A site to transform Pubmed publications into these bibliographic reference formats: ADS, BibTeX, EndNote, ISI used by the Web of Knowledge, RIS, MEDLINE, Microsoft's Word 2007 XML.

Joanna Lewis - Top 30 Publications

Changes in chlamydia prevalence and duration of infection estimated from testing and diagnosis rates in England: a model-based analysis using surveillance data, 2000-15.

Chlamydia screening programmes have been implemented in several countries, but the effects of screening on incidence, prevalence, and reproductive sequelae remain unclear. In England, despite increases in testing with the rollout of the National Chlamydia Screening Programme (NCSP; 2003-08), prevalence estimated in 10-yearly population-based surveys was similar before (1999-2001) and after (2010-12) the programme. However, the precision of these previous estimates was limited by the low numbers of infections. We aimed to establish annual, rather than 10-yearly, estimates of chlamydia prevalence and infection duration.

Re: Recovery of CD4 T Cells in HIV/HCV Coinfected Children: Is it Really Impaired?

Thymic Output and CD4 T-Cell Reconstitution in HIV-Infected Children on Early and Interrupted Antiretroviral Treatment: Evidence from the Children with HIV Early Antiretroviral Therapy Trial.

Early treatment of HIV-infected children and adults is important for optimal immune reconstitution. Infants' immune systems are more plastic and dynamic than older children's or adults', and deserve particular attention. This study aimed to understand the response of the HIV-infected infant immune system to early antiretroviral therapy (ART) and planned ART interruption and restart.

Genital Chlamydia trachomatis Infections Clear More Slowly in Men Than Women, but Are Less Likely to Become Established.

Rigorous estimates for clearance rates of untreated chlamydia infections are important for understanding chlamydia epidemiology and designing control interventions, but were previously only available for women.

Modelling CD4 T Cell Recovery in Hepatitis C and HIV Co-infected Children Receiving Antiretroviral Therapy.

The effect of hepatitis C virus (HCV) coinfection on CD4 T cell recovery in treated HIV-infected children is poorly understood.

Estimating Local Chlamydia Incidence and Prevalence Using Surveillance Data.

Understanding patterns of chlamydia prevalence is important for addressing inequalities and planning cost-effective control programs. Population-based surveys are costly; the best data for England come from the Natsal national surveys, which are only available once per decade, and are nationally representative but not powered to compare prevalence in different localities. Prevalence estimates at finer spatial and temporal scales are required.

Through the Google Glass: The impact of heads-up displays on visual attention.

In five experiments, we evaluated how secondary information presented on a heads-up display (HUD) impacts performance of a concurrent visual attention task. To do so, we had participants complete a primary visual search task under a variety of secondary load conditions (a single word presented on Google Glass during each search trial). Processing of secondary information was measured through a recognition memory task. Other manipulations included relevance (Experiments 1-4) and temporal onset of secondary information relative to the primary task (Experiment 3). Secondary information was always disruptive to the visual search, regardless of temporal onset and even when participants were instructed to ignore it. These patterns were evident in search tasks reflective of both selective (Experiments 1-3) and preattentive (Experiment 4) attentional mechanisms, and were not a result of onset-offset attentional capture (Experiment 5). Recognition memory for secondary information was always above chance. Our findings suggest that HUD-based visual information is profoundly disruptive to attentional processes and largely immune to user-centric prioritization.

Where next for the reproducibility agenda in computational biology?

The concept of reproducibility is a foundation of the scientific method. With the arrival of fast and powerful computers over the last few decades, there has been an explosion of results based on complex computational analyses and simulations. The reproducibility of these results has been addressed mainly in terms of exact replicability or numerical equivalence, ignoring the wider issue of the reproducibility of conclusions through equivalent, extended or alternative methods.

ENERGY AND ENVIRONMENT. Understanding China's non-fossil energy targets.

Fixation not required: characterizing oculomotor attention capture for looming stimuli.

A stimulus moving toward us, such as a ball being thrown in our direction or a vehicle braking suddenly in front of ours, often represents a stimulus that requires a rapid response. Using a visual search task in which target and distractor items were systematically associated with a looming object, we explored whether this sort of looming motion captures attention, the nature of such capture using eye movement measures (overt/covert), and the extent to which such capture effects are more closely tied to motion onset or the motion itself. We replicated previous findings indicating that looming motion induces response time benefits and costs during visual search Lin, Franconeri, & Enns(Psychological Science 19(7): 686-693, 2008). These differences in response times were independent of fixation, indicating that these capture effects did not necessitate overt attentional shifts to a looming object for search benefits or costs to occur. Interestingly, we found no differences in capture benefits and costs associated with differences in looming motion type. Combined, our results suggest that capture effects associated with looming motion are more likely subserved by covert attentional mechanisms rather than overt mechanisms, and attention capture for looming motion is likely related to motion itself rather than the onset of motion.

Reactivity of routine HIV antibody tests in children who initiated antiretroviral therapy in early infancy as part of the Children with HIV Early Antiretroviral Therapy (CHER) trial: a retrospective analysis.

Early antiretroviral therapy (ART) and virological suppression can affect evolving antibody responses to HIV infection. We aimed to assess frequency and predictors of seronegativity in infants starting early ART.

Ten simple rules for a successful cross-disciplinary collaboration.

Using CD4 percentage and age to optimize pediatric antiretroviral therapy initiation.

Quantifying pediatric immunologic recovery by highly active antiretroviral therapy (HAART) initiation at different CD4 percentage (CD4%) and age thresholds may inform decisions about timing of treatment initiation.

Pharmacokinetic/pharmacodynamic modelling approaches in paediatric infectious diseases and immunology.

Pharmacokinetic/pharmacodynamic (PKPD) modelling is used to describe and quantify dose-concentration-effect relationships. Within paediatric studies in infectious diseases and immunology these methods are often applied to developing guidance on appropriate dosing. In this paper, an introduction to the field of PKPD modelling is given, followed by a review of the PKPD studies that have been undertaken in paediatric infectious diseases and immunology. The main focus is on identifying the methodological approaches used to define the PKPD relationship in these studies. The major findings were that most studies of infectious diseases have developed a PK model and then used simulations to define a dose recommendation based on a pre-defined PD target, which may have been defined in adults or in vitro. For immunological studies much of the modelling has focused on either PK or PD, and since multiple drugs are usually used, delineating the relative contributions of each is challenging. The use of dynamical modelling of in vitro antibacterial studies, and paediatric HIV mechanistic PD models linked with the PK of all drugs, are emerging methods that should enhance PKPD-based recommendations in the future.

A mechanistic model for naive CD4 T cell homeostasis in healthy adults and children.

The size and composition of the T lymphocyte compartment is subject to strict homeostatic regulation and is remarkably stable throughout life in spite of variable dynamics in cell production and death during T cell development and immune responses. Homeostasis is achieved by careful orchestration of lymphocyte survival and cell division. New T cells are generated from the thymus and the number of peripheral T cells is regulated by controlling survival and proliferation. How these processes combine is however very complex. Thymic output increases in the first year of life and then decreases but is crucial for establishing repertoire diversity. Proliferation of new naive T cells plays a crucial role for maintaining numbers but at a potential cost to TCR repertoire diversity. A mechanistic two-compartment model of T cell homeostasis is described here that includes specific terms for thymic output, cell proliferation, and cell death of both resting and dividing cells. The model successfully predicts the homeostatic set point for T cells in adults and identifies variables that determine the total number of T cells. It also accurately predicts T cell numbers in children in early life despite rapid changes in thymic output and growth over this period.

Transforming food culture in schools, communities and throughout the life course.

Predicting patterns of long-term CD4 reconstitution in HIV-infected children starting antiretroviral therapy in sub-Saharan Africa: a cohort-based modelling study.

Long-term immune reconstitution on antiretroviral therapy (ART) has important implications for HIV-infected children, who increasingly survive into adulthood. Children's response to ART differs from adults', and better descriptive and predictive models of reconstitution are needed to guide policy and direct research. We present statistical models characterising, qualitatively and quantitatively, patterns of long-term CD4 recovery.

Antiretroviral therapy increases thymic output in children with HIV.

Disease progression and response to antiretroviral therapy (ART) in HIV-infected children is different to that of adults. Immune reconstitution in adults is mainly from memory T cells, whereas in children it occurs predominantly from the naive T-cell pool. It is unclear however what proportion of reconstituted CD4 T cells comes from thymic export and homeostatic proliferation in the periphery. Thymic output is often estimated by measuring T-cell receptor excision circles and markers such as CD31 expressed on recent thymic emigrants but these are confounded by peripheral T-cell division and cannot in themselves be used as quantitative estimates of thymic output.

CD31+ cell percentage correlation with speed of CD4+ T-cell count recovery in HIV-infected adults is reversed in children: higher thymic output may be responsible.

Age and CD4 count at initiation of antiretroviral therapy in HIV-infected children: effects on long-term T-cell reconstitution.

Effective therapies and reduced AIDS-related morbidity and mortality have shifted the focus in pediatric human immunodeficiency virus (HIV) from minimizing short-term disease progression to maintaining optimal long-term health. We describe the effects of children's age and pre-antiretroviral therapy (ART) CD4 count on long-term CD4 T-cell reconstitution.

Cost savings and increased efficiency using a stratified specimen pooling strategy for Chlamydia trachomatis and Neisseria gonorrhoeae.

Idaho Chlamydia trachomatis-Neisseria gonorrhoeae specimens from July 2009 were pooled by stratified specimen pooling, an approach that removes high-risk specimens from the pooling population and pools low-risk specimens to maximize pooling efficiency. This approach reduced pool positivity rates by 8%, repeated tests by 9%, and saved 47.4% in direct costs.