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1.  Quantifying Trends in Disease Impact to Produce a Consistent and Reproducible Definition of an Emerging Infectious Disease 
PLoS ONE  2013;8(8):e69951.
The proper allocation of public health resources for research and control requires quantification of both a disease's current burden and the trend in its impact. Infectious diseases that have been labeled as “emerging infectious diseases” (EIDs) have received heightened scientific and public attention and resources. However, the label ‘emerging’ is rarely backed by quantitative analysis and is often used subjectively. This can lead to over-allocation of resources to diseases that are incorrectly labelled “emerging,” and insufficient allocation of resources to diseases for which evidence of an increasing or high sustained impact is strong. We suggest a simple quantitative approach, segmented regression, to characterize the trends and emergence of diseases. Segmented regression identifies one or more trends in a time series and determines the most statistically parsimonious split(s) (or joinpoints) in the time series. These joinpoints in the time series indicate time points when a change in trend occurred and may identify periods in which drivers of disease impact change. We illustrate the method by analyzing temporal patterns in incidence data for twelve diseases. This approach provides a way to classify a disease as currently emerging, re-emerging, receding, or stable based on temporal trends, as well as to pinpoint the time when the change in these trends happened. We argue that quantitative approaches to defining emergence based on the trend in impact of a disease can, with appropriate context, be used to prioritize resources for research and control. Implementing this more rigorous definition of an EID will require buy-in and enforcement from scientists, policy makers, peer reviewers and journal editors, but has the potential to improve resource allocation for global health.
doi:10.1371/journal.pone.0069951
PMCID: PMC3743838  PMID: 23967065
2.  A framework for the study of zoonotic disease emergence and its drivers: spillover of bat pathogens as a case study 
Many serious emerging zoonotic infections have recently arisen from bats, including Ebola, Marburg, SARS-coronavirus, Hendra, Nipah, and a number of rabies and rabies-related viruses, consistent with the overall observation that wildlife are an important source of emerging zoonoses for the human population. Mechanisms underlying the recognized association between ecosystem health and human health remain poorly understood and responding appropriately to the ecological, social and economic conditions that facilitate disease emergence and transmission represents a substantial societal challenge. In the context of disease emergence from wildlife, wildlife and habitat should be conserved, which in turn will preserve vital ecosystem structure and function, which has broader implications for human wellbeing and environmental sustainability, while simultaneously minimizing the spillover of pathogens from wild animals into human beings. In this review, we propose a novel framework for the holistic and interdisciplinary investigation of zoonotic disease emergence and its drivers, using the spillover of bat pathogens as a case study. This study has been developed to gain a detailed interdisciplinary understanding, and it combines cutting-edge perspectives from both natural and social sciences, linked to policy impacts on public health, land use and conservation.
doi:10.1098/rstb.2012.0228
PMCID: PMC3427567  PMID: 22966143
bat; zoonosis; emergence; collaborative framework
3.  Ecology and evolution of mammalian biodiversity 
Mammals have incredible biological diversity, showing extreme flexibility in eco-morphology, physiology, life history and behaviour across their evolutionary history. Undoubtedly, mammals play an important role in ecosystems by providing essential services such as regulating insect populations, seed dispersal and pollination and act as indicators of general ecosystem health. However, the macroecological and macroevolutionary processes underpinning past and present biodiversity patterns are only beginning to be explored on a global scale. It is also particularly important, in the face of the global extinction crisis, to understand these processes in order to be able to use this knowledge to prevent future biodiversity loss and loss of ecosystem services. Unfortunately, efforts to understand mammalian biodiversity have been hampered by a lack of data. New data compilations on current species' distributions, ecologies and evolutionary histories now allow an integrated approach to understand this biodiversity. We review and synthesize these new studies, exploring the past and present ecology and evolution of mammalian biodiversity, and use these findings to speculate about the mammals of our future.
doi:10.1098/rstb.2011.0090
PMCID: PMC3138616  PMID: 21807728
biogeography; conservation; diversification; phylogeny; life-history traits; species richness
4.  Can unified theories of biodiversity explain mammalian macroecological patterns? 
The idea of a unifying theory of biodiversity linking the diverse array of macroecological patterns into a common theoretical framework is very appealing. We explore this idea to examine currently proposed unified theories of biodiversity (UTBs) and their predictions. Synthesizing the literature on the macroecological patterns of mammals, we critically evaluate the evidence to support these theories. We find general qualitative support for the UTBs' predictions within mammals, but rigorous testing is hampered by the types of data typically collected in studies of mammals. In particular, abundance is rarely estimated for entire mammalian communities or of individual species in multiple locations, reflecting the logistical challenges of studying wild mammal populations. By contrast, there are numerous macroecological patterns (especially allometric scaling relationships) that are extremely well characterized for mammals, but which fall outside the scope of current UTBs. We consider how these theories might be extended to explain mammalian biodiversity patterns more generally. Specifically, we suggest that UTBs need to incorporate the dimensions of geographical space, species' traits and time to reconcile theory with pattern.
doi:10.1098/rstb.2011.0119
PMCID: PMC3138617  PMID: 21807736
abundance; body size; distribution; metabolic energy; species richness; species' traits
5.  What is macroecology? 
Biology Letters  2012;8(6):904-906.
The symposium ‘What is Macroecology?’ was held in London on 20 June 2012. The event was the inaugural meeting of the Macroecology Special Interest Group of the British Ecological Society and was attended by nearly 100 scientists from 11 countries. The meeting reviewed the recent development of the macroecological agenda. The key themes that emerged were a shift towards more explicit modelling of ecological processes, a growing synthesis across systems and scales, and new opportunities to apply macroecological concepts in other research fields.
doi:10.1098/rsbl.2012.0672
PMCID: PMC3497138  PMID: 22915630
macroecology; spatial scale; process-based model; theory; ecosystem; disease
6.  Reconstruction of Exposure to m-Xylene from Human Biomonitoring Data Using PBPK Modelling, Bayesian Inference, and Markov Chain Monte Carlo Simulation 
Journal of Toxicology  2012;2012:760281.
There are numerous biomonitoring programs, both recent and ongoing, to evaluate environmental exposure of humans to chemicals. Due to the lack of exposure and kinetic data, the correlation of biomarker levels with exposure concentrations leads to difficulty in utilizing biomonitoring data for biological guidance values. Exposure reconstruction or reverse dosimetry is the retrospective interpretation of external exposure consistent with biomonitoring data. We investigated the integration of physiologically based pharmacokinetic modelling, global sensitivity analysis, Bayesian inference, and Markov chain Monte Carlo simulation to obtain a population estimate of inhalation exposure to m-xylene. We used exhaled breath and venous blood m-xylene and urinary 3-methylhippuric acid measurements from a controlled human volunteer study in order to evaluate the ability of our computational framework to predict known inhalation exposures. We also investigated the importance of model structure and dimensionality with respect to its ability to reconstruct exposure.
doi:10.1155/2012/760281
PMCID: PMC3376947  PMID: 22719759
7.  Biological monitoring of pesticide exposures in residents living near agricultural land 
BMC Public Health  2011;11:856.
Background
There is currently a lack of reliable information on the exposures of residents and bystanders to pesticides in the UK. Previous research has shown that the methods currently used for assessing pesticide exposure for regulatory purposes are appropriate for farm workers [1]. However, there were indications that the exposures of bystanders may sometimes be underestimated. The previous study did not collect data for residents. Therefore, this study aims to collect measurements to determine if the current methods and tools are appropriate for assessing pesticide exposure for residents living near agricultural fields.
Methods/design
The study will recruit owners of farms and orchards (hereafter both will be referred to as farms) that spray their agricultural crops with certain specified pesticides, and which have residential areas in close proximity to these fields. Recruited farms will be asked to provide details of their pesticide usage throughout the spray season. Informed consenting residents (adults (18 years and over) and children (aged 4-12 years)) will be asked to provide urine samples and accompanying activity diaries during the spraying season and in addition for a limited number of weeks before/after the spray season to allow background pesticide metabolite levels to be determined. Selected urine samples will be analysed for the pesticide metabolites of interest. Statistical analysis and mathematical modelling will use the laboratory results, along with the additional data collected from the farmers and residents, to determine systemic exposure levels amongst residents. Surveys will be carried out in selected areas of the United Kingdom over two years (2011 and 2012), covering two spraying seasons and the time between the spraying seasons.
Discussion
The described study protocol was implemented for the sample and data collection procedures carried out in 2011. Based on experience to date, no major changes to the protocol are anticipated for the 2012 spray season although the pesticides and regional areas for inclusion in 2012 are still to be confirmed.
doi:10.1186/1471-2458-11-856
PMCID: PMC3236113  PMID: 22074397
8.  Labeling of Multiple HIV-1 Proteins with the Biarsenical-Tetracysteine System 
PLoS ONE  2011;6(2):e17016.
Due to its small size and versatility, the biarsenical-tetracysteine system is an attractive way to label viral proteins for live cell imaging. This study describes the genetic labeling of the human immunodeficiency virus type 1 (HIV-1) structural proteins (matrix, capsid and nucleocapsid), enzymes (protease, reverse transcriptase, RNAse H and integrase) and envelope glycoprotein 120 with a tetracysteine tag in the context of a full-length virus. We measure the impact of these modifications on the natural virus infection and, most importantly, present the first infectious HIV-1 construct containing a fluorescently-labeled nucleocapsid protein. Furthermore, due to the high background levels normally associated with the labeling of tetracysteine-tagged proteins we have also optimized a metabolic labeling system that produces infectious virus containing the natural envelope glycoproteins and specifically labeled tetracysteine-tagged proteins that can easily be detected after virus infection of T-lymphocytes. This approach can be adapted to other viral systems for the visualization of the interplay between virus and host cell during infection.
doi:10.1371/journal.pone.0017016
PMCID: PMC3037950  PMID: 21347302
10.  Use of the out-of-hours emergency dental service at two south-east London hospitals 
BMC Oral Health  2009;9:19.
Background
Prior to the introduction of the 2006 NHS dental contract in England and Wales, general dental practitioners (GDPs) were responsible for the provision of out-of-hours (OOH) emergency dental services (EDS); however there was great national variation in service provision. Under the contractual arrangements introduced 1st April 2006, local commissioning agencies became formally responsible for the provision of out-of-hours emergency dental services. This study aimed to examine patients' use of an out-of-hours emergency dental service and to determine whether the introduction of the 2006 national NHS dental contract had resulted in a change in service use, with a view to informing future planning and commissioning of care.
Methods
A questionnaire was administered to people attending the out-of-hours emergency dental service at two inner city London hospitals over two time periods; four weeks before and six months after the introduction of the dental contract in April 2006. The questionnaire explored: reasons for attending; dental registration status and attendance; method of access; knowledge and use of NHS Direct; satisfaction with the service; future preferences for access and use of out-of-hours dental services. Data were compared to determine any impact of the new contract on how and why people accessed the emergency dental service.
Results
The response rate was 73% of attendees with 981 respondents for the first time period and 546 for the second. There were no significant differences between the two time periods in the gender, age, ethnic distribution or main language of service users accessing the service. Overall, the main dental problem was toothache (72%) and the main reason for choosing this service was due to the inability to access another emergency dental service (42%). Significantly fewer service users attended the out-of-hours emergency dental service during the second period because they could not get an appointment with their own dentist (p = 0.002 from 28% to 20%) and significantly more service users in the second period felt the emergency dental service was easier to get to than their own dentist (P = 0.003 from 8% to 14%). Service users found out about the service from multiple sources, of which family and friends were the most common source (30%). In the second period fewer service users were obtaining information about the service from dental receptionists (P = 0.002 from 14% to 9%) and increased use of NHS Direct for a dental problem was reported (P = 0.002 from 16% to 22%) along with more service users being referred to the service by NHS Direct (P = 0.02 from 19% to 24%). The most common preference for future emergency dental care was face-to-face with a dentist (79%).
Conclusion
This study has provided an insight into how and why people use an out-of-hours emergency dental service and has helped to guide future commissioning of these services. Overall, the service was being used in much the same way both before and after the 2006 dental contract. Significantly more use was being made of NHS Direct after April 2006; however, informal information networks such as friends and family remain an important source of information about accessing emergency dental services.
doi:10.1186/1472-6831-9-19
PMCID: PMC2729730  PMID: 19630986
11.  The predictability of extinction: biological and external correlates of decline in mammals 
Extinction risk varies among species, and comparative analyses can help clarify the causes of this variation. Here we present a phylogenetic comparative analysis of species-level extinction risk across nearly the whole of the class Mammalia. Our aims were to examine systematically the degree to which general predictors of extinction risk can be identified, and to investigate the relative importance of different types of predictors (life history, ecological, human impact and environmental) in determining extinction risk. A single global model explained 27.3% of variation in mammal extinction risk, but explanatory power was lower for region-specific models (median R2=0.248) and usually higher for taxon-specific models (median R2=0.383). Geographical range size, human population density and latitude were the most consistently significant predictors of extinction risk, but otherwise there was little evidence for general, prescriptive indicators of high extinction risk across mammals. Our results therefore support the view that comparative models of relatively narrow taxonomic scope are likely to be the most precise.
doi:10.1098/rspb.2008.0179
PMCID: PMC2602711  PMID: 18367443
Red List; phylogenetically independent contrasts; supertree
12.  Primary T-lymphocytes rescue the replication of HIV-1 DIS RNA mutants in part by facilitating reverse transcription 
Nucleic Acids Research  2008;36(5):1578-1588.
The dimerization initiation site (DIS) stem-loop within the HIV-1 RNA genome is vital for the production of infectious virions in T-cell lines but not in primary cells. In comparison to peripheral blood mononuclear cells (PBMCs), which can support the replication of both wild type and HIV-1 DIS RNA mutants, we have found that DIS RNA mutants are up to 100 000-fold less infectious than wild-type HIV-1 in T-cell lines. We have also found that the cell-type-dependent replication of HIV-1 DIS RNA mutants is largely producer cell-dependent, with mutants displaying a greater defect in viral cDNA synthesis when viruses were not derived from PBMCs. While many examples exist of host–pathogen interplays that are mediated via proteins, analogous examples which rely on nucleic acid triggers are limited. Our data provide evidence to illustrate that primary T-lymphocytes rescue, in part, the replication of HIV-1 DIS RNA mutants through mediating the reverse transcription process in a cell-type-dependent manner. Our data also suggest the presence of a host cell factor that acts within the virus producer cells. In addition to providing an example of an RNA-mediated cell-type-dependent block to viral replication, our data also provides evidence which help to resolve the dilemma of how HIV-1 genomes with mismatched DIS sequences can recombine to generate chimeric viral RNA genomes.
doi:10.1093/nar/gkm1149
PMCID: PMC2275147  PMID: 18216043
13.  Mating system and brain size in bats 
The contribution of sexual selection to brain evolution has been little investigated. Through comparative analyses of bats, we show that multiple mating by males, in the absence of multiple mating by females, has no evolutionary impact on relative brain dimension. In contrast, bat species with promiscuous females have relatively smaller brains than do species with females exhibiting mate fidelity. This pattern may be a consequence of the demonstrated negative evolutionary relationship between investment in testes and investment in brains, both metabolically expensive tissues. These results have implications for understanding the correlated evolution of brains, behaviour and extravagant sexually selected traits.
doi:10.1098/rspb.2005.3367
PMCID: PMC1560082  PMID: 16608692
brain; neocortex; cognition; testes; Chiroptera; sexual selection

Results 1-14 (14)