Associations between maternal iron supplementation in pregnancy and offspring growth and cardiometabolic risk outcomes in infancy and childhood

It was previously observed that maternal iron supplementation in pregnancy was associated with increased offspring size and adiposity at birth, possibly mediated through increased risk of gestational diabetes. In this study we investigated potential long-term associations of maternal iron supplementation in pregnancy with offspring growth in infancy, and growth and cardiometabolic risk factors in mid-childhood to seek evidence of nutritional programming. Using a nested case-control format, markers of growth and adiposity were measured at 3, 12 and 24 months of age in 341 infants from the Cambridge Baby Growth Study whose mothers supplemented with iron in pregnancy and 222 infants whose mothers did not. Measures of growth, glucose tolerance (using a 30 minute 1.75 g glucose/kg body weight oral glucose tolerance test), insulin sensitivity (HOMA IR) and blood pressure were collected in 122 and 79 of these children, respectively, at around 9.5 years of age. In infancy adiposity-promoting associations with maternal iron supplementation in pregnancy were evident at 3 months of age (e.g. mean difference in skinfold thickness: β = +0.15 mm, p = 0.02, in n = 341 whose mothers supplemented versus 222 that did not; waist circumference: β = +0.7 cm, p = 0.04, in n = 159 and 78, respectively) but differences lessened after this time (e.g. 3–12 month change in mean difference in skinfold thickness: β = -0.2 mm, p = 0.03, in n = 272 and 178, respectively). At ~9.5 years of age children whose mothers supplemented with iron in pregnancy had lower mean arterial blood pressures (β = -1.0 mmHg, p = 0.03, in n = 119 and 78, respectively). There were no apparent differences in markers of growth or other cardiometabolic factors. These results suggest that most of the associations of maternal iron supplementation in pregnancy on growth and adiposity evident at birth disappear during infancy, but there may be some evidence of long-term nutritional programming of blood pressure in mid-childhood.

Bedtime Routines Intervention for Children (BRIC) project: results from a non-randomised feasibility, proof-of concept study

BACKGROUND

Bedtime routines are highly recurrent family activities with implications for children's wellbeing, development and health.

AIMS

The objective of this study is to co-develop and test in a feasibility, proof-of-concept study a bedtime routines intervention using text messages aimed at first-time parents with young children.

METHODS

Fifty first-time parents with children aged 1-3 years were recruited for this study. Parents received a text message-based intervention for 7-consecutive nights which provided support and information on achieving optimal bedtime routines. Parents completed pre- and post-intervention questionnaires focusing on children's sleep, bedtime routines and parental mood disturbance. Feedback was provided at the end of the study.

RESULTS

Recruitment target and high retention with 98%, or 49 out of 50 participants completing the study were achieved. Pre- and post-intervention, there were improvements in total children's sleep with children sleeping longer and having less disrupted sleep overall (MD = - 7.77 (SD = 17.91), t(48) = - 3.03, p = .004, CI (- 12.91, - 2.63) and in overall quality of bedtime routines (MD = - 5.00, SD = 7.01, t(48) = - 4.98, p < .001, CI (- 7.01, - 2.98). Parental mood disturbance decreased pre- to post-intervention (MD = 5.87, SD = 15.43, t(48) = 2.66), p = .010, CI (1.44, 10.30). Parents provided positive feedback about the intervention and valued the support that was provided to them.

CONCLUSIONS

Bedtime routines were successfully altered with short-term benefits for children's sleep and parental mood. Future research will need to utilize a more robust, longitudinal approach for a definite exploration of sustained changes in bedtime routines and their long-term implications for children and parents.

A numerically stable algorithm for integrating Bayesian models using Markov melding

When statistical analyses consider multiple data sources, Markov melding provides a method for combining the source-specific Bayesian models. Markov melding joins together submodels that have a common quantity. One challenge is that the prior for this quantity can be implicit, and its prior density must be estimated. We show that error in this density estimate makes the two-stage Markov chain Monte Carlo sampler employed by Markov melding unstable and unreliable. We propose a robust two-stage algorithm that estimates the required prior marginal self-density ratios using weighted samples, dramatically improving accuracy in the tails of the distribution. The stabilised version of the algorithm is pragmatic and provides reliable inference. We demonstrate our approach using an evidence synthesis for inferring HIV prevalence, and an evidence synthesis of A/H1N1 influenza.

A computationally tractable birth-death model that combines phylogenetic and epidemiological data

Inferring the dynamics of pathogen transmission during an outbreak is an important problem in infectious disease epidemiology. In mathematical epidemiology, estimates are often informed by time series of confirmed cases, while in phylodynamics genetic sequences of the pathogen, sampled through time, are the primary data source. Each type of data provides different, and potentially complementary, insight. Recent studies have recognised that combining data sources can improve estimates of the transmission rate and the number of infected individuals. However, inference methods are typically highly specialised and field-specific and are either computationally prohibitive or require intensive simulation, limiting their real-time utility. We present a novel birth-death phylogenetic model and derive a tractable analytic approximation of its likelihood, the computational complexity of which is linear in the size of the dataset. This approach combines epidemiological and phylodynamic data to produce estimates of key parameters of transmission dynamics and the unobserved prevalence. Using simulated data, we show (a) that the approximation agrees well with existing methods, (b) validate the claim of linear complexity and (c) explore robustness to model misspecification. This approximation facilitates inference on large datasets, which is increasingly important as large genomic sequence datasets become commonplace.

ReIMAGINE: a prostate cancer research consortium with added value through its patient and public involvement and engagement

BACKGROUND

ReIMAGINE aims to improve the current prostate specific antigen (PSA)/biopsy risk stratification for prostate cancer (PCa) and develop a new image-based method (with biomarkers) for diagnosing high/low risk PCa in men. ReIMAGINE's varied patient and public involvement (PPI) and engagement (PE) strategy maximises the impact of its scientific output by informing and shaping the different stages of research.

AIMS

Through including the voice of patients and the public, the ReIMAGINE Consortium aims to translate these different perspectives into the design and implementation process. This will improve the overall quality of the research by: reflecting the needs and priorities of patients and the public, ensuring methods and procedures are feasible and appropriate ensuring information is relevant and accessible to those being recruited to the study identifying dissemination channels relevant to patients/the public and developing outputs that are accessible to a lay audience With support from our patient/user groups, the ReIMAGINE Consortium aims to improve our ability to derive prognostic information and allocate men to the most appropriate and effective therapies, using a novel image-based risk stratification with investigation of non-imaging biomarkers.

FINDINGS

We have been working with patients and the public from initiation of the project to ensure that the research is relevant to men and their families. Our PPI Sub-Committee, led by a PCa patient, has been involved in our dissemination strategy, outreach activities, and study design recommendations. For example, the sub-committee have developed a variety of informative videos relevant and accessible to those being recruited, and organised multiple online research engagement events that are accessible to a lay audience. As quoted by one of the study participants, "the more we present the benefits and opportunities to patients and the public, the more research commitment we obtain, and the sooner critical clinical questions such as PCa diagnostics will be addressed".

Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability

Identifying causative variants in cis-regulatory elements (CRE) in neurodevelopmental disorders has proven challenging. We have used in vivo functional analyses to categorize rigorously filtered CRE variants in a clinical cohort that is plausibly enriched for causative CRE mutations: 48 unrelated males with a family history consistent with X-linked intellectual disability (XLID) in whom no detectable cause could be identified in the coding regions of the X chromosome (chrX). Targeted sequencing of all chrX CRE identified six rare variants in five affected individuals that altered conserved bases in CRE targeting known XLID genes and segregated appropriately in families. Two of these variants, FMR1CRE and TENM1CRE, showed consistent site- and stage-specific differences of enhancer function in the developing zebrafish brain using dual-color fluorescent reporter assay. Mouse models were created for both variants. In male mice Fmr1CRE induced alterations in neurodevelopmental Fmr1 expression, olfactory behavior and neurophysiological indicators of FMRP function. The absence of another likely causative variant on whole genome sequencing further supported FMR1CRE as the likely basis of the XLID in this family. Tenm1CRE mice showed no phenotypic anomalies. Following the release of gnomAD 2.1, reanalysis showed that TENM1CRE exceeded the maximum plausible population frequency of a XLID causative allele. Assigning causative status to any ultra-rare CRE variant remains problematic and requires disease-relevant in vivo functional data from multiple sources. The sequential and bespoke nature of such analyses renders them time-consuming and challenging to scale for routine clinical use.

Shigella-specific antibodies in the first year of life among Zambian infants: A longitudinal cohort study

Introduction

Shigellosis, is a leading cause of moderate-to-severe diarrhoea and related mortality in young children in low and middle income countries (LMICs). Knowledge on naturally acquired immunity can support the development of Shigella candidate vaccines mostly needed in LMICs. We aimed to quantify Shigella-specific antibodies of maternal origin and those naturally acquired in Zambian infants.

Methods

Plasma samples collected from infants at age 6, 14 and 52-weeks were tested for Shigella (S. sonnei and S. flexneri 2a) lipopolysaccharide (LPS) antigen specific immunoglobulin G (IgG) and A (IgA) by enzyme-linked immunosorbent assay.

Results

At 6 weeks infant age, the IgG geometric mean titres (GMT) against S. sonnei (N = 159) and S. flexneri 2a (N = 135) LPS were 311 (95% CI 259–372) and 446 (95% CI 343–580) respectively. By 14 weeks, a decline in IgG GMT was observed for both S. sonnei to 104 (95% CI 88–124), and S. flexneri 2a to 183 (95% CI 147–230). Both S. sonnei and S. flexneri 2a specific IgG GMT continued to decrease by 52 weeks infant age when compared to 6 weeks. In 27% and 8% of infants a significant rise in titre (4 fold and greater) against S. flexneri 2a and S. sonnei LPS, respectively, was detected between the ages of 14 and 52 weeks.

IgA levels against both species LPS were very low at 6 and 14 weeks and raised significantly against S. flexneri 2a and S. sonnei LPS in 29% and 10% of the infants, respectively.

Conclusion

In our setting, transplacental IgG anti-Shigella LPS is present at high levels in early infancy, and begins to decrease by age 14 weeks. Our results are consistent with early exposure to Shigella and indicate naturally acquired IgG and IgA antibodies to S. flexneri 2a and S. sonnei LPS in part of infants between 14 and 52 weeks of age. These results suggest that a potential timing of vaccination would be after 14 and before 52 weeks of age to ensure early infant protection against shigellosis.

The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape

The world continues to face a life-threatening viral pandemic. The virus underlying the Coronavirus Disease 2019 (COVID-19), Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has caused over 98 million confirmed cases and 2.2 million deaths since January 2020. Although the most recent respiratory viral pandemic swept the globe only a decade ago, the way science operates and responds to current events has experienced a cultural shift in the interim. The scientific community has responded rapidly to the COVID-19 pandemic, releasing over 125,000 COVID-19-related scientific articles within 10 months of the first confirmed case, of which more than 30,000 were hosted by preprint servers. We focused our analysis on bioRxiv and medRxiv, 2 growing preprint servers for biomedical research, investigating the attributes of COVID-19 preprints, their access and usage rates, as well as characteristics of their propagation on online platforms. Our data provide evidence for increased scientific and public engagement with preprints related to COVID-19 (COVID-19 preprints are accessed more, cited more, and shared more on various online platforms than non-COVID-19 preprints), as well as changes in the use of preprints by journalists and policymakers. We also find evidence for changes in preprinting and publishing behaviour: COVID-19 preprints are shorter and reviewed faster. Our results highlight the unprecedented role of preprints and preprint servers in the dissemination of COVID-19 science and the impact of the pandemic on the scientific communication landscape.

UK prevalence of underlying conditions which increase the risk of severe COVID-19 disease: a point prevalence study using electronic health records

BACKGROUND

Characterising the size and distribution of the population at risk of severe COVID-19 is vital for effective policy and planning. Older age, and underlying health conditions, are associated with higher risk of death from COVID-19. This study aimed to describe the population at risk of severe COVID-19 due to underlying health conditions across the United Kingdom.

METHODS

We used anonymised electronic health records from the Clinical Practice Research Datalink GOLD to estimate the point prevalence on 5 March 2019 of the at-risk population following national guidance. Prevalence for any risk condition and for each individual condition is given overall and stratified by age and region with binomial exact confidence intervals. We repeated the analysis on 5 March 2014 for full regional representation and to describe prevalence of underlying health conditions in pregnancy. We additionally described the population of cancer survivors, and assessed the value of linked secondary care records for ascertaining COVID-19 at-risk status.

RESULTS

On 5 March 2019, 24.4% of the UK population were at risk due to a record of at least one underlying health condition, including 8.3% of school-aged children, 19.6% of working-aged adults, and 66.2% of individuals aged 70 years or more. 7.1% of the population had multimorbidity. The size of the at-risk population was stable over time comparing 2014 to 2019, despite increases in chronic liver disease and diabetes and decreases in chronic kidney disease and current asthma. Separately, 1.6% of the population had a new diagnosis of cancer in the past 5 y.

CONCLUSIONS

The population at risk of severe COVID-19 (defined as either aged ≥70 years, or younger with an underlying health condition) comprises 18.5 million individuals in the UK, including a considerable proportion of school-aged and working-aged individuals. Our national estimates broadly support the use of Global Burden of Disease modelled estimates in other countries. We provide age- and region- stratified prevalence for each condition to support effective modelling of public health interventions and planning of vaccine resource allocation. The high prevalence of health conditions among older age groups suggests that age-targeted vaccination strategies may efficiently target individuals at higher risk of severe COVID-19.

Wide distribution of prion infectivity in the peripheral tissues of vCJD and sCJD patients

Sporadic Creutzfeldt-Jakob disease (sCJD) is the commonest human prion disease, occurring most likely as the consequence of spontaneous formation of abnormal prion protein in the central nervous system (CNS). Variant Creutzfeldt–Jakob disease (vCJD) is an acquired prion disease that was first identified in 1996. In marked contrast to vCJD, previous investigations in sCJD revealed either inconsistent levels or an absence of PrP^Sc in peripheral tissues. These findings contributed to the consensus that risks of transmitting sCJD as a consequence of non-CNS invasive clinical procedures were low. In this study, we systematically measured prion infectivity levels in CNS and peripheral tissues collected from vCJD and sCJD patients. Unexpectedly, prion infectivity was detected in a wide variety of peripheral tissues in sCJD cases. Although the sCJD infectivity levels varied unpredictably in the tissues sampled and between patients, these findings could impact on our perception of the possible transmission risks associated with sCJD.

Complexome profile of Toxoplasma gondii mitochondria identifies divergent subunits of respiratory chain complexes including new subunits of cytochrome bc1 complex

The mitochondrial electron transport chain (mETC) and F1Fo-ATP synthase are of central importance for energy and metabolism in eukaryotic cells. The Apicomplexa, important pathogens of humans causing diseases such as toxoplasmosis and malaria, depend on their mETC in every known stage of their complicated life cycles. Here, using a complexome profiling proteomic approach, we have characterised the Toxoplasma mETC complexes and F1Fo-ATP synthase. We identified and assigned 60 proteins to complexes II, IV and F1Fo-ATP synthase of Toxoplasma, of which 16 have not been identified previously. Notably, our complexome profile elucidates the composition of the Toxoplasma complex III, the target of clinically used drugs such as atovaquone. We identified two new homologous subunits and two new parasite-specific subunits, one of which is broadly conserved in myzozoans. We demonstrate all four proteins are essential for complex III stability and parasite growth, and show their depletion leads to decreased mitochondrial potential, supporting their assignment as complex III subunits. Our study highlights the divergent subunit composition of the apicomplexan mETC and F1Fo-ATP synthase complexes and sets the stage for future structural and drug discovery studies.

Is social camouflaging associated with anxiety and depression in autistic adults?

BACKGROUND

There is inconsistent evidence for a clear pattern of association between 'camouflaging' (strategies used to mask and/or compensate for autism characteristics during social interactions) and mental health.

METHODS

This study explored the relationship between self-reported camouflaging and generalised anxiety, depression, and social anxiety in a large sample of autistic adults and, for the first time, explored the moderating effect of gender, in an online survey.

RESULTS

Overall, camouflaging was associated with greater symptoms of generalised anxiety, depression, and social anxiety, although only to a small extent beyond the contribution of autistic traits and age. Camouflaging more strongly predicted generalised and social anxiety than depression. No interaction between camouflaging and gender was found.

LIMITATIONS

These results cannot be generalised to autistic people with intellectual disability, or autistic children and young people. The sample did not include sufficient numbers of non-binary people to run separate analyses; therefore, it is possible that camouflaging impacts mental health differently in this population.

CONCLUSIONS

The findings suggest that camouflaging is a risk factor for mental health problems in autistic adults without intellectual disability, regardless of gender. We also identified levels of camouflaging at which risk of mental health problems is highest, suggesting clinicians should be particularly aware of mental health problems in those who score at or above these levels.

Evidence use in E-cigarettes debates: scientific showdowns in a 'wild west' of research

BACKGROUND

Against a backdrop of declining tobacco use, e-cigarette markets are growing. The UK now has a higher percentage of e-cigarette users than any other European country. These developments have prompted fierce discussions in scientific, advocacy and policy communities about how best to respond. This article is one of the first to examine the role of evidence in these debates.

METHODS

We analysed 121 submissions to two Scottish policy consultations on e-cigarettes (in 2014 and 2015) and undertook interviews with 26 key informants in 2015-2016, following up with a sub-set in 2019-2020. All data were thematically coded, and our analysis was informed by insights from policy studies and the sociology of science.

RESULTS

First, we affirm previous research in suggesting that e-cigarettes appeared to have triggered a breakdown of old public health alliances. Second, we demonstrate that, amid concerns about research quality and quantity, actors are guided by normative outlooks (and/or economic interests) in their assessments of evidence. Third, we show that, despite describing e-cigarette debates as contentious and polarised, actors engaging in Scottish policy debates exhibit a spectrum of views, with most interviewees occupying an uncertain 'middle ground' that is responsive to new evidence. Fourth, we suggest that the perceived divisiveness of e-cigarette debates is attributed to recurrent media simplifications and tensions arising from the behaviours of some actors with settled positions working to promote particular policy responses (including by strategically enrolling supportive evidence). Fifth, we argue that the actions of these actors are potentially explained by the prospect that e-cigarettes could usher in a new tobacco 'policy paradigm'. Finally, we show how scientific authority is employed as a tool within these debates.

CONCLUSIONS

E-cigarette debates are likely to reconcile only if a clear majority of participants in the uncertain 'middle ground' settle on a more fixed position. Our results suggest that many participants in Scottish e-cigarette debates occupy this 'middle ground' and express concerns that can be empirically assessed, implying evidence has the potential to play a more important role in settling e-cigarette debates than previous research suggests.

The gut microbiome: a key player in the complexity of amyotrophic lateral sclerosis (ALS)

BACKGROUND

Much progress has been made in mapping genetic abnormalities linked to amyotrophic lateral sclerosis (ALS), but the majority of cases still present with no known underlying cause. Furthermore, even in families with a shared genetic abnormality there is significant phenotypic variability, suggesting that non-genetic elements may modify pathogenesis. Identification of such disease-modifiers is important as they might represent new therapeutic targets. A growing body of research has begun to shed light on the role played by the gut microbiome in health and disease with a number of studies linking abnormalities to ALS.

MAIN BODY

The microbiome refers to the genes belonging to the myriad different microorganisms that live within and upon us, collectively known as the microbiota. Most of these microbes are found in the intestines, where they play important roles in digestion and the generation of key metabolites including neurotransmitters. The gut microbiota is an important aspect of the environment in which our bodies operate and inter-individual differences may be key to explaining the different disease outcomes seen in ALS. Work has begun to investigate animal models of the disease, and the gut microbiomes of people living with ALS, revealing changes in the microbial communities of these groups. The current body of knowledge will be summarised in this review. Advances in microbiome sequencing methods will be highlighted, as their improved resolution now enables researchers to further explore differences at a functional level. Proposed mechanisms connecting the gut microbiome to neurodegeneration will also be considered, including direct effects via metabolites released into the host circulation and indirect effects on bioavailability of nutrients and even medications.

CONCLUSION

Profiling of the gut microbiome has the potential to add an environmental component to rapidly advancing studies of ALS genetics and move research a step further towards personalised medicine for this disease. Moreover, should compelling evidence of upstream neurotoxicity or neuroprotection initiated by gut microbiota emerge, modification of the microbiome will represent a potential new avenue for disease modifying therapies. For an intractable condition with few current therapeutic options, further research into the ALS microbiome is of crucial importance.

Associations between breast cancer survivorship and adverse mental health outcomes: A matched population-based cohort study in the United Kingdom

BACKGROUND

Breast cancer is the most common cancer diagnosed in women globally, and 5-year net survival probabilities in high-income countries are generally >80%. A cancer diagnosis and treatment are often traumatic events, and many women struggle to cope during this period. Less is known, however, about the long-term mental health impact of the disease, despite many women living several years beyond their breast cancer and mental health being a major source of disability in modern societies. The objective of this study was to quantify the risk of several adverse mental health-related outcomes in women with a history of breast cancer followed in primary care in the United Kingdom National Health Service, compared to similar women who never had cancer.

METHODS AND FINDINGS

We conducted a matched cohort study using data routinely collected in primary care across the UK to quantify associations between breast cancer history and depression, anxiety, and other mental health-related outcomes. All women with incident breast cancer in the Clinical Practice Research Datalink (CPRD) GOLD primary care database between 1988 and 2018 (N = 57,571, mean = 62 ± 14 years) were matched 1:4 to women with no prior cancer (N = 230,067) based on age, primary care practice, and eligibility of the data for linkage to hospital data sources. Cox models were used to estimate associations between breast cancer survivorship and each mental health-related outcome, further adjusting for diabetes, body mass index (BMI), and smoking and drinking status at baseline. Breast cancer survivorship was positively associated with anxiety (adjusted hazard ratio (HR) = 1.33; 95% confidence interval (CI): 1.29-1.36; p < 0.001), depression (1.35; 1.32-1.38; p < 0.001), sexual dysfunction (1.27; 1.17-1.38; p < 0.001), and sleep disorder (1.68; 1.63-1.73; p < 0.001), but not with cognitive dysfunction (1.00; 0.97-1.04; p = 0.88). Positive associations were also found for fatigue (HR = 1.28; 1.25-1.31; p < 0.001), pain (1.22; 1.20-1.24; p < 0.001), receipt of opioid analgesics (1.86; 1.83-1.90; p < 0.001), and fatal and nonfatal self-harm (1.15; 0.97-1.36; p = 0.11), but CI was wide, and the relationship was not statistically significant for the latter. HRs for anxiety and depression decreased over time (p-interaction <0.001), but increased risks persisted for 2 and 4 years, respectively, after cancer diagnosis. Increased levels of pain and sleep disorder persisted for 10 years. Younger age was associated with larger HRs for depression, cognitive dysfunction, pain, opioid analgesics use, and sleep disorders (p-interaction <0.001 in each case). Limitations of the study include the potential for residual confounding by lifestyle factors and detection bias due to cancer survivors having greater healthcare contact.

CONCLUSIONS

In this study, we observed that compared to women with no prior cancer, breast cancer survivors had higher risk of anxiety, depression, sleep problems, sexual dysfunction, fatigue, receipt of opioid analgesics, and pain. Relative risks estimates tended to decrease over time, but anxiety and depression were significantly increased for 2 and 4 years after breast cancer diagnosis, respectively, while associations for fatigue, pain, and sleep disorders were elevated for at least 5-10 years after diagnosis. Early diagnosis and increased awareness among patients, healthcare professionals, and policy makers are likely to be important to mitigate the impacts of these raised risks.

An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia

Background

Chikungunya virus (CHIKV) is an important emerging and re-emerging public health problem worldwide. In Indonesia, where the virus is endemic, epidemiological information from outside of the main islands of Java and Bali is limited.

Methodology/Principal Findings

Four hundred and seventy nine acutely febrile patients presenting between September 2017–2019 were recruited from three city hospitals situated in Ambon, Maluku; Banjarmasin, Kalimantan; and Batam, Batam Island as part of a multi-site observational study. CHIKV RNA was detected in a single serum sample while a separate sample was IgM positive. IgG seroprevalence was also low across all three sites, ranging from 1.4–3.2%. The single RT-PCR positive sample from this study and 24 archived samples collected during other recent outbreaks throughout Indonesia were subjected to complete coding region sequencing to assess the genetic diversity of Indonesian strains. Phylogenetic analysis revealed all to be of a single clade, which was distinct from CHIKV strains recently reported from neighbouring regions including the Philippines and the Pacific Islands.

Conclusions/Significance

Chikungunya virus strains from recent outbreaks across Indonesia all belong to a single clade. However, low-level seroprevalence and molecular detection of CHIKV across the three study sites appears to contrast with the generally high seroprevalences that have been reported for non-outbreak settings in Java and Bali, and may account for the relative lack of CHIKV epidemiological data from other regions of Indonesia.

Outbreaks of chikungunya virus (CHIKV) are a common occurrence in Indonesia. However, limited data is available on CHIKV from regions outside of the main, central islands of Java and Bali. We recruited hospital patients from three cities located in the east (Ambon), west (Batam) and north (Banjarmasin) of the country, and screened their blood for evidence of CHIKV infection. Our results showed that CHIKV infections were relatively uncommon across patients from all three sites, suggesting that CHIKV transmission is currently relatively rare in these regions.

Additional analysis of 25 recent Indonesian CHIKV genome sequences revealed that a new lineage of CHIKV has recently emerged in Indonesia. Several reports have highlighted Indonesia as a major source of imported CHIKV cases, suggesting that this new lineage has the potential to be introduced into neighbouring countries in the near future, with unknown consequences. Overall, our results indicate that additional CHIKV surveillance studies in Indonesia and Southeast Asia are needed in order to gain a clearer understanding of transmission routes and hot spots throughout the region.

Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies

BACKGROUND

Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Fast and accurate tracking of MTBC strains is therefore crucial for infection control, and our previous work developed a 62-single nucleotide polymorphism (SNP) barcode to inform on the phylogenetic identity of 7 human lineages and 64 sub-lineages.

METHODS

To update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~ 1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. bovis, M. tuberculosis var. caprae and M. tuberculosis var. orygis). The data was partitioned into training (N = 17,903, 50.7%) and test (N = 17,395, 49.3%) sets and were analysed using an integrated phylogenetic tree and population differentiation (FST) statistical approach.

RESULTS

By constructing a phylogenetic tree on the training MTBC isolates, we characterised 90 lineages or sub-lineages or species, of which 30 are new, and identified 421 robust barcoding mutations, of which a minimal set of 90 was selected that included 20 markers from the 62-SNP barcode. The barcoding SNPs (90 and 421) discriminated perfectly the 86 MTBC isolate (sub-)lineages in the test set and could accurately reconstruct the clades across the combined 35k samples.

CONCLUSIONS

The validated 90 SNPs can be used for the rapid diagnosis and tracking of MTBC strains to assist public health surveillance and control. To facilitate this, the SNP markers have now been incorporated into the TB-Profiler informatics platform ( https://github.com/jodyphelan/TBProfiler ).

Identifying frailty in trials: an analysis of individual participant data from trials of novel pharmacological interventions

BACKGROUND

Frailty is common in clinical practice, but trials rarely report on participant frailty. Consequently, clinicians and guideline-developers assume frailty is largely absent from trials and have questioned the relevance of trial findings to frail people. Therefore, we examined frailty in phase 3/4 industry-sponsored clinical trials of pharmacological interventions for three exemplar conditions: type 2 diabetes mellitus (T2DM), rheumatoid arthritis (RA), and chronic obstructive pulmonary disease (COPD).

METHODS

We constructed a 40-item frailty index (FI) in 19 clinical trials (7 T2DM, 8 RA, 4 COPD, mean age 42-65 years) using individual-level participant data. Participants with a FI > 0.24 were considered 'frail'. Baseline disease severity was assessed using HbA1c for T2DM, Disease Activity Score-28 (DAS28) for RA, and % predicted FEV1 for COPD. Using generalised gamma regression, we modelled FI on age, sex, and disease severity. In negative binomial regression, we modelled serious adverse event rates on FI and combined results for each index condition in a random-effects meta-analysis.

RESULTS

All trials included frail participants: prevalence 7-21% in T2DM trials, 33-73% in RA trials, and 15-22% in COPD trials. The 99th centile of the FI ranged between 0.35 and 0.45. Female sex was associated with higher FI in all trials. Increased disease severity was associated with higher FI in RA and COPD, but not T2DM. Frailty was associated with age in T2DM and RA trials, but not in COPD. Across all trials, and after adjusting for age, sex, and disease severity, higher FI predicted increased risk of serious adverse events; the pooled incidence rate ratios (per 0.1-point increase in FI scale) were 1.46 (95% CI 1.21-1.75), 1.45 (1.13-1.87), and 1.99 (1.43-2.76) for T2DM, RA, and COPD, respectively.

CONCLUSION

The upper limit of frailty in trials is lower than has been described in the general population. However, mild to moderate frailty was common, suggesting trial data may be harnessed to inform disease management in people living with frailty. Participants with higher FI experienced more serious adverse events, suggesting screening for frailty in trial participants would enable identification of those that merit closer monitoring. Frailty is identifiable and prevalent among middle-aged and older participants in phase 3/4 drug trials and has clinically important safety implications.

Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections

BACKGROUND

Asymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures.

METHODS

Using reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever ≥ 37.5 °C, cough, shortness of breath, sudden onset of anosmia, ageusia or dysgeusia illness) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the baseline case fatality ratio (CFR), which was adjusted for delays and under-ascertainment, then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment.

RESULTS

Based on reported cases and deaths, we estimated that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.4% (Bangladesh) to 100% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6 July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 18 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. As of 7 June, our seroprevalence estimates range from 0% (many countries) to 13% (95% CrI 5.6-24%) (Belgium).

CONCLUSIONS

We found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each country's population infected with SARS-CoV-2 worldwide is generally low.

What makes advocacy work? Stakeholders' voices and insights from prioritisation of maternal and child health programme in Nigeria

BACKGROUND

The Nigerian government introduced and implemented a health programme to improve maternal and child health (MCH) called Subsidy Reinvestment and Empowerment programme for MCH (SURE-P/MCH). It ran from 2012 and ended abruptly in 2015 and was followed by increased advocacy for sustaining the MCH (antenatal, delivery, postnatal and immunization) services as a policy priority. Advocacy is important in allowing social voice, facilitating prioritization, and bringing different forces/actors together. Therefore, the study set out to understand how advocacy works - through understanding what effective advocacy implementation processes comprise and what mechanisms are triggered by which contexts to produce the intended outcomes.

METHODS

The study used a Realist Evaluation design through a mixed quantitative and qualitative methods case study approach. The programme theory (PT) was developed from three substantive social theories (power politics, media influence communication theory, and the three-streams theory of agenda-setting), data and programme design documentation, and subsequently tested. We report information from 22 key informant interviews including national and State policy and law makers, policy implementers, CSOs, Development partners, NGOs, health professional groups, and media practitioners and review of relevant documents on advocacy events post-SURE-P.

RESULTS

Key advocacy organizations and individuals including health professional groups, the media, civil society organizations, powerful individuals, and policymakers were involved in advocacy activities. The nature of their engagement included organizing workshops, symposiums, town hall meetings, individual meetings, press conferences, demonstrations, and engagements with media. Effective advocacy mechanism involved alliance brokering to increase influence, the media supporting and engaging in advocacy, and the use of champions, influencers, and spouses (Leadership and Elite Gendered Power Dynamics). The key contextual influences which determined the effectiveness of advocacy measures for MCH included the political cycle, availability of evidence on the issue, networking with powerful and interested champions, and alliance building in advocacy. All these enhanced the entrenchment of MCH on the political and financial agenda at the State and Federal levels.

CONCLUSIONS

Our result suggest that advocacy can be a useful tool to bring together different forces by allowing expression of voices and ensuring accountability of different actors including policymakers. In the context of poor health outcomes, interest from policymakers and politicians in MCH, combined with advocacy from key policy actors armed with evidence, can improve prioritization and sustained implementation of MCH services.

Spatial spillover analysis of a cluster-randomized trial against dengue vectors in Trujillo, Venezuela

BACKGROUND

The ability of cluster-randomized trials to capture mass or indirect effects is one reason for their increasing use to test interventions against vector-borne diseases such as malaria and dengue. For the same reason, however, the independence of clusters may be compromised if the distances between clusters is too small to ensure independence. In other words they may be subject to spillover effects.

METHODS

We distinguish two types of spatial spillover effect: between-cluster dependence in outcomes, or spillover dependence; and modification of the intervention effect according to distance to the intervention arm, or spillover indirect effect. We estimate these effects in trial of insecticide-treated materials against the dengue mosquito vector, Aedes aegypti, in Venezuela, the endpoint being the Breteau index. We use a novel random effects Poisson spatial regression model. Spillover dependence is incorporated via an orthogonalized intrinsic conditional autoregression (ICAR) model. Spillover indirect effects are incorporated via the number of locations within a certain radius, set at 200m, that are in the intervention arm.

RESULTS

From the model with ICAR spatial dependence, and the degree of surroundedness, the intervention effect is estimated as 0.74-favouring the intervention-with a 95% credible interval of 0.34 to 1.69. The point estimates are stronger with increasing surroundedness within intervention locations.

CONCLUSION

In this trial there is some evidence of a spillover indirect effect of the intervention, with the Breteau index tending to be lower in locations which are more surrounded by locations in the intervention arm.

Use of a highly specific kinase inhibitor for rapid, simple and precise synchronization of Plasmodium falciparum and Plasmodium knowlesi asexual blood-stage parasites

During the course of the asexual erythrocytic stage of development, Plasmodium spp. parasites undergo a series of morphological changes and induce alterations in the host cell. At the end of this stage, the parasites egress from the infected cell, after which the progeny invade a new host cell. These processes are rapid and occur in a time-dependent manner. Of particular importance, egress and invasion of erythrocytes by the parasite are difficult to capture in an unsynchronized culture, or even a culture that has been synchronized within a window of one to several hours. Therefore, precise synchronization of parasite cultures is of paramount importance for the investigation of these processes. Here we describe a method for synchronizing Plasmodium falciparum and Plasmodium knowlesi asexual blood stage parasites with ML10, a highly specific inhibitor of the cGMP-dependent protein kinase (PKG) that arrests parasite growth approximately 15 minutes prior to egress. This inhibitor allows parasite cultures to be synchronized so that all parasites are within a window of development of several minutes, with a simple wash step. Furthermore, we show that parasites remain viable for several hours after becoming arrested by the compound and that ML10 has advantages, owing to its high specificity and low EC50, over the previously used PKG inhibitor Compound 2. Here, we demonstrate that ML10 is an invaluable tool for the study of Plasmodium spp. asexual blood stage biology and for the routine synchronization of P. falciparum and P. knowlesi cultures.

Life course exposures continually shape antibody profiles and risk of seroconversion to influenza

Complex exposure histories and immune mediated interactions between influenza strains contribute to the life course of human immunity to influenza. Antibody profiles can be generated by characterizing immune responses to multiple antigenically variant strains, but how these profiles vary across individuals and determine future responses is unclear. We used hemagglutination inhibition titers from 21 H3N2 strains to construct 777 paired antibody profiles from people aged 2 to 86, and developed novel metrics to capture features of these profiles. Total antibody titer per potential influenza exposure increases in early life, then decreases in middle age. Increased titers to one or more strains were seen in 97.8% of participants during a roughly four-year interval, suggesting widespread influenza exposure. While titer changes were seen to all strains, recently circulating strains exhibited the greatest titer rise. Higher pre-existing, homologous titers at baseline reduced the risk of seroconversion to recent strains. After adjusting for homologous titer, we also found an increased frequency of seroconversion against recent strains among those with higher immunity to older previously exposed strains. Including immunity to previously exposures also improved the deviance explained by the models. Our results suggest that a comprehensive quantitative description of immunity encompassing past exposures could lead to improved correlates of risk of influenza infection.

Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS

We present long-read Tet-assisted pyridine borane sequencing (lrTAPS) for targeted base-resolution sequencing of DNA methylation and hydroxymethylation in regions up to 10 kb from nanogram-level input. Compatible with both Oxford Nanopore and PacBio Single-Molecule Real-Time (SMRT) sequencing, lrTAPS detects methylation with accuracy comparable to short-read Illumina sequencing but with long-range epigenetic phasing. We applied lrTAPS to sequence difficult-to-map regions in mouse embryonic stem cells and to identify distinct methylation events in the integrated hepatitis B virus genome.

DNA methylation-based measures of accelerated biological ageing and the risk of dementia in the oldest-old: a study of the Lothian Birth Cohort 1921

BACKGROUND

Previous studies have demonstrated an association between DNA methylation-based measures of accelerated ageing and age-related health outcomes and mortality. As a disease closely associated with advancing age, we hypothesized that DNA methylation-based measures of accelerated ageing might be associated with risk for dementia. This study therefore aimed to examine the association between four recognised measures of age acceleration and subsequent dementia.

METHODS

Study subjects (n = 488) were members of the Lothian Birth Cohort 1921. Dementia case ascertainment used data from death certificates, electronic hospital records, and clinical reviews. Venous blood samples were taken at baseline, at age 79 years. DNA methylation and measures of epigenetic age were calculated in accordance with Horvath's epigenetic clock tutorial, using the online calculator (https://dnamage.genetics.ucla.edu/). From these values, four measures of accelerated ageing were calculated: extrinsic epigenetic age acceleration (EEAA), intrinsic epigenetic age acceleration (IEAA), AgeAccelPheno and AgeAccelGrim. Competing risk regression models - with death as a competing risk - were performed to examine the association between each measure of accelerated ageing and incident dementia. APOE ɛ4 status, sex, age, smoking status, history of cardiovascular disease, cerebrovascular disease, hypertension, and diabetes were included as covariates.

RESULTS

None of the multivariate models revealed a positive association between increased epigenetic age acceleration and dementia risk. Across all included models, never-smoking increased risk for dementia (HR 1.69 [1.06, 2.71], p = 0.03), and having no APOE ɛ4 alleles reduced risk for dementia (HR 0.44 [0.29, 0.67], p < 0.001).

CONCLUSIONS

The present study did not demonstrate any consistent association between DNA methylation-based measures of accelerated ageing and dementia in subjects aged over 79 years. Further, larger studies - including separate analyses of dementia subtypes - are required to further investigate the potential association between DNA methylation-based measures of accelerated ageing and dementia.

Emergency imaging in paediatric oncology: a pictorial review

Despite the decline in mortality rates over the last 20 years, cancer remains one of the leading causes of death in children worldwide. Early recognition and treatment for acute oncological emergencies are vital in preventing mortality and poor outcomes, such as irreversible end-organ damage and a compromised quality of life.Imaging plays a pivotal and adjunctive role to clinical examination, and a high level of interpretative acumen by the radiologist can make the difference between life and death. In contrast to adults, the most accessible cross-sectional imaging tool in children typically involves ultrasound. The excellent soft tissue differentiation allows for careful delineation of malignant masses and along with colour Doppler imaging, thromboses and large haematomas can be easily identified. Neurological imaging, particularly in older children is an exception. Here, computed tomography (CT) is required for acute intracranial pathologies, with magnetic resonance imaging (MRI) providing more definitive results later.This review is divided into a 'body systems' format covering a range of pathologies including neurological complications (brainstem herniation, hydrocephalus, spinal cord compression), thoracic complications (airway obstruction, superior vena cava syndrome, cardiac tamponade), intra-abdominal complications (bowel obstruction and perforation, hydronephrosis, abdominal compartment syndrome) and haematological-related emergencies (thrombosis, infection, massive haemorrhage). Within each subsection, we highlight pertinent clinical and imaging considerations.The overall objective of this pictorial review is to illustrate how primary childhood malignancies may present with life-threatening complications, and emphasise the need for imminent patient management.

Development of a healthy ageing index in Latin American countries - a 10/66 dementia research group population-based study

BACKGROUND

Our population is ageing and in 2050 more than one out of five people will be 60 years or older; 80% of whom will be living in a low-and-middle income country. Living longer does not entail living healthier; however, there is not a widely accepted measure of healthy ageing hampering policy and research. The World Health Organization defines healthy ageing as the process of developing and maintaining functional ability that will enable well-being in older age. We aimed to create a healthy ageing index (HAI) in a subset of six low-and-middle income countries, part of the 10/66 study, by using items of functional ability and intrinsic capacity.

METHODS

The study sample included residents 65-years old and over (n = 12,865) from catchment area sites in Cuba, Dominican Republic, Peru, Venezuela, Mexico and Puerto Rico. Items were collected by interviewing participants or key informants between 2003 and 2010. Two-stage factor analysis was employed and we compared one-factor, second-order and bifactor models. The psychometric properties of the index, including reliability, replicability, unidimensionality and concurrent convergent validity as well as measurement invariance per ethnic group and gender were further examined in the best fit model.

RESULTS

The bifactor model displayed superior model fit statistics supporting that a general factor underlies the various items but other subdomain factors are also needed. The HAI indicated excellent reliability (ω = 0.96, ωΗ = 0.84), replicability (H = 0.96), some support for unidimensionality (Explained Common Variance = 0.65) and some concurrent convergent validity with self-rated health. Scalar measurement invariance per ethnic group and gender was supported.

CONCLUSIONS

A HAI with excellent psychometric properties was created by using items of functional ability and intrinsic capacity in a subset of six low-and-middle income countries. Further research is needed to explore sub-population differences and to validate this index to other cultural settings.

Validation and characterisation of a DNA methylation alcohol biomarker across the life course

BACKGROUND

Recently, an alcohol predictor was developed using DNA methylation at 144 CpG sites (DNAm-Alc) as a biomarker for improved clinical or epidemiologic assessment of alcohol-related ill health. We validate the performance and characterise the drivers of this DNAm-Alc for the first time in independent populations.

RESULTS

In N = 1049 parents from the Avon Longitudinal Study of Parents and Children (ALSPAC) Accessible Resource for Integrated Epigenomic Studies (ARIES) at midlife, we found DNAm-Alc explained 7.6% of the variation in alcohol intake, roughly half of what had been reported previously, and interestingly explained a larger 9.8% of Alcohol Use Disorders Identification Test (AUDIT) score, a scale of alcohol use disorder. Explanatory capacity in participants from the offspring generation of ARIES measured during adolescence was much lower. However, DNAm-Alc explained 14.3% of the variation in replication using the Head and Neck 5000 (HN5000) clinical cohort that had higher average alcohol consumption. To investigate whether this relationship was being driven by genetic and/or earlier environment confounding, we examined how earlier versus concurrent DNAm-Alc measures predicted AUDIT scores. In both ARIES parental and offspring generations, we observed associations between AUDIT and concurrent, but not earlier DNAm-Alc, suggesting independence from genetic and stable environmental contributions.

CONCLUSIONS

The stronger relationship between DNAm-Alcs and AUDIT in parents at midlife compared to adolescents despite similar levels of consumption suggests that DNAm-Alc likely reflects long-term patterns of alcohol abuse. Such biomarkers may have potential applications for biomonitoring and risk prediction, especially in cases where reporting bias is a concern.

Participatory learning and action to address type 2 diabetes in rural Bangladesh: a qualitative process evaluation

BACKGROUND

Diabetes is 7th largest cause of death worldwide, and prevalence is increasing rapidly in low-and middle-income countries. There is an urgent need to develop and test interventions to prevent and control diabetes and develop the theory about how such interventions can be effective. We conducted a participatory learning and action (PLA) intervention with community groups in rural Bangladesh which was evaluated through a cluster randomised controlled trial. There was a large reduction in the combined prevalence of type 2 diabetes and intermediate hyperglycaemia in the PLA group compared with the control group. We present findings from qualitative process evaluation research to explore how this intervention was effective.

METHODS

We conducted group interviews and focus group discussions using photovoice with purposively sampled group attenders and non-attenders, and intervention implementers. Data were collected before the trial analysis. We used inductive content analysis to generate theory from the data.

RESULTS

The intervention increased the health literacy of individuals and communities - developing their knowledge, capacity and self-confidence to enact healthy behaviours. Community, household and individual capacity increased through social support and social networks, which then created an enabling community context, further strengthening agency and enabling community action. This increased opportunities for healthy behaviour. Community actions addressed lack of awareness about diabetes, gendered barriers to physical activity and lack of access to blood glucose testing. The interaction between the individual, household, and community contexts amplified change, and yet there was limited engagement with macro level, or 'state', barriers to healthy behaviour.

CONCLUSIONS

The participatory approach enabled groups to analyse how context affected their ability to have healthy behaviours and participants engaged with issues as a community in the ways that they felt comfortable. We suggest measuring health literacy and social networks in future interventions and recommend specific capacity strengthening to develop public accountability mechanisms and health systems strengthening to complement community-based interventions.

TRIAL REGISTRATION

Registered at ISRCTN on 30th March 2016 (Retrospectively Registered) Registration number: ISRCTN41083256 .

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets

Gene expression governs cell fate, and is regulated via a complex interplay of transcription factors and molecules that change chromatin structure. Advances in sequencing-based assays have enabled investigation of these processes genome-wide, leading to large datasets that combine information on the dynamics of gene expression, transcription factor binding and chromatin structure as cells differentiate. While numerous studies focus on the effects of these features on broader gene regulation, less work has been done on the mechanisms of gene-specific transcriptional control. In this study, we have focussed on the latter by integrating gene expression data for the in vitro differentiation of murine ES cells to macrophages and cardiomyocytes, with dynamic data on chromatin structure, epigenetics and transcription factor binding. Combining a novel strategy to identify communities of related control elements with a penalized regression approach, we developed individual models to identify the potential control elements predictive of the expression of each gene. Our models were compared to an existing method and evaluated using the existing literature and new experimental data from embryonic stem cell differentiation reporter assays. Our method is able to identify transcriptional control elements in a gene specific manner that reflect known regulatory relationships and to generate useful hypotheses for further testing.

ChromaClade: combined visualisation of phylogenetic and sequence data

BACKGROUND

Studying site-specific amino acid frequencies by eye can reveal biologically significant variability and lineage-specific adaptation. This so-called 'sequence gazing' often informs bioinformatics and experimental research. But it is important to also account for the underlying phylogeny, since similarities may be due to common descent rather than selection pressure, and because it is important to distinguish between founder effects and convergent evolution. We set out to combine phylogenetic and sequence data to produce evolutionarily insightful visualisations.

RESULTS

We present ChromaClade, a convenient tool with a graphical user-interface that works in concert with popular tree viewers to produce colour-annotated phylogenies highlighting residues found in each taxon and at each site in a sequence alignment. Colouring branches according to residues found at descendent tips also quickly identifies lineage-specific residues and those internal branches where key substitutions have occurred. We demonstrate applications of ChromaClade to human immunodeficiency virus and influenza A virus datasets, illustrating cases of conservative, adaptive and convergent evolution.

CONCLUSIONS

We find this to be a powerful approach for visualising site-wise residue distributions and detecting evolutionary patterns, especially in large datasets. ChromaClade is available for Windows, macOS and Unix or Linux; program executables and source code are available at github.com/chrismonit/chroma_clade .

Improved co-registration of ex-vivo and in-vivo cardiovascular magnetic resonance images using heart-specific flexible 3D printed acrylic scaffold combined with non-rigid registration

BACKGROUND

Ex-vivo cardiovascular magnetic resonance (CMR) imaging has played an important role in the validation of in-vivo CMR characterization of pathological processes. However, comparison between in-vivo and ex-vivo imaging remains challenging due to shape changes occurring between the two states, which may be non-uniform across the diseased heart. A novel two-step process to facilitate registration between ex-vivo and in-vivo CMR was developed and evaluated in a porcine model of chronic myocardial infarction (MI).

METHODS

Seven weeks after ischemia-reperfusion MI, 12 swine underwent in-vivo CMR imaging with late gadolinium enhancement followed by ex-vivo CMR 1 week later. Five animals comprised the control group, in which ex-vivo imaging was undertaken without any support in the LV cavity, 7 animals comprised the experimental group, in which a two-step registration optimization process was undertaken. The first step involved a heart specific flexible 3D printed scaffold generated from in-vivo CMR, which was used to maintain left ventricular (LV) shape during ex-vivo imaging. In the second step, a non-rigid co-registration algorithm was applied to align in-vivo and ex-vivo data. Tissue dimension changes between in-vivo and ex-vivo imaging were compared between the experimental and control group. In the experimental group, tissue compartment volumes and thickness were compared between in-vivo and ex-vivo data before and after non-rigid registration. The effectiveness of the alignment was assessed quantitatively using the DICE similarity coefficient.

RESULTS

LV cavity volume changed more in the control group (ratio of cavity volume between ex-vivo and in-vivo imaging in control and experimental group 0.14 vs 0.56, p < 0.0001) and there was a significantly greater change in the short axis dimensions in the control group (ratio of short axis dimensions in control and experimental group 0.38 vs 0.79, p < 0.001). In the experimental group, prior to non-rigid co-registration the LV cavity contracted isotropically in the ex-vivo condition by less than 20% in each dimension. There was a significant proportional change in tissue thickness in the healthy myocardium (change = 29 ± 21%), but not in dense scar (change = - 2 ± 2%, p = 0.034). Following the non-rigid co-registration step of the process, the DICE similarity coefficients for the myocardium, LV cavity and scar were 0.93 (±0.02), 0.89 (±0.01) and 0.77 (±0.07) respectively and the myocardial tissue and LV cavity volumes had a ratio of 1.03 and 1.00 respectively.

CONCLUSIONS

The pattern of the morphological changes seen between the in-vivo and the ex-vivo LV differs between scar and healthy myocardium. A 3D printed flexible scaffold based on the in-vivo shape of the LV cavity is an effective strategy to minimize morphological changes in the ex-vivo LV. The subsequent non-rigid registration step further improved the co-registration and local comparison between in-vivo and ex-vivo data.

How community resources mitigate the association between household poverty and the incidence of adverse childhood experiences

OBJECTIVES

To assess what proportion of the association between household low income and incidence of adverse childhood experiences (ACE) would be eliminated if all households had access to housing, transportation and childcare services, breastfeeding counselling, and parks.

METHODS

Using Growing Up in Scotland birth cohort data (N = 2816), an inverse probability-weighted regression-based mediation technique was applied to assess associations between low-income status (< £11,000 in 2004/5), resource access, and cumulative 8-year ACE incidence (≥ 1, ≥ 3 ACEs). Resource access was measured based on households' self-reported difficulties (yes/no) in accessing housing, transportation, childcare, and breastfeeding counselling, and park proximity (within 10 min from the residence).

RESULTS

The protective effects of resources were heterogeneous. Only access to transportation was associated with lower ACE incidence in both low- and higher-income households. If all had access to transportation, 21% (95% CI 3%, 41%) of the income-based inequality in incidence of 3 or more ACEs could be eliminated.

CONCLUSIONS

While second best to the elimination of child poverty, measures to improve families' access to community resources such as transportation may mitigate the effects of poverty on ACE incidence.

Arrhythmia mechanisms and spontaneous calcium release: Bi-directional coupling between re-entrant and focal excitation

Spontaneous sub-cellular calcium release events (SCRE) are conjectured to promote rapid arrhythmias associated with conditions such as heart failure and atrial fibrillation: they can underlie the emergence of spontaneous action potentials in single cells which can lead to arrhythmogenic triggers in tissue. The multi-scale mechanisms of the development of SCRE into arrhythmia triggers, and their dynamic interaction with the tissue substrate, remain elusive; rigorous and simultaneous study of dynamics from the nanometre to the centimetre scale is a major challenge. The aim of this study was to develop a computational approach to overcome this challenge and study potential bi-directional coupling between sub-cellular and tissue-scale arrhythmia phenomena. A framework comprising a hierarchy of computational models was developed, which includes detailed single-cell models describing spatio-temporal calcium dynamics in 3D, efficient non-spatial cell models, and both idealised and realistic tissue models. A phenomenological approach was implemented to reproduce SCRE morphology and variability in the efficient cell models, comprising the definition of analytical Spontaneous Release Functions (SRF) whose parameters may be randomly sampled from appropriate distributions in order to match either the 3D cell models or experimental data. Pro-arrhythmogenic pacing protocols were applied to initiate re-entry and promote calcium overload, leading to the emergence of SCRE. The SRF accurately reproduced the dynamics of SCRE and its dependence on environment variables under multiple different conditions. Sustained re-entrant excitation promoted calcium overload, and led to the emergence of focal excitations after termination. A purely functional mechanism of re-entry and focal activity localisation was demonstrated, related to the unexcited spiral wave core. In conclusion, a novel approach has been developed to dynamically model SCRE at the tissue scale, which facilitates novel, detailed multi-scale mechanistic analysis. It was revealed that complex re-entrant excitation patterns and SCRE may be bi-directionally coupled, promoting novel mechanisms of arrhythmia perpetuation.

Estimating undetected Ebola spillovers

The preparedness of health systems to detect, treat, and prevent onward transmission of Ebola virus disease (EVD) is central to mitigating future outbreaks. Early detection of outbreaks is critical to timely response, but estimating detection rates is difficult because unreported spillover events and outbreaks do not generate data. Using three independent datasets available on the distributions of secondary infections during EVD outbreaks across West Africa, in a single district (Western Area) of Sierra Leone, and in the city of Conakry, Guinea, we simulated realistic outbreak size distributions and compared them to reported outbreak sizes. These three empirical distributions lead to estimates for the proportion of detected spillover events and small outbreaks of 26% (range 8-40%, based on the full outbreak data), 48% (range 39-62%, based on the Sierra Leone data), and 17% (range 11-24%, based on the Guinea data). We conclude that at least half of all spillover events have failed to be reported since EVD was first recognized. We also estimate the probability of detecting outbreaks of different sizes, which is likely less than 10% for single-case spillover events. Comparing models of the observation process also suggests the probability of detecting an outbreak is not simply the cumulative probability of independently detecting any one individual. Rather, we find that any individual's probability of detection is highly dependent upon the size of the cluster of cases. These findings highlight the importance of primary health care and local case management to detect and contain undetected early stage outbreaks at source.

The reflective component of the Mellow Bumps parenting intervention: Implementation, engagement and mechanisms of change

Understanding why parenting programmes work or do not work, and for whom, is crucial for development of more effective parenting interventions. In this paper we focus on a specific component of Mellow Bumps: reflection on one's own childhood/past/life. We explore how this component was implemented, how participants engaged with it, the facilitating and constraining factors shaping this, whether and how it appeared to work, or not, and for whom. The paper analyses data from the Process Evaluation of the Trial of Healthy Relationships Initiatives for the Very Early years, which is evaluating two antenatal interventions delivered to vulnerable women, one of which is Mellow Bumps. Data were collected from January 2014 to June 2018 for 28 groups, 108 participants and 24 facilitators in a comprehensive and rigorous Process Evaluation designed to complement the Outcome Evaluation. Data were gathered at various time points using multiple methods, and were synthesised to triangulate findings. The reflective component was implemented with fidelity and participants engaged with it to varying degrees, dependent largely on the coherence of the group. Patchy attendance compromised the coherence of some groups, with the development of rapport, which is key to delivering reflective exercises, more difficult when group composition varied from week to week. Where there was a coherent group, powerful mechanisms of change, leading to stress reduction, included: relief through unburdening, empowerment through support given and received, reduced isolation through sharing anxieties, and control through self-care advice. A minority of highly vulnerable mothers seemed not to benefit from the reflective exercises and were marginalised within their groups. In order to minimise potential harmful effects of such exercises, allocation of participants to groups should strive to maximise group homogeneity. More research is needed to explore how very vulnerable parents can be supported in attending parenting interventions from start to finish.

The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection

Host innate immune defences play a critical role in restricting the intracellular propagation and pathogenesis of invading viral pathogens. Here we show that the histone H3.3 chaperone HIRA (histone cell cycle regulator) associates with promyelocytic leukaemia nuclear bodies (PML-NBs) to stimulate the induction of innate immune defences against herpes simplex virus 1 (HSV-1) infection. Following the activation of innate immune signalling, HIRA localized at PML-NBs in a Janus-Associated Kinase (JAK), Cyclin Dependent Kinase (CDK), and Sp100-dependent manner. RNA-seq analysis revealed that HIRA promoted the transcriptional upregulation of a broad repertoire of host genes that regulate innate immunity to HSV-1 infection, including those involved in MHC-I antigen presentation, cytokine signalling, and interferon stimulated gene (ISG) expression. ChIP-seq analysis revealed that PML, the principle scaffolding protein of PML-NBs, was required for the enrichment of HIRA onto ISGs, identifying a role for PML in the HIRA-dependent regulation of innate immunity to virus infection. Our data identifies independent roles for HIRA in the intrinsic silencing of viral gene expression and the induction of innate immune defences to restrict the initiation and propagation of HSV-1 infection, respectively. These intracellular host defences are antagonized by the HSV-1 ubiquitin ligase ICP0, which disrupts the stable recruitment of HIRA to infecting viral genomes and PML-NBs at spatiotemporally distinct phases of infection. Our study highlights the importance of histone chaperones to regulate multiple phases of intracellular immunity to virus infection, findings that are likely to be highly pertinent in the cellular restriction of many clinically important viral pathogens.

Host innate immune defences play critical roles in the cellular restriction of invading viral pathogens and the stimulation of adaptive immune responses. A key component in the regulation of this arm of host immunity is the rapid induction of cytokine signalling and the expression of interferon stimulated gene products (ISGs), which confer a refractory antiviral state to limit virus propagation and pathogenesis. While the signal transduction cascades that activate innate immune defences are well established, little is known about the cellular host factors that expedite the expression of this broad repertoire of antiviral host genes in response to pathogen invasion. Here we show that HIRA, a histone H3.3 chaperone, associates with PML-NBs to stimulate the induction of innate immune defences in response to HSV-1 infection. Our study highlights the importance of histone chaperones in the coordinated regulation of multiple phases of host immunity in response to pathogen invasion and identifies a key role for HIRA in the induction of innate immunity to virus infection.

BA08: An open-label, single-arm, non-randomised, phase 2 trial of cisplatin, methotrexate and vinblastine (CMV) for pure squamous cell cancer of the urinary tract

BACKGROUND

Pure squamous cell carcinoma (SCC) of the urinary tract is rare in the UK and has a poor prognosis compared with transitional cell carcinoma (TCC). Cisplatin based chemotherapy has been shown to be effective in TCC.

METHODS

Patients with T3-T4, pelvic relapsed, nodal or metastatic SCC of the urinary tract were recruited into an open-label, single-arm, non-randomised, phase 2 trial evaluating the activity and safety of cisplatin, methotrexate and vinblastine (CMV) chemotherapy. CMV was given as three 21-day cycles of methotrexate 30mg/m2 (day 1 & 8), vinblastine 4mg/m2 (day 1 & 8) and cisplatin 100mg/m2 (day 2).

RESULTS

38 patients were recruited. Overall response was 39% (95% CI 24%, 55%)-13% CR and 26% PR. Median OS was 7.8 months (95% CI 3.4, 12.6) with 39% 1-year survival. Toxicity was acceptable.

CONCLUSION

CMV is well tolerated and active in patients with pure SCC of the urinary tract.

A robust intracellular metabolite extraction protocol for human neutrophil metabolic profiling

Neutrophils are phagocytic innate immune cells that play essential roles in host defence, but are also implicated in inflammatory diseases such as rheumatoid arthritis (RA) where they contribute to systemic inflammation and joint damage. Transcriptomic analysis of neutrophils has revealed significant changes in gene expression in neutrophils activated in vitro by cytokines and in vivo during inflammation in RA. However, there are no reports on the global metabolomic changes that occur as a consequence of this activation. The aim of this study was to establish protocols for the study of changes in the metabolome of human neutrophils using 1H NMR spectroscopy. Sample preparation and spectral analysis protocols were optimised using neutrophils isolated by Ficoll-Paque, with decreased washing steps and inclusion of a heat-shock step to quench metabolite turnover. Cells were incubated ± PMA for 15 min in HEPES-free media and samples were analysed by NMR using a 700 MHz NMR Avance IIIHD Bruker NMR spectrometer equipped with a TCI cryoprobe. Chenomx, Bruker TopSpin and AMIX software were used to process spectra and identify metabolites. Principal Component Analysis (PCA) and signalling pathway analysis was carried out using Metaboanalyst. Cell number and number of scans (NS) were optimised as >3.6 million cells and 512 NS. 327 spectral bins were defined in the neutrophil spectra, of which 287 (87.7%) were assigned to 110 metabolites that included: amino acids, peptides and analogues; carbohydrates, carbonyls and alcohols; nucleotides, nucleosides and analogues; lipids and lipid-like molecules; benzenoids; and other organic compounds. 43 metabolites changed at least 1.5 fold (increase or decrease) after the addition of PMA for 5 or 15 min. Pathway analysis revealed that PMA affected nicotinate and nicotinamide metabolism, aminoacyl-tRNA biosynthesis and glycolysis, suggesting a redirection of glucose metabolism from glycolysis to the pentose phosphate pathway and production of NADPH for activation of the NADPH oxidase and subsequent respiratory burst. We have developed protocols for the study of human neutrophils by 1H NMR spectroscopy. Importantly, this methodology has sufficient sensitivity and reproducibility to detect changes in metabolite abundance from cell numbers typically collected from clinical samples or experiments with multiple assay conditions.

Levofloxacin versus placebo for the prevention of tuberculosis disease in child contacts of multidrug-resistant tuberculosis: study protocol for a phase III cluster randomised controlled trial (TB-CHAMP)

BACKGROUND

Multidrug-resistant (MDR) tuberculosis (TB) presents a challenge for global TB control. Treating individuals with MDR-TB infection to prevent progression to disease could be an effective public health strategy. Young children are at high risk of developing TB disease following infection and are commonly infected by an adult in their household. Identifying young children with household exposure to MDR-TB and providing them with MDR-TB preventive therapy could reduce the risk of disease progression. To date, no trials of MDR-TB preventive therapy have been completed and World Health Organization guidelines suggest close observation with no active treatment.

METHODS

The tuberculosis child multidrug-resistant preventive therapy (TB-CHAMP) trial is a phase III cluster randomised placebo-controlled trial to assess the efficacy of levofloxacin in young child contacts of MDR-TB cases. The trial is taking place at three sites in South Africa where adults with MDR-TB are identified. If a child aged < 5 years lives in their household, we assess the adult index case, screen all household members for TB disease and evaluate any child aged < 5 years for trial eligibility. Eligible children are randomised by household to receive daily levofloxacin (15-20 mg/kg) or matching placebo for six months. Children are closely monitored for disease development, drug tolerability and adverse events. The primary endpoint is incident TB disease or TB death by one year after recruitment. We will enrol 1556 children from approximately 778 households with an average of two eligible children per household. Recruitment will run for 18-24 months with all children followed for 18 months after treatment. Qualitative and health economic evaluations are embedded in the trial.

DISCUSSION

If the TB-CHAMP trial demonstrates that levofloxacin is effective in preventing TB disease in young children who have been exposed to MDR-TB and that it is safe, well tolerated, acceptable and cost-effective, we would expect that that this intervention would rapidly transfer into policy.

TRIAL REGISTRATION

ISRCTN Registry, ISRCTN92634082 . Registered on 31 March 2016.

Investigating clinical handover and healthcare communication for outpatients with chronic disease in India: A mixed-methods study

OBJECTIVES

Research concentrating on continuity of care for chronic, non-communicable disease (NCD) patients in resource-constrained settings is currently limited and focusses on inpatients. Outpatient care requires attention as this is where NCD patients often seek treatment and optimal handover of information is essential. We investigated handover, healthcare communication and barriers to continuity of care for chronic NCD outpatients in India. We also explored potential interventions for improving storage and exchange of healthcare information.

METHODS

A mixed-methods design was used across five healthcare facilities in Kerala and Himachal Pradesh states. Questionnaires from 513 outpatients with cardiovascular disease, chronic respiratory disease, or diabetes covered the form and comprehensiveness of information exchange between healthcare professionals (HCPs) and between HCPs and patients. Semi-structured interviews with outpatients and HCPs explored handover, healthcare communication and intervention ideas. Barriers to continuity of care were identified through triangulation of all data sources.

RESULTS

Almost half (46%) of patients self-referred to hospital outpatient clinics (OPCs). Patient-held healthcare information was often poorly recorded on unstructured sheets of paper; 24% of OPC documents contained the following: diagnosis, medication, long-term care and follow-up information. Just 55% of patients recalled receiving verbal follow-up and medication instructions during OPC appointments. Qualitative themes included patient preference for hospital visits, system factors, inconsistent doctor-patient communication and attitudes towards medical documents. Barriers were hospital time constraints, inconsistent referral practices and absences of OPC medical record-keeping, structured patient-held medical documents and clinical handover training. Patients and HCPs were in favour of the introduction of patient-held booklets for storing and transporting medical documents.

CONCLUSIONS

Deficiencies in communicative practices are compromising the continuity of chronic NCD outpatient care. Targeted systems-based interventions are urgently required to improve information provision and exchange. Our findings indicate that well-designed patient-held booklets are likely to be an acceptable, affordable and effective part of the solution.

Exploring variability in basal ganglia connectivity with functional MRI in healthy aging

Changes in functional connectivity (FC) measured using resting state fMRI within the basal ganglia network (BGN) have been observed in pathologies with altered neurotransmitter systems and conditions involving motor control and dopaminergic processes. However, less is known about non-disease factors affecting FC in the BGN. The aim of this study was to examine associations of FC within the BGN with dopaminergic processes in healthy older adults. We explored the relationship between FC in the BGN and variables related to demographics, impulsive behavior, self-paced tasks, mood, and motor correlates in 486 participants in the Whitehall-II imaging sub-study using both region-of-interest- and voxel-based approaches. Age was the only correlate of FC in the BGN that was consistently significant with both analyses. The observed adverse effect of aging on FC may relate to alterations of the dopaminergic system, but no unique dopamine-related function seemed to have a link with FC beyond those detectable in and linearly correlated with healthy aging.

Reactive and pre-emptive vaccination strategies to control hepatitis E infection in emergency and refugee settings: A modelling study

BACKGROUND

Hepatitis E Virus (HEV) is the leading cause of acute viral hepatitis globally. Symptomatic infection is associated with case fatality rates of ~20% in pregnant women and it is estimated to account for ~10,000 annual pregnancy-related deaths in southern Asia alone. Recently, large and well-documented outbreaks with high mortality have occurred in displaced population camps in Sudan, Uganda and South Sudan. However, the epidemiology of HEV is poorly defined, and the value of different immunisation strategies in outbreak settings uncertain. We aimed to estimate the critical epidemiological parameters for HEV and to evaluate the potential impact of both reactive vaccination (initiated in response to an epidemic) and pre-emptive vaccination.

METHODS

We analysed data from one of the world's largest recorded HEV epidemics, which occurred in internally-displaced persons camps in Uganda (2007-2009), using transmission dynamic models to estimate epidemiological parameters and assess the potential impact of reactive and pre-emptive vaccination strategies.

RESULTS

Under baseline assumptions we estimated the basic reproduction number of HEV in three separate camps to range from 3.7 (95% Credible Interval [CrI] 2.8, 5.1) to 8.5 (5.3, 11.4). Mean latent and infectious periods were estimated to be 34 (95% CrI 28, 39) and 40 (95% CrI 23, 71) days respectively. Assuming 90% vaccine coverage, reactive two-dose vaccination of those aged 16-65 years excluding pregnant women (for whom vaccine is not licensed), if initiated after 50 reported cases, led to mean camp-specific reductions in mortality of 10 to 29%. Pre-emptive vaccination with two doses reduced mortality by 35 to 65%. Both strategies were more effective if coverage was extended to groups for whom the vaccine is not currently licensed. For example, two dose pre-emptive vaccination, if extended to include pregnant women, led to mean reductions in mortality of 66 to 82%.

CONCLUSIONS

HEV has a high transmission potential in displaced population settings. Substantial reductions in mortality through vaccination are expected, even if used reactively. There is potential for greater impact if vaccine safety and effectiveness can be established in pregnant women.

Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria

Clostridium difficile is a Gram-positive spore-forming anaerobe and a major cause of antibiotic-associated diarrhoea. Disruption of the commensal microbiota, such as through treatment with broad-spectrum antibiotics, is a critical precursor for colonisation by C. difficile and subsequent disease. Furthermore, failure of the gut microbiota to recover colonisation resistance can result in recurrence of infection. An unusual characteristic of C. difficile among gut bacteria is its ability to produce the bacteriostatic compound para-cresol (p-cresol) through fermentation of tyrosine. Here, we demonstrate that the ability of C. difficile to produce p-cresol in vitro provides a competitive advantage over gut bacteria including Escherichia coli, Klebsiella oxytoca and Bacteroides thetaiotaomicron. Metabolic profiling of competitive co-cultures revealed that acetate, alanine, butyrate, isobutyrate, p-cresol and p-hydroxyphenylacetate were the main metabolites responsible for differentiating the parent strain C. difficile (630Δerm) from a defined mutant deficient in p-cresol production. Moreover, we show that the p-cresol mutant displays a fitness defect in a mouse relapse model of C. difficile infection (CDI). Analysis of the microbiome from this mouse model of CDI demonstrates that colonisation by the p-cresol mutant results in a distinctly altered intestinal microbiota, and metabolic profile, with a greater representation of Gammaproteobacteria, including the Pseudomonales and Enterobacteriales. We demonstrate that Gammaproteobacteria are susceptible to exogenous p-cresol in vitro and that there is a clear divide between bacterial Phyla and their susceptibility to p-cresol. In general, Gram-negative species were relatively sensitive to p-cresol, whereas Gram-positive species were more tolerant. This study demonstrates that production of p-cresol by C. difficile has an effect on the viability of intestinal bacteria as well as the major metabolites produced in vitro. These observations are upheld in a mouse model of CDI, in which p-cresol production affects the biodiversity of gut microbiota and faecal metabolite profiles, suggesting that p-cresol production contributes to C. difficile survival and pathogenesis.

New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images

The precise anatomical location of gene expression is an essential component of the study of gene function. For most model organisms this task is usually undertaken via visual inspection of gene expression images by interested researchers. Computational analysis of gene expression has been developed in several model organisms, notably in Drosophila which exhibits a uniform shape and outline in the early stages of development. Here we address the challenge of computational analysis of gene expression in Xenopus, where the range of developmental stages of interest encompasses a wide range of embryo size and shape. Embryos may have different orientation across images, and, in addition, embryos have a pigmented epidermis that can mask or confuse underlying gene expression. Here we report the development of a set of computational tools capable of processing large image sets with variable characteristics. These tools efficiently separate the Xenopus embryo from the background, separately identify both histochemically stained and naturally pigmented regions within the embryo, and can sort images from the same gene and developmental stage according to similarity of gene expression patterns without information about relative orientation. We tested these methods on a large, but highly redundant, collection of 33,289 in situ hybridization images, allowing us to select representative images of expression patterns at different embryo orientations. This has allowed us to put a much smaller subset of these images into the public domain in an effective manner. The ‘isimage’ module and the scripts developed are implemented in Python and freely available on https://pypi.python.org/pypi/isimage/.

An important component of research into the function of genes in the developing organism is an understanding of both when and where the gene is expressed. Well established molecular techniques can be used to colour the embryo in regions where the gene of interest appears, and researchers will photograph such treated embryos at different stages of development to build up the story of the gene’s use. Small numbers of these expression pattern images may easily be examined by eye, but getting usable information from large collections of such images would take an enormous investment in time by trained scientists. Computational analysis is much to be preferred, but the task is complex and difficult to generalise. The frog Xenopus is an important model for studying vertebrate development, but up till now has had no purely computational methods available for analysing gene expression. Here we present a suite of computational tools based on a range of mathematical methods, capable of recognising the outline of the embryo against a variety of backgrounds, and within the embryo separately recognising areas of both gene expression and natural pigmentation. These tools work over a wide range of embryo shapes and imaging conditions, and, in our opinion, represent a major step towards full automation of anatomical gene expression annotation in vertebrate embryology.

Pro-inflammatory cytokines attenuate glucose-stimulated insulin secretion from INS-1E insulinoma cells by restricting mitochondrial pyruvate oxidation capacity - Novel mechanistic insight from real-time analysis of oxidative phosphorylation

Pro-inflammatory cytokines cause pancreatic beta cell failure during the development of type 2 diabetes. This beta cell failure associates with mitochondrial dysfunction, but the precise effects of cytokines on mitochondrial respiration remain unclear. To test the hypothesis that pro-inflammatory cytokines impair glucose-stimulated insulin secretion (GSIS) by inhibiting oxidative ATP synthesis, we probed insulin release and real-time mitochondrial respiration in rat INS-1E insulinoma cells that were exposed to a combination of 2 ng/mL interleukin-1-beta and 50 ng/mL interferon-gamma. We show that 24-h exposure to these cytokines dampens both glucose- and pyruvate-stimulated insulin secretion (P < 0.0001 and P < 0.05, respectively), but does not affect KCl-induced insulin release. Mirroring secretory defects, glucose- and pyruvate-stimulated mitochondrial respiration are lowered after cytokine exposure (P < 0.01). Further analysis confirms that cytokine-induced mitochondrial respiratory defects occur irrespective of whether fuel oxidation is coupled to, or uncoupled from, ATP synthesis. These observations demonstrate that pro-inflammatory cytokines attenuate GSIS by restricting mitochondrial pyruvate oxidation capacity. Interleukin-1-beta and interferon-gamma also increase mitochondrial superoxide levels (P < 0.05), which may reinforce the inhibition of pyruvate oxidation, and cause a modest (20%) but significant (P < 0.01) loss of INS-1E cells. Cytokine-induced INS-1E cell failure is insensitive to palmitoleate and linoleate, which is at odds with the cytoprotection offered by unsaturated fatty acids against harm caused by nutrient excess. Our data disclose a mitochondrial mechanism for cytokine-impaired GSIS in INS-1E cells, and suggest that inflammatory and nutrient-related beta cell failure emerge, at least partly, through distinct paths.

Detection of Plasmodium berghei infected Anopheles stephensi using near-infrared spectroscopy

BACKGROUND

The proportion of mosquitoes infected with malaria is an important entomological metric used to assess the intensity of transmission and the impact of vector control interventions. Currently, the prevalence of mosquitoes with salivary gland sporozoites is estimated by dissecting mosquitoes under a microscope or using molecular methods. These techniques are laborious, subjective, and require either expensive equipment or training. This study evaluates the potential of near-infrared spectroscopy (NIRS) to identify laboratory reared mosquitoes infected with rodent malaria.

METHODS

Anopheles stephensi mosquitoes were reared in the laboratory and fed on Plasmodium berghei infected blood. After 12 and 21 days post-feeding mosquitoes were killed, scanned and analysed using NIRS and immediately dissected by microscopy to determine the number of oocysts on the midgut wall or sporozoites in the salivary glands. A predictive classification model was used to determine parasite prevalence and intensity status from spectra.

RESULTS

The predictive model correctly classifies infectious and uninfectious mosquitoes with an overall accuracy of 72%. The false negative and false positive rates were 30 and 26%, respectively. While NIRS was able to differentiate between uninfectious and highly infectious mosquitoes, differentiating between mid-range infectious groups was less accurate. Multiple scans of the same specimen, with repositioning the mosquito between scans, is shown to improve accuracy. On a smaller dataset NIRS was unable to predict whether mosquitoes harboured oocysts.

CONCLUSIONS

To our knowledge, we provide the first evidence that NIRS can differentiate between infectious and uninfectious mosquitoes. Currently, distinguishing between different intensities of infection is challenging. The classification model provides a flexible framework and allows for different error rates to be optimised, enabling the sensitivity and specificity of the technique to be varied according to requirements.

Exploratory studies to decide whether and how to proceed with full-scale evaluations of public health interventions: a systematic review of guidance

BACKGROUND

Evaluations of complex interventions in public health are frequently undermined by problems that can be identified before the effectiveness study stage. Exploratory studies, often termed pilot and feasibility studies, are a key step in assessing the feasibility and value of progressing to an effectiveness study. Such studies can provide vital information to support more robust evaluations, thereby reducing costs and minimising potential harms of the intervention. This systematic review forms the first phase of a wider project to address the need for stand-alone guidance for public health researchers on designing and conducting exploratory studies. The review objectives were to identify and examine existing recommendations concerning when such studies should be undertaken, questions they should answer, suitable methods, criteria for deciding whether to progress to an effectiveness study and appropriate reporting.

METHODS

We searched for published and unpublished guidance reported between January 2000 and November 2016 via bibliographic databases, websites, citation tracking and expert recommendations. Included papers were thematically synthesized.

RESULTS

The search retrieved 4095 unique records. Thirty papers were included, representing 25 unique sources of guidance/recommendations. Eight themes were identified: pre-requisites for conducting an exploratory study, nomenclature, guidance for intervention assessment, guidance surrounding any future evaluation study design, flexible versus fixed design, progression criteria to a future evaluation study, stakeholder involvement and reporting of exploratory studies. Exploratory studies were described as being concerned with the intervention content, the future evaluation design or both. However, the nomenclature and endorsed methods underpinning these aims were inconsistent across papers. There was little guidance on what should precede or follow an exploratory study and decision-making surrounding this.

CONCLUSIONS

Existing recommendations are inconsistent concerning the aims, designs and conduct of exploratory studies, and guidance is lacking on the evidence needed to inform when to proceed to an effectiveness study.

TRIAL REGISTRATION

PROSPERO 2016, CRD42016047843.

Estimating city-level travel patterns using street imagery: A case study of using Google Street View in Britain

Background

Street imagery is a promising and growing big data source providing current and historical images in more than 100 countries. Studies have reported using this data to audit road infrastructure and other built environment features. Here we explore a novel application, using Google Street View (GSV) to predict travel patterns at the city level.

Methods

We sampled 34 cities in Great Britain. In each city, we accessed 2000 GSV images from 1000 random locations. We selected archived images from time periods overlapping with the 2011 Census and the 2011–2013 Active People Survey (APS). We manually annotated the images into seven categories of road users. We developed regression models with the counts of images of road users as predictors. The outcomes included Census-reported commute shares of four modes (combined walking plus public transport, cycling, motorcycle, and car), as well as APS-reported past-month participation in walking and cycling.

Results

We found high correlations between GSV counts of cyclists (‘GSV-cyclists’) and cycle commute mode share (r = 0.92)/past-month cycling (r = 0.90). Likewise, GSV-pedestrians was moderately correlated with past-month walking for transport (r = 0.46), GSV-motorcycles was moderately correlated with commute share of motorcycles (r = 0.44), and GSV-buses was highly correlated with commute share of walking plus public transport (r = 0.81). GSV-car was not correlated with car commute mode share (r = –0.12). However, in multivariable regression models, all outcomes were predicted well, except past-month walking. The prediction performance was measured using cross-validation analyses. GSV-buses and GSV-cyclists are the strongest predictors for most outcomes.

Conclusions

GSV images are a promising new big data source to predict urban mobility patterns. Predictive power was the greatest for those modes that varied the most (cycle and bus). With its ability to identify mode of travel and capture street activity often excluded in routinely carried out surveys, GSV has the potential to be complementary to new and traditional data. With half the world’s population covered by street imagery, and with up to 10 years historical data available in GSV, further testing across multiple settings is warranted both for cross-sectional and longitudinal assessments.