are widely used in the synthesis of chiral pharmaceuticals, flavors and functional materials and appropriate whole-cell biocatalysts offer a highly enantioselective, minimally polluting route to these valuable compounds. The recently isolated strain Acetobacter sp. CCTCC M209061 showed exclusive anti-Prelog stereoselectivity for the reduction of prochiral ketones, but the low biomass has limited its commercialization and industrial applications. To tackle this problem, the effects of medium components and culture conditions on the strain's growth and reduction activity were explored. Results By using a one-at-a-time method and a central composite rotatable design (CCRD), the optimal medium and culture conditions were found to be as follows: glucose 8.26 g/L, fructose 2.50 g/L, soy peptone 83.92 g/L, MnSO4·H2O 0.088 g/L, pH 5.70, 30°C and 10% (v/v) inoculum. Under the above-mentioned conditions, the biomass after 30 h cultivation reached 1.10 ± 0.03 g/L, which was 9.5-fold higher than that obtained with basic medium. Also, the reduction activity towards 4'-chloroacetophenone was markedly enhanced to 39.49 ± 0.96 μmol/min/g from 29.34 ± 0.65 μmol/min/g, with the product e.e. being above 99%. Comparable improvements were also seen with the enantioselective bioreduction of 4-(trimethylsilyl)-3-butyn-2-one to the key pharmaceutical precursor (R) - 4-(trimethylsilyl)-3-butyn-2-ol. Conclusions The biomass and reduction activity of Acetobacter sp. CCTCC M209061 can be greatly enhanced through the optimization strategy. This facilitates use of the strain in the anti-Prelog stereoselective reduction of prochiral ketones to enantiopure chiral alcohols as building blocks for many industries.

Abstract Background Clostridium botulinum, an obligate anaerobic spore-forming bacterium, produces seven antigenic variants of botulinum toxin that are distinguished serologically and termed "serotypes". Botulinum toxin blocks the release of acetylcholine at neuromuscular junctions resulting in flaccid paralysis. The potential lethality of the disease warrants a fast and accurate means of diagnosing suspected instances of food contamination or human intoxication. Currently, the Food and Drug Administration (FDA)-accepted assay to detect and type botulinum neurotoxins (BoNTs) is the mouse protection bioassay. While specific and sensitive, this assay requires the use of laboratory animals, may take up to four days to achieve a diagnosis, and is unsuitable for high-throughput analysis. We report here a two-step PCR assay that identifies all toxin types, that achieves the specificity of the mouse bioassay while surpassing it in equivalent sensitivity, that has capability for high-throughput analysis, and that provides quantitative results within hours. The first step of our assay consists of a conventional PCR that detects the presence of C. botulinum regardless of the neurotoxin type. The second step uses quantitative PCR (qPCR) technology to determine the specific serotype of the neurotoxin. Results We assayed purified C. botulinum DNA and crude toxin preparations, as well as food and stool from healthy individuals spiked with purified BoNT DNA, and one stool sample from a case of infant botulism for the presence of the NTNH gene, which is part of the BoNT gene cluster, and for the presence of serotype-specific BoNT genes. The PCR surpassed the mouse bioassay both in specificity and sensitivity, detecting positive signals in BoNT preparations containing well below the 1 LD50 required for detection via the mouse bioassay. These results were type-specific and we were reliably able to quantify as few as 10 genomic copies. Conclusions While other studies have reported conventional or quantitative PCR-based assays for the detection of C. botulinum genes, our procedure's high-throughput capability and its portability allows most laboratories to quickly assess the possible presence of BoNTs either in food processing samples or in suspected cases of botulism. Thus, this assay provides rapid and specific detection of BoNT and toxin complex genes and would enable the targeting of appropriate therapeutics to infected individuals in a timely manner.

Abstract Background The communities of Namawala and Idete villages in southern Tanzania experienced extremely high malaria transmission in the 1990s. By 2001-03, following high usage rates (75% of all age groups) of untreated bed nets, a 4.2-fold reduction in malaria transmission intensity was achieved. Since 2006, a national-scale programme has promoted the use of longer-lasting insecticide treatment kits (consisting of an insecticide plus binder) co-packaged with all bed nets manufactured in the country. Methods The entomological inoculation rate (EIR) was estimated through monthly surveys in 72 houses randomly selected in each of the two villages. Mosquitoes were caught using CDC light traps placed beside occupied bed nets between January and December 2008 (n = 1,648 trap nights). Sub-samples of mosquitoes were taken from each trap to determine parity status, sporozoite infection and Anopheles gambiae complex sibling species identity. Results Compared with a historical mean EIR of ~1400 infectious bites/person/year (ib/p/y) in 1990-94; the 2008 estimate of 81 ib/p/y represents an 18-fold reduction for an unprotected person without a net. The combined impact of longer-lasting insecticide treatments as well as high bed net coverage was associated with a 4.6-fold reduction in EIR, on top of the impact from the use of untreated nets alone. The scale-up of bed nets and subsequent insecticidal treatment has reduced the density of the anthropophagic, endophagic primary vector species, Anopheles gambiae sensu stricto, by 79%. In contrast, the reduction in density of the zoophagic, exophagic sibling species Anopheles arabiensis was only 38%. Conclusion Insecticide treatment of nets reduced the intensity of malaria transmission in addition to that achieved by the untreated nets alone. Impacts were most pronounced against the highly anthropophagic, endophagic primary vector, leading to a shift in the sibling species composition of the A. gambiae complex.

Abstract Background Avian influenza virus (AIV) is an important public health issue because pandemic influenza viruses in people have contained genes from viruses that infect birds. The H5 and H7 AIV subtypes have periodically mutated from low pathogenicity to high pathogenicity form. Analysis of the geographic distribution of AIV can identify areas where reassortment events might occur and how high pathogenicity influenza might travel if it enters wild bird populations in the US. Modelling the number of AIV cases is important because the rate of co-infection with multiple AIV subtypes increases with the number of cases and co-infection is the source of reassortment events that give rise to new strains of influenza, which occurred before the 1968 pandemic. Aquatic birds in the orders Anseriformes and Charadriiformes have been recognized as reservoirs of AIV since the 1970s. However, little is known about influenza prevalence in terrestrial birds in the order Passeriformes. Since passerines share the same habitat as poultry, they may be more effective transmitters of the disease to humans than aquatic birds. We analyze 152 passerine species including the American Robin (Turdus migratorius) and Swainson's Thrush (Catharus ustulatus). Methods We formulate a regression model to predict AIV cases throughout the US at the county scale as a function of 12 environmental variables, sampling effort, and proximity to other counties with influenza outbreaks. Our analysis did not distinguish between types of influenza, including low or highly pathogenic forms. Results Analysis of 13,046 cloacal samples collected from 225 bird species in 41 US states between 2005 and 2008 indicates that the average prevalence of influenza in passerines is greater than the prevalence in eight other avian orders. Our regression model identifies the Great Plains and the Pacific Northwest as high-risk areas for AIV. Highly significant predictors of AIV include the amount of harvested cropland and the first day of the year when a county is snow free. Conclusions Although the prevalence of influenza in waterfowl has long been appreciated, we show that 22 species of song birds and perching birds (order Passeriformes) are influenza reservoirs in the contiguous US.

Abstract Background Individuals in a malaria endemic community differ from one another. Many of these differences, such as heterogeneities in transmission or treatment-seeking behaviour, affect malaria epidemiology. The different kinds of heterogeneity are likely to be correlated. Little is known about their impact on the shape of age-prevalence and incidence curves. In this study, the effects of heterogeneity in transmission, treatment-seeking and risk of co-morbidity were simulated. Methods Simple patterns of heterogeneity were incorporated into a comprehensive individual-based model of Plasmodium falciparum malaria epidemiology. The different types of heterogeneity were systematically simulated individually, and in independent and co-varying pairs. The effects on age-curves for parasite prevalence, uncomplicated and severe episodes, direct and indirect mortality and first-line treatments and hospital admissions were examined. Results Different heterogeneities affected different outcomes with large effects reserved for outcomes which are directly affected by the action of the heterogeneity rather than via feedback on acquired immunity or fever thresholds. Transmission heterogeneity affected the age-curves for all outcomes. The peak parasite prevalence was reduced and all age-incidence curves crossed those of the reference scenario with a lower incidence in younger children and higher in older age-groups. Heterogeneity in the probability of seeking treatment reduced the peak incidence of first-line treatment and hospital admissions. Heterogeneity in co-morbidity risk showed little overall effect, but high and low values cancelled out for outcomes directly affected by its action. Independently varying pairs of heterogeneities produced additive effects. More variable results were produced for co-varying heterogeneities, with striking differences compared to independent pairs for some outcomes which were affected by both heterogeneities individually. Conclusions Different kinds of heterogeneity both have different effects and affect different outcomes. Patterns of co-variation are also important. Alongside the absolute levels of different factors affecting age-curves, patterns of heterogeneity should be considered when parameterizing or validating models, interpreting data and inferring from one outcome to another.

Abstract Background Molecular monitoring of parasite resistance has become an important complementary tool in establishing rational anti-malarial drug policies. Community surveys provide a representative sample of the parasite population and can be carried out more rapidly than accrual of samples from clinical cases, but it is not known whether the frequencies of genetic resistance markers in clinical cases differ from those in the overall population, or whether such community surveys can provide good predictions of treatment failure rates. Methods Between 2003 and 2005, in vivo drug efficacy of amodiaquine or chloroquine plus sulphadoxine-pyrimethamine was determined at three sites in Papua New Guinea. The genetic drug resistance profile (i.e., 33 single nucleotide polymorphisms in Plasmodium falciparum crt, mdr1, dhfr, dhps, and ATPase6) was concurrently assessed in 639 community samples collected in the catchment areas of the respective health facilities by using a DNA microarray-based method. Mutant allele and haplotype frequencies were determined and their relationship with treatment failure rates at each site in each year was investigated. Results PCR-corrected in vivo treatment failure rates were between 12% and 28% and varied by site and year with variable longitudinal trends. In the community samples, the frequencies of mutations in pfcrt and pfmdr1 were high and did not show significant changes over time. Mutant allele frequencies in pfdhfr were moderate and those in pfdhps were low. No mutations were detected in pfATPase6. There was much more variation between sites than temporal, within-site, variation in allele and haplotype frequencies. This variation did not correlate well with treatment failure rates. Allele and haplotype frequencies were very similar in clinical and community samples from the same site. Conclusions The relationship between parasite genetics and in vivo treatment failure rate is not straightforward. The frequencies of genetic anti-malarial resistance markers appear to be very similar in community and clinical samples, but cannot be used to make precise predictions of clinical outcome. Thus, indicators based on molecular data have to be considered with caution and interpreted in the local context, especially with regard to prior drug usage and level of pre-existing immunity. Testing community samples for molecular drug resistance markers is a complementary tool that should help decision-making for the best treatment options and appropriate potential alternatives.

Abstract Background Clostridium botulinum is a taxonomic designation for at least four diverse species that are defined by the expression of one (monovalent) or two (bivalent) of seven different C. botulinum neurotoxins (BoNTs, A-G). The four species have been classified as C. botulinum Groups I-IV. The presence of bont genes in strains representing the different Groups is probably the result of horizontal transfer of the toxin operons between the species. Results Chromosome and plasmid sequences of several C. botulinum strains representing A, B, E and F serotypes and a C. butyricum type E strain were compared to examine their genomic organization, or synteny, and the location of the botulinum toxin complex genes. These comparisons identified synteny among proteolytic (Group I) strains or nonproteolytic (Group II) strains but not between the two Groups. The bont complex genes within the strains examined were not randomly located but found within three regions of the chromosome or in two specific sites within plasmids. A comparison of sequences from a Bf strain revealed homology to the plasmid pCLJ with similar locations for the bont/bv b genes but with the bont/a4 gene replaced by the bont/f gene. An analysis of the toxin cluster genes showed that many recombination events have occurred, including several events within the ntnh gene. One such recombination event resulted in the integration of the bont/a1 gene into the serotype toxin B ha cluster, resulting in a successful lineage commonly associated with food borne botulism outbreaks. In C. botulinum type E and C. butyricum type E strains the location of the bont/e gene cluster appears to be the result of insertion events that split a rarA, recombination-associated gene, independently at the same location in both species. Conclusion The analysis of the genomic sequences representing different strains reveals the presence of insertion sequence (IS) elements and other transposon-associated proteins such as recombinases that could facilitate the horizontal transfer of the bonts; these events, in addition to recombination among the toxin complex genes, have led to the lineages observed today within the neurotoxin-producing clostridia.