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Journal: Wellcome open research

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Background: Relative blood flow in the two middle cerebral arteries can be measured using functional transcranial Doppler sonography (fTCD) to give an index of lateralisation as participants perform a specific task. Language laterality has mostly been studied with fTCD using a word generation task, but it is not clear whether this is optimal. Methods: Using fTCD, we evaluated a sentence generation task that has shown good reliability and strong left lateralisation in fMRI. We interleaved trials of word generation, sentence generation and list generation and assessed agreement of these tasks in 31 participants (29 right-handers). Results: Although word generation and sentence generation both gave robust left-lateralisation, Bland-Altman analysis showed that these two methods were not equivalent. The comparison list generation task was not systematically lateralised, but nevertheless laterality indices (LIs) from this task were significantly correlated with the other two tasks. Subtracting list generation LI from sentence generation LI did not affect the strength of the laterality index. Conclusions: This was a pre-registered methodological study designed to explore novel approaches to optimising measurement of language lateralisation using fTCD. It confirmed that sentence generation gives robust left lateralisation in most people, but is not equivalent to the classic word generation task. Although list generation does not show left-lateralisation at the group level, the LI on this task was correlated with left-lateralised tasks. This suggests that word and sentence generation involve adding a constant directional bias to an underlying continuum of laterality that is reliable in individuals but not biased in either direction. In future research we suggest that consistency of laterality across tasks might have more functional significance than strength or direction of laterality on any one task.

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Here we describe the ways in which the sequence and annotation of the Plasmodium falciparum reference genome has changed since its publication in 2002. As the malaria species responsible for the most deaths worldwide, the richness of annotation and accuracy of the sequence are important resources for the P. falciparum research community as well as the basis for interpreting the genomes of subsequently sequenced species. At the time of publication in 2002 over 60% of predicted genes had unknown functions. As of March 2019, this number has been significantly decreased to 33%. The reduction is due to the inclusion of genes that were subsequently characterised experimentally and genes with significant similarity to others with known functions. In addition, the structural annotation of genes has been significantly refined; 27% of gene structures have been changed since 2002, comprising changes in exon-intron boundaries, addition or deletion of exons and the addition or deletion of genes. The sequence has also undergone significant improvements. In addition to the correction of a large number of single-base and insertion or deletion errors, a major miss-assembly between the subtelomeres of chromosome 7 and 8 has been corrected. As the number of sequenced isolates continues to grow rapidly, a single reference genome will not be an adequate basis for interpreting intra-species sequence diversity. We therefore describe in this publication a population reference genome of P. falciparum, called Pfref1. This reference will enable the community to map to regions that are not present in the current assembly. P. falciparum 3D7 will continue to be maintained, with ongoing curation ensuring continual improvements in annotation quality.

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Background: Radon (and its decay products) is a known human carcinogen and the leading cause of lung cancer in never-smokers and the second in ever-smokers. The carcinogenic mechanism from radiation is a combination of genetic and epigenetic processes, but compared to the genetic mechanisms, epigenetic processes remain understudied in humans. This study aimed to explore associations between residential radon exposure and DNA methylation in the general population. Methods: Potential residential radon exposure for 75-metre area buffers was linked to genome-wide DNA methylation measured in peripheral blood from children and mothers of the Accessible Resource for Integrated Epigenomic Studies subsample of the ALSPAC birth cohort. Associations with DNA methylation were tested at over 450,000 CpG sites at ages 0, 7 and 17 years (children) and antenatally and during middle-age (mothers). Analyses were adjusted for potential residential and lifestyle confounding factors and were determined for participants with complete data (n = 786 to 980). Results: Average potential exposure to radon was associated in an exposure-dependent manner with methylation at cg25422346 in mothers during pregnancy, with no associations at middle age. For children, radon potential exposure was associated in an exposure-dependent manner with methylation of cg16451995 at birth, cg01864468 at age 7, and cg04912984, cg16105117, cg23988964, cg04945076, cg08601898, cg16260355 and cg26056703 in adolescence. Conclusions: Residential radon exposure was associated with DNA methylation in an exposure-dependent manner. Although chance and residual confounding cannot be excluded, the identified associations may show biological mechanisms involved in early biological effects from radon exposure.

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Background: Protein-conjugate capsular polysaccharide vaccines can potentially control invasive meningococcal disease (IMD) caused by five (A, C, W, X, Y) of the six IMD-associated serogroups.  Concerns raised by immunological similarity of the serogroup B capsule to human neural cell carbohydrates, meant that ‘serogroup B substitute’ vaccines target more variable subcapsular protein antigens.  A successful approach using outer membrane vesicles (OMVs) as major vaccine components had limited strain coverage. In 4CMenB (Bexsero ®), recombinant proteins have been added to ameliorate this problem.  Methods: Scalable, portable, genomic techniques were used to investigate the Bexsero ® OMV protein diversity in meningococcal populations. Shotgun proteomics identified 461 proteins in the OMV, defining a complex proteome. Amino acid sequences for the 24 proteins most likely to be involved in cross-protective immune responses were catalogued within the PubMLST.org/neisseria database using a novel OMV peptide Typing (OMVT) scheme. Results: Among these proteins there was variation in the extent of diversity and association with meningococcal lineages, identified as clonal complexes (ccs), ranging from the most conserved peptides (FbpA, NEISp0578, and putative periplasmic protein, NEISp1063) to the most diverse (TbpA, NEISp1690).  There were 1752 unique OMVTs identified amongst 2492/3506 isolates examined by whole-genome sequencing (WGS). These OMVTs were grouped into clusters (sharing ≥18 identical OMVT peptides), with 45.3% of isolates assigned to one of 27 OMVT clusters. OMVTs and OMVT clusters were strongly associated with cc, genogroup, and Bexsero ® antigen variants, demonstrating that combinations of OMV proteins exist in discrete, non-overlapping combinations associated with genogroup and Bexsero ® Antigen Sequence Type. This highly structured population of IMD-associated meningococci is consistent with strain structure models invoking host immune and/or metabolic selection. Conclusions: The OMVT scheme facilitates region-specific WGS investigation of meningococcal diversity and is an open-access, portable tool with applications for vaccine development, especially in the choice of antigen combinations, assessment and implementation.

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Background: The extraction of data from the reports of primary studies, on which the results of systematic reviews depend, needs to be carried out accurately. To aid reliability, it is recommended that two researchers carry out data extraction independently. The extraction of statistical data from graphs in PDF files is particularly challenging, as the process is usually completely manual, and reviewers need sometimes to revert to holding a ruler against the page to read off values: an inherently time-consuming and error-prone process. Methods: To mitigate some of the above problems we integrated and customised two existing JavaScript libraries to create a new web-based graphical data extraction tool to assist reviewers in extracting data from graphs. This tool aims to facilitate more accurate and timely data extraction through a user interface which can be used to extract data through mouse clicks. We carried out a non-inferiority evaluation to examine its performance in comparison with participants' standard practice for extracting data from graphs in PDF documents. Results: We found that the customised graphical data extraction tool is not inferior to users' (N=10) prior standard practice. Our study was not designed to show superiority, but suggests that, on average, participants saved around 6 minutes per graph using the new tool, accompanied by a substantial increase in accuracy. Conclusions: Our study suggests that the incorporation of this type of tool in online systematic review software would be beneficial in facilitating the production of accurate and timely evidence synthesis to improve decision-making.

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Background: Down syndrome (DS) is associated with poor language skills that seem disproportionate to general nonverbal ability, but the nature and causes of this deficit are unclear. We assessed how individuals with DS understand complex linguistic constructions, and considered how cognitive ability and memory and impact the ability of those with DS to process these sentence types. Methods: There were three groups participating in the study: children with DS (n = 33) and two control groups composed of children with cognitive impairment of unknown aetiology (CI) (n = 32) and children with typical development (n = 33). The three groups did not differ on raw scores on a test of non-verbal cognitive ability. Using a newly devised animation task, we examined how well individuals with DS (n = 33) could understand relative clauses, complement clauses and adverbial clauses compared to children with CI and typically developing controls. Participants also completed the Test for the Reception of Grammar-2, three measures of memory (forward and backward digit recall, visuo-spatial memory) and a hearing screen. Results: Results indicated that (1) with the exception of intransitive subject relative clauses, children with DS performed at floor on all other complex sentences, (2) they performed at a significantly lower level than both control groups, and (3) DS status accounted for a significant proportion of the variance over and above memory skills. Conclusions: Our findings suggest that children with DS have a disproportionate difficulty understanding complex sentences compared to two control groups matched on mental age. Furthermore, their understanding of syntax is not completely explained by poor cognitive or memory skills, rather it appears to be a specific deficit that may distinguish children with DS from other neurodevelopmental disorders.

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Background: Genome-wide association studies have identified genetic variants associated with coronary artery disease (CAD) in adults - the leading cause of death worldwide. It often occurs later in life, but variants may impact CAD-relevant phenotypes early and throughout the life-course. Cohorts with longitudinal and genetic data on thousands of individuals are letting us explore the antecedents of this adult disease. Methods: 148 metabolites, with a focus on the lipidome, measured using nuclear magnetic resonance ( 1H-NMR) spectroscopy, and genotype data were available from 5,907 individuals at ages 7, 15, and 17 years from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Linear regression was used to assess the association between the metabolites and an adult-derived genetic risk score (GRS) of CAD comprising 146 variants. Individual variant-metabolite associations were also examined. Results: The CAD-GRS associated with 118 of 148 metabolites (false discovery rate [FDR] < 0.05), the strongest associations being with low-density lipoprotein (LDL) and atherogenic non-LDL subgroups. Nine of 146 variants in the GRS associated with one or more metabolites (FDR < 0.05). Seven of these are within lipid loci: rs11591147 PCSK9, rs12149545 HERPUD1-CETP, rs17091891 LPL, rs515135 APOB, rs602633 CELSR2-PSRC1, rs651821 APOA5, rs7412 APOE-APOC1. All associated with metabolites in the LDL or atherogenic non-LDL subgroups or both including aggregate cholesterol measures. The other two variants identified were rs112635299 SERPINA1 and rs2519093 ABO.Conclusions: Genetic variants that influence CAD risk in adults are associated with large perturbations in metabolite levels in individuals as young as seven. The variants identified are mostly within lipid-related loci and the metabolites they associated with are primarily linked to lipoproteins. Along with further research, this knowledge could allow for preventative measures, such as increased monitoring of at-risk individuals and perhaps treatment earlier in life, to be taken years before any symptoms of the disease arise.

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Background: Incentives play a role in introducing health-related benefits, but no interventions using mixed incentives, i.e. a combination of individual and group incentives, have been tested in individuals with type 2 diabetes mellitus (T2DM). We evaluated the feasibility of implementing individual- and mixed-incentives, with and without a supportive partner, on glycated haemoglobin (HbA1c) control and weight loss among patients with T2DM. Methods: This is a feasibility, sex-stratified, single-blinded, randomized controlled study in individuals with T2DM. All participants received diabetes education and tailored goal setting for weight and glycated haemoglobin (HbA1c). Participants were randomly assigned into three arms: individual incentives (Arm 1), mixed incentives-altruism (Arm 2), and mixed incentives-cooperation (Arm 3). Participants were accompanied by a diabetes educator every other week to monitor targets, and the intervention period lasted 3 months. The primary outcome was the change in HbA1c at 3 months from baseline. Weight and change body mass index (BMI) were considered as secondary outcomes. Results: Out of 783 patients screened, a total of 54 participants, 18 per study arm, were enrolled and 44 (82%) completed the 3-month follow-up. Mean baseline HbA1c values were 8.5%, 7.9% and 8.2% in Arm 1, Arm 2, and Arm 3, respectively. At 3 months, participants in all three study arms showed reductions in HbA1c ranging from -0.9% in Arm 2 to -1.4% in Arm 1. Weight and BMI also showed reductions. Conclusions: Individual and mixed cash incentives show important reductions in HbA1c, weight and BMI in patients with type 2 diabetes mellitus after 3 months.  Recruitment and uptake of the intervention were successfully accomplished demonstrating feasibility to conduct larger effectiveness studies to test individual and mixed economic incentives for diabetes management. Registration: ClinicalTrials.gov Identifier NCT02891382.

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Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine.  Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.

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Background: The arbovirus vector, Aedes albopictus, originating from Asia, has recently invaded African countries, including the Republic of the Congo, where it was associated with a chikungunya outbreak. Up until now, little was known about its distribution in relation to the native Aedes aegypti and how the invasion will modify the epidemiology of arboviral diseases. Here, we assessed the current distribution of Ae. albopictus and Ae. aegypti in the Republic of the Congo and explored the genetic diversity of the invading species, Ae. albopictus. Methods: Immature stages of Aedes were collected in nine locations in the Republic of the Congo in 2017 following a north-south transect and reared to adult stage. Adults were morphologically identified, counted and grouped according to species and location. Genetic diversity of Ae. albopictus was assessed by analyzing the cytochrome oxidase I ( COI) gene. Results:Ae.albopictus and Ae. aegypti were found together across the country in all the locations investigated. The invasive species is predominant over the native species in all locations except Brazzaville, suggesting that Ae. albopictus is displacing Ae. aegypti across Congo. When comparing the species distributions across the two largest cities, Brazzaville and Pointe Noire, Ae. albopictus was more prevalent than Ae. aegypti in the suburbs whereas the opposite situation was reported in the city centre. Mitochondrial DNA analysis revealed very low genetic diversity of Ae. albopictus with only three haplotypes recorded across the country supporting the recent introduction of this species in the Republic of the Congo. Phylogenetic tree analysis revealed that Ae. albopictus from Congo originated from other tropical Asian countries such as China, likely as a result of increasing trade links. Conclusion: These findings are important for the implementation of vector control strategies and can serve as a foundation for further research on these vectors in the country.