Hiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity in Fusarium oxysporum f.sp. ciceris.

Understanding the origins of variation in agricultural pathogens is of fundamental interest and practical importance, especially for diseases that threaten food security. Fusarium oxysporum is among the most important of soil-borne pathogens, with a global distribution and an extensive host range. The pathogen is considered to be asexual, with horizontal transfer of chromosomes providing an analog of assortment by meiotic recombination. Here, we challenge those assumptions based on the results of population genomic analyses, describing the pathogen's diversity and inferring its origins and functional consequences in the context of a single, long-standing agricultural system. We identify simultaneously low nucleotide distance among strains, and unexpectedly high levels of genetic and genomic variability. We determine that these features arise from a combination of genome-scale recombination, best explained by widespread sexual reproduction, and presence-absence variation consistent with chromosomal rearrangement. Pangenome analyses document an accessory genome more than twice the size of the core genome, with contrasting evolutionary dynamics. The core genome is stable, with low diversity and high genetic differentiation across geographic space, while the accessory genome is paradoxically more diverse and unstable but with lower genetic differentiation and hallmarks of contemporary gene flow at local scales. We suggest a model in which episodic sexual reproduction generates haplotypes that are selected and then maintained through clone-like dynamics, followed by contemporary genomic rearrangements that reassort the accessory genome among sympatric strains. Taken together, these processes contribute unique genome content, including reassortment of virulence determinants that may explain observed variation in pathogenic potential.

Seed color patterns in domesticated common bean are regulated by MYB-bHLH-WD40 transcription factors and temperature.

Seed colors and color patterns are critical for the survival of wild plants and the consumer appeal of crops. In common bean, a major global staple, these patterns are also essential in determining market classes, yet the genetic and environmental control of many pigmentation patterns remains unresolved. In this study, we genetically mapped variation for several important seed pattern loci, including T, Bip, phbw, and Z, which co-segregated with candidate genes PvTTG1, PvMYC1, PvTT8, and PvTT2, respectively. Proteins encoded by these genes are predicted to work together in MYB-bHLH-WD40 (MBW) complexes, propagating flavonoid biosynthesis across the seed coat as observed in Arabidopsis. Whole-genome sequencing of 37 accessions identified mutations, including seven unique parallel mutations in T (PvTTG1) and non-synonymous SNPs in highly conserved residues in bipana (PvMYC1) and z (PvTT2). A 612 bp intron deletion in phbw (PvTT8) eliminated motifs conserved since the Papilionoideae origin and corresponded to a 20-fold reduction in transcript abundance. In multi-location field trials of seven varieties with partial seed coat pigmentation patterning, the pigmented seed coat area correlated positively with ambient temperature, with up to 11-fold increases in the pigmented area from the coolest to the warmest environments. In controlled growth chamber conditions, an increase of 4°C was sufficient to cause pigmentation on an average additional 21% of the seed coat area. Our results shed light on key steps of flavonoid biosynthesis in common bean. They will inform breeding efforts for seed coat color/patterning to improve consumer appeal in this nutritious staple crop.

Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes.

The Genome Context Viewer is a web application for identifying, aligning, and visualizing genomic regions based on their micro and macrosyntenic structures. By using functional elements such as gene annotations as the unit of search and comparison, the Genome Context Viewer can compute and display relationships between regions across many assemblies from federated data sources in real-time, enabling users to rapidly explore multiple annotated genomes and identify divergence and structural events that can help provide insight into evolutionary mechanisms associated with functional consequences. In this work, we introduce version 2 of the Genome Context Viewer and highlight new features that enhance usability, performance, and ease of deployment.

Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance.

Medicago truncatula, model legume and alfalfa relative, has served as an essential resource for advancing our understanding of legume physiology, functional genetics, and crop improvement traits. Necrotrophic fungus, Ascochyta medicaginicola, the causal agent of spring black stem (SBS) and leaf spot is a devasting foliar disease of alfalfa affecting stand survival, yield, and forage quality. Host resistance to SBS disease is poorly understood, and control methods rely on cultural practices. Resistance has been observed in M. truncatula accession SA27063 (HM078) with two recessively inherited quantitative-trait loci (QTL), rnpm1 and rnpm2, previously reported. To shed light on host resistance, we carried out a de novo genome assembly of HM078. The genome, referred to as MtHM078 v1.0, is comprised of 23 contigs totaling 481.19 Mbp. Notably, this assembly contains a substantial amount of novel centromere-related repeat sequences due to deep long-read sequencing. Genome annotation resulted in 98.4% of BUSCO fabales proteins being complete. The assembly enabled sequence-level analysis of rnpm1 and rnpm2 for gene content, synteny, and structural variation between SBS-resistant accession SA27063 (HM078) and SBS-susceptible accession A17 (HM101). Fourteen candidate genes were identified, and some have been implicated in resistance to necrotrophic fungi. Especially interesting candidates include loss-of-function events in HM078 because they fit the inverse gene-for-gene model, where resistance is recessively inherited. In rnpm1, these include a loss-of-function in a disease resistance gene due to a premature stop codon, and a 10.85 kbp retrotransposon-like insertion disrupting a ubiquitin conjugating E2. In rnpm2, we identified a frameshift mutation causing a loss-of-function in a glycosidase, as well as a missense and frameshift mutation altering an F-box family protein. This study generated a high-quality genome of HM078 and has identified promising candidates, that once validated, could be further studied in alfalfa to enhance disease resistance.

Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean.

BACKGROUND: Mung bean (Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous traits for adaptation to northern and southern latitudes. This study investigates the genetic basis of the Days-to-Flowering trait (DTF) in mung bean, combining genome-wide association studies (GWAS) in mung bean and comparisons with orthologous genes involved with control of DTF responses in soybean (Glycine max (L) Merr) and Arabidopsis (Arabidopsis thaliana). RESULTS: The most significant associations for DTF were on mung bean chromosomes 1, 2, and 4. Only the SNPs on chromosomes 1 and 4 were heavily investigated using downstream analysis. The chromosome 1 DTF association is tightly linked with a cluster of locally duplicated FERONIA (FER) receptor-like protein kinase genes, and the SNP occurs within one of the FERONIA genes. In Arabidopsis, an orthologous FERONIA gene (AT3G51550), has been reported to regulate the expression of the FLOWERING LOCUS C (FLC). For the chromosome 4 DTF locus, the strongest candidates are Vradi04g00002773 and Vradi04g00002778, orthologous to the Arabidopsis PhyA and PIF3 genes, encoding phytochrome A (a photoreceptor protein sensitive to red to far-red light) and phytochrome-interacting factor 3, respectively. The soybean PhyA orthologs include the classical loci E3 and E4 (genes GmPhyA3, Glyma.19G224200, and GmPhyA2, Glyma.20G090000). The mung bean PhyA ortholog has been previously reported as a candidate for DTF in studies conducted in South Korea. CONCLUSION: The top two identified SNPs accounted for a significant proportion (~ 65%) of the phenotypic variability in mung bean DTF by the six significant SNPs (39.61%), with a broad-sense heritability of 0.93. The strong associations of DTF with genes that have orthologs with analogous functions in soybean and Arabidopsis provide strong circumstantial evidence that these genes are causal for this trait. The three reported loci and candidate genes provide useful targets for marker-assisted breeding in mung beans.

Factors associated with multimorbidity in England: an analysis of the English Longitudinal Study of Ageing.

BACKGROUND: Multimorbidity, defined as the presence of two or more long-term conditions, is a growing public health challenge, especially in terms of prevention and accumulation of long-term conditions among particular population cohorts. To date, efforts to understand multimorbidity has focused mainly on specific disease combinations, with little known about the sociodemographic factors associated with it. The study aimed to assess the factors associated with multimorbidity in England. METHODS: A cross-sectional study was conducted using the English Longitudinal Study of Ageing (ELSA), a dataset of people aged 50 years and older. The study identified ten long-term conditions from waves 2 to 9. Wave 2 to 9 were conducted between June 2004 to July 2005, May 2006 to August 2007, May 2008 to July 2009, June 2010 to July 2011, May 2012 to June 2013, June 2014 to May 2015, May 2016 to June 2017 and June 2018 to July 2019, respectively. The study included people with two or more long-term conditions. We identified the number of long-term conditions and multimorbidity, and we examined their association with age, gender, ethnicity, marital status, employment status, education, weekly contact with relative, and feeling lonely, sad or depressed using multinomial logistic regression. FINDINGS: Of 16 731 people recruited from wave 2 to wave 9, we identified 10 026 people with multimorbidity aged 50 years and older. The majority had two conditions (39%) and were female (55%), aged 50-69 years (32%), of white ethnicity (96%), married (69%) and unemployed (65·3%). The adjusted odds ratio (aOR) of having more than two long-term conditions increased with age, after adjusting for sex and ethnicity (≥5 conditions: aOR 12·89, 95% CI 2·23-3·76). Being female was associated with an increased risk of having more than two long-term conditions (≥5 conditions: aOR 1·21, 1·04-1·42). Similarly, being separated, divorced, or widowed were associated with having more than two long-term conditions (≥5 conditions: aOR 1·45, 1·21-1·74). Not owning a home was independently associated with more than two long-term conditions (≥5 conditions: aOR 1·59, 1·35-1·88). INTERPRETATION: The current analysis used only ten long-term conditions that were available in the ELSA data, so a different association might have arisen if other conditions had been considered. Our findings provide insights into which particular groups of the multimorbid population could be the target of preventive public health strategies and wider clinical and social care interventions in England to reduce the burden of multimorbidity. FUNDING: National Institute for Health and Care Research (NIHR).

Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange.

The narrow genetics of most crops is a fundamental vulnerability to food security. This makes wild crop relatives a strategic resource of genetic diversity that can be used for crop improvement and adaptation to new agricultural challenges. Here, we uncover the contribution of one wild species accession, Arachis cardenasii GKP 10017, to the peanut crop (Arachis hypogaea) that was initiated by complex hybridizations in the 1960s and propagated by international seed exchange. However, until this study, the global scale of the dispersal of genetic contributions from this wild accession had been obscured by the multiple germplasm transfers, breeding cycles, and unrecorded genetic mixing between lineages that had occurred over the years. By genetic analysis and pedigree research, we identified A. cardenasii-enhanced, disease-resistant cultivars in Africa, Asia, Oceania, and the Americas. These cultivars provide widespread improved food security and environmental and economic benefits. This study emphasizes the importance of wild species and collaborative networks of international expertise for crop improvement. However, it also highlights the consequences of the implementation of a patchwork of restrictive national laws and sea changes in attitudes regarding germplasm that followed in the wake of the Convention on Biological Diversity. Today, the botanical collections and multiple seed exchanges which enable benefits such as those revealed by this study are drastically reduced. The research reported here underscores the vital importance of ready access to germplasm in ensuring long-term world food security.

Implementing a text message-based intervention to support type 2 diabetes medication adherence in primary care: a qualitative study with general practice staff.

BACKGROUND: The Support through Mobile Messaging and digital health Technology for Diabetes (SuMMiT-D) project has developed, and is evaluating, a mobile phone-based intervention delivering brief messages targeting identified behaviour change techniques promoting medication use to people with type 2 diabetes in general practice. The present study aimed to inform refinement and future implementation of the SuMMiT-D intervention by investigating general practice staff perceptions of how a text message-based intervention to support medication adherence should be implemented within current and future diabetes care. METHODS: Seven focus groups and five interviews were conducted with 46 general practice staff (including GPs, nurses, healthcare assistants, receptionists and linked pharmacists) with a potential role in the implementation of a text message-based intervention for people with type 2 diabetes. Interviews and focus groups were audio-recorded, transcribed and analysed using an inductive thematic analysis approach. RESULTS: Five themes were developed. One theme 'The potential of technology as a patient ally' described a need for diabetes support and the potential of technology to support medication use. Two themes outlined challenges to implementation, 'Limited resources and assigning responsibility' and 'Treating the patient; more than diabetes medication adherence'. The final two themes described recommendations to support implementation, 'Selling the intervention: what do general practice staff need to see?' and 'Fitting the mould; complementing current service delivery'. CONCLUSIONS: Staff see the potential for a text message-based support intervention to address unmet needs and to enhance care for people with diabetes. Digital interventions, such as SuMMiT-D, need to be compatible with existing systems, demonstrate measurable benefits, be incentivised and be quick and easy for staff to engage with. Interventions also need to be perceived to address general practice priorities, such as taking a holistic approach to care and having multi-cultural reach and relevance. Findings from this study are being combined with parallel work with people with type 2 diabetes to ensure stakeholder views inform further refinement and implementation of the SuMMiT-D intervention.

Assessment of glycaemic status in adult hospital patients for the detection of undiagnosed diabetes mellitus: A systematic review.

AIM: In-hospital blood glucose testing is commonplace, particularly in acute care. In-hospital screening for hyperglycaemia may present a valuable opportunity for early diabetes diagnosis by identifying at-risk individuals. This systematic review investigates the extent to which random blood glucose testing in acute and inpatient hospital settings predicts undiagnosed diabetes. METHODS: Two databases were systematically searched for studies in which adult patients received an in-hospital random blood glucose test, followed by a diagnostic HbA1c test. The primary outcome was the proportion of hyperglycaemic individuals diagnosed with diabetes by HbA1c. RESULTS: A total of 3245 unique citations were identified, and 12 were eligible for inclusion. Ten different blood glucose thresholds, ranging from 5.5 to 11.1 mmol/L, were used to detect hyperglycaemia, indicating that there is no consistent clinical definition for hyperglycaemia. The proportion of participants with hyperglycaemia in each study ranged from 3.3% to 62.1%, with a median (Q1 , Q3 ) of 34.5% (5.95%, 61.1%). The proportion of hyperglycaemic participants found to have a diabetes-range HbA1c varied from 4.1% to 90%, with a median (Q1 , Q3 ) of 18.9% (11.5%, 61.1%). Meta-analysis was not possible due to substantial heterogeneity between study protocols. CONCLUSIONS: All studies consistently identified a proportion of hyperglycaemic hospital patients as having a diabetes-range HbA1c, showing that in-hospital blood glucose screening can facilitate diabetes diagnosis. The proportion of hyperglycaemic participants with undiagnosed diabetes varied substantially, indicating a need for further research and consistency in defining in-hospital hyperglycaemia. This may aid the development of a standardised screening protocol to identify people with possible undiagnosed diabetes.

The diagnostic accuracy of HbA1c , compared to the oral glucose tolerance test, for screening for type 2 diabetes mellitus in Africa-A systematic review and meta-analysis.

OBJECTIVE: To assess the diagnostic accuracy of glycated haemoglobin A1c (HbA1c ), compared to fasting plasma glucose (FPG) and the oral glucose tolerance test (OGTT), in screening for type 2 diabetes (T2D) in Africa. METHODS: We systematically searched databases for studies that compared the HbA1c to either the OGTT, or the FPG for T2D diagnosis were included. The QUADAS 2 tool was used for assessing the quality of included studies. We used the split component synthesis (SCS) method for the meta-analysis of diagnostic accuracy studies to pool the studies for meta-analysis of sensitivity and specificity, primarily at the HbA1c ≥48 mmol/mol (6.5%) cut-off and at other cut-offs. We assessed heterogeneity using the I2  statistic and publication bias using Doi plots. RESULTS: Eleven studies, from seven African countries, with 12,925 participants, were included. Against the OGTT, HbA1c ≥48 mmol/mol (6.5%) had a pooled sensitivity of 57.7% (95% confidence interval [CI] 43.4-70.9) and specificity of 92.3% (95% CI 83.9-96.5). Against the FPG, HbA1c ≥48 mmol/mol (6.5%) had a pooled sensitivity of 64.5% (95% CI 50.5-76.4) and specificity of 94.3% (95% CI 87.9-97.5). The highest sensitivity for HbA1c , against the OGTT, was at the 42 mmol/mol (6.0%) cut-off. CONCLUSION: In Africa, the HbA1c ≥48 mmol/mol (6.5%) cut-off may miss almost half of the individuals with T2D based on blood glucose measures.

The potential for utilising in-hospital glucose measurements to detect individuals at high risk of previously undiagnosed diabetes: Retrospective cohort study.

BACKGROUND: Many people with undiagnosed diabetes have hyperglycaemia when admitted to hospital. Inpatient hyperglycaemia can be an indication of diabetes mellitus but can also indicate a stress response. This study reports the extent to which an in-hospital maximum observed random glucose measurement is an indicator of the need for in-hospital (or subsequent) HbA1c measurement to look for undiagnosed diabetes. METHODS: Blood glucose, HbA1c, age and sex were collected for all adults following admission to a UK NHS trust hospital from 1 January 2019 to 31 December 2020. We restricted the analysis to those participants who were registered with a GP practice that uses the trust laboratory and who had at least some tests requested by those practices since 2008. We stratified individuals according to their maximum in-hospital glucose measurement and report the number of these with HbA1c measurement ≥48 mmol/mol (6.5%) prior to the index admission, and during and after admission. We calculated an estimated proportion of individuals in each blood glucose stratum without a follow-up HbA1c who could have undiagnosed diabetes. RESULTS: In toal, 764,241 glucose measurements were recorded for 81,763 individuals who were admitted to the Oxford University Hospitals Trust. The median (Q1, Q3) age was 70 (56, 81) years, and 53% were males. Of the population, 70.7% of individuals declared themselves to be of White ethnicity, 3.1% of Asian background, and 1.1% of Black background, with 23.1% unstated. Of those individuals, 22,375 (27.4%) had no previous HbA1c measurement recorded. A total of 1689 individuals had a diabetes-range HbA1c during or after their hospital admission (2.5%) while we estimate an additional 1496 (2.2%) may have undiagnosed diabetes, with the greatest proportion of these having an in-hospital glucose of ≥15 mmol/L. We estimate that the number needed to detect a possible new case of diabetes falls from 16 (in-hospital glucose 8 mmol/L to <9 mmol/L) to 4 (14 mmol/L to <15 mmol/L). CONCLUSION: The number of people who need to be tested to identify an individual who may have diabetes decreases as a testing threshold based on maximum in-hospital glucose concentration increases. Among those with hyperglycaemia and no previous HbA1c measurement in the diabetes range, there appears to be a lack of subsequent HbA1c measurement. This work identifies the potential for integrating the testing and follow-up of people, with apparently unrecognised hospital hyperglycaemia across primary and secondary care.

The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress.

BACKGROUND: Medicago ruthenica, a wild and perennial legume forage widely distributed in semi-arid grasslands, is distinguished by its outstanding tolerance to environmental stress. It is a close relative of commonly cultivated forage of alfalfa (Medicago sativa). The high tolerance of M. ruthenica to environmental stress makes this species a valuable genetic resource for understanding and improving traits associated with tolerance to harsh environments. RESULTS: We sequenced and assembled genome of M. ruthenica using an integrated approach, including PacBio, Illumina, 10×Genomics, and Hi-C. The assembled genome was 904.13 Mb with scaffold N50 of 99.39 Mb, and 50,162 protein-coding genes were annotated. Comparative genomics and transcriptomic analyses were used to elucidate mechanisms underlying its tolerance to environmental stress. The expanded FHY3/FAR1 family was identified to be involved in tolerance of M. ruthenica to drought stress. Many genes involved in tolerance to abiotic stress were retained in M. ruthenica compared to other cultivated Medicago species. Hundreds of candidate genes associated with drought tolerance were identified by analyzing variations in single nucleotide polymorphism using accessions of M. ruthenica with varying tolerance to drought. Transcriptomic data demonstrated the involvements of genes related to transcriptional regulation, stress response, and metabolic regulation in tolerance of M. ruthenica. CONCLUSIONS: We present a high-quality genome assembly and identification of drought-related genes in the wild species of M. ruthenica, providing a valuable resource for genomic studies on perennial legume forages.

Effects of Aspirin for Primary Prevention in Persons with Diabetes Mellitus.

BACKGROUND: Diabetes mellitus is associated with an increased risk of cardiovascular events. Aspirin use reduces the risk of occlusive vascular events but increases the risk of bleeding; the balance of benefits and hazards for the prevention of first cardiovascular events in patients with diabetes is unclear. METHODS: We randomly assigned adults who had diabetes but no evident cardiovascular disease to receive aspirin at a dose of 100 mg daily or matching placebo. The primary efficacy outcome was the first serious vascular event (i.e., myocardial infarction, stroke or transient ischemic attack, or death from any vascular cause, excluding any confirmed intracranial hemorrhage). The primary safety outcome was the first major bleeding event (i.e., intracranial hemorrhage, sight-threatening bleeding event in the eye, gastrointestinal bleeding, or other serious bleeding). Secondary outcomes included gastrointestinal tract cancer. RESULTS: A total of 15,480 participants underwent randomization. During a mean follow-up of 7.4 years, serious vascular events occurred in a significantly lower percentage of participants in the aspirin group than in the placebo group (658 participants [8.5%] vs. 743 [9.6%]; rate ratio, 0.88; 95% confidence interval [CI], 0.79 to 0.97; P=0.01). In contrast, major bleeding events occurred in 314 participants (4.1%) in the aspirin group, as compared with 245 (3.2%) in the placebo group (rate ratio, 1.29; 95% CI, 1.09 to 1.52; P=0.003), with most of the excess being gastrointestinal bleeding and other extracranial bleeding. There was no significant difference between the aspirin group and the placebo group in the incidence of gastrointestinal tract cancer (157 participants [2.0%] and 158 [2.0%], respectively) or all cancers (897 [11.6%] and 887 [11.5%]); long-term follow-up for these outcomes is planned. CONCLUSIONS: Aspirin use prevented serious vascular events in persons who had diabetes and no evident cardiovascular disease at trial entry, but it also caused major bleeding events. The absolute benefits were largely counterbalanced by the bleeding hazard. (Funded by the British Heart Foundation and others; ASCEND Current Controlled Trials number, ISRCTN60635500 ; ClinicalTrials.gov number, NCT00135226 .).

Effects of n-3 Fatty Acid Supplements in Diabetes Mellitus.

BACKGROUND: Increased intake of n-3 fatty acids has been associated with a reduced risk of cardiovascular disease in observational studies, but this finding has not been confirmed in randomized trials. It remains unclear whether n-3 (also called omega-3) fatty acid supplementation has cardiovascular benefit in patients with diabetes mellitus. METHODS: We randomly assigned 15,480 patients with diabetes but without evidence of atherosclerotic cardiovascular disease to receive 1-g capsules containing either n-3 fatty acids (fatty acid group) or matching placebo (olive oil) daily. The primary outcome was a first serious vascular event (i.e., nonfatal myocardial infarction or stroke, transient ischemic attack, or vascular death, excluding confirmed intracranial hemorrhage). The secondary outcome was a first serious vascular event or any arterial revascularization. RESULTS: During a mean follow-up of 7.4 years (adherence rate, 76%), a serious vascular event occurred in 689 patients (8.9%) in the fatty acid group and in 712 (9.2%) in the placebo group (rate ratio, 0.97; 95% confidence interval [CI], 0.87 to 1.08; P=0.55). The composite outcome of a serious vascular event or revascularization occurred in 882 patients (11.4%) and 887 patients (11.5%), respectively (rate ratio, 1.00; 95% CI, 0.91 to 1.09). Death from any cause occurred in 752 patients (9.7%) in the fatty acid group and in 788 (10.2%) in the placebo group (rate ratio, 0.95; 95% CI, 0.86 to 1.05). There were no significant between-group differences in the rates of nonfatal serious adverse events. CONCLUSIONS: Among patients with diabetes without evidence of cardiovascular disease, there was no significant difference in the risk of serious vascular events between those who were assigned to receive n-3 fatty acid supplementation and those who were assigned to receive placebo. (Funded by the British Heart Foundation and others; Current Controlled Trials number, ISRCTN60635500 ; ClinicalTrials.gov number, NCT00135226 .).

The early use of Antibiotics for at Risk CHildren with InfluEnza-like illness (ARCHIE): a double-blind randomised placebo-controlled trial.

INTRODUCTION: The UK government stockpiles co-amoxiclav to treat bacterial complications during influenza pandemics. This pragmatic trial examines whether early co-amoxiclav use reduces reconsultation due to clinical deterioration in "at risk" children presenting with influenza-like illness (ILI) in primary or ambulatory care. METHODS: "At risk" children aged from 6 months to 12 years presenting within 5 days of ILI onset were randomly assigned to oral co-amoxiclav 400/57 or a placebo twice daily for 5 days (dosing based on age±weight). "At risk" groups included children with respiratory, cardiac and neurological conditions. Randomisation was stratified by region and used a non-deterministic minimisation algorithm to balance age and current seasonal influenza vaccination status. Our target sample size was 650 children which would have allowed us to detect a reduction in the proportion of children reconsulting due to clinical deterioration from 40% to 26%, with 90% power and 5% two-tailed alpha error (including allowance for 25% loss to follow-up and an inflation factor of 1.041). Participants, caregivers and investigators were blinded to treatment allocation. Intention-to-treat analysis included all randomised participants with primary outcome data on reconsultation due to clinical deterioration within 28 days. Safety analysis included all randomised participants. TRIAL REGISTRATION: ISRCTN 70714783. EudraCT 2013-002822-21. RESULTS: We recruited 271 children between February 11, 2015 and April 20, 2018. Primary outcome data were available for 265 children. Only 61 out of 265 children (23.0%) reconsulted due to clinical deterioration. No evidence of a treatment effect was observed for reconsultation due to clinical deterioration (33 out of 133 for co-amoxiclav (24.8%) and 28 out of 132 (21.2%) for placebo; adjusted risk ratio (RR) 1.16, 95% confidence interval (CI) 0.75-1.80). There was also no evidence of a difference between groups in the proportion of children for whom one or more adverse events (AEs) were reported (32 out of 136 (23.5%) for co-amoxiclav and 22 out of 135 (16.3%) for placebo; adjusted RR 1.45, 95% CI 0.90-2.34). In total, 66 AEs were reported (co-amoxiclav, n=37; placebo, n=29). Nine serious AEs were reported per group, although none were considered related to study medication. CONCLUSION: Our trial did not find evidence that treatment with co-amoxiclav reduces risk of reconsultation due to clinical deterioration in "at risk" children who present early with ILI during influenza season. Our findings therefore do not support early co-amoxiclav use in children with seasonal ILI.

Intervention development of a brief messaging intervention for a randomised controlled trial to improve diabetes treatment adherence in sub-Saharan Africa.

BACKGROUND: Brief messaging interventions, including Short Message Service (SMS) text-messages, delivered via mobile device platforms, show promise to support and improve treatment adherence. To understand how these interventions work, and to facilitate transparency, we need clear descriptions of the intervention development process. METHOD: We describe and reflect on the process of designing and pretesting an evidence- and theory-informed brief messaging intervention, to improve diabetes treatment adherence in sub-Saharan Africa. We followed the stepwise approach recommended by the Medical Research Council, United Kingdom (MRC UK) Framework for Development and Evaluation of Complex Health Interventions and guidance for mobile health intervention development. RESULTS: We used a four-phase, iterative approach that first generated primary and secondary evidence on the lived experience of diabetes, diabetes treatment services and mobile-phone use. Second, we designed a type 2 diabetes-specific, brief text-message library, building on our previous hypertension text-message library, as well as drawing on the primary and secondary data from phase one, and on expert opinion. We then mapped the brief text-messages onto behaviour change (COM-B) theoretical constructs. Third, we refined and finalised the newly developed brief text-message library through stakeholder consultation and translated it into three local languages. Finally, we piloted the intervention by pre-testing the automated delivery of the brief text-messages in the trial sites in Malawi and South Africa. The final SMS text Adherence suppoRt for people with type 2 diabetes (StAR2D) intervention was tested in a randomised controlled trial in Malawi and South Africa (trial registration: ISRCTN70768808 ). CONCLUSION: The complexity of public health interventions requires that we give more attention to intervention development work. Our documentation and reflection on the StAR2D intervention development process promotes transparency, replicability, assessment of intervention quality, and comparison with other studies.

Understanding acceptability in the context of text messages to encourage medication adherence in people with type 2 diabetes.

BACKGROUND: Acceptability is recognised as a key concept in the development of health interventions, but there has been a lack of consensus about how acceptability should be conceptualised. The theoretical framework of acceptability (TFA) provides a potential tool for understanding acceptability. It has been proposed that acceptability measured before use of an intervention (anticipated acceptability) may differ from measures taken during and after use (experienced acceptability), but thus far this distinction has not been tested for a specific intervention. This paper 1) directly compares ratings of anticipated and experienced acceptability of a text message-based intervention, 2) explores the applicability of the TFA in a technology-based intervention, and 3) uses these findings to inform suggestions for measuring acceptability over the lifespan of technology-based health interventions. METHODS: Data were obtained from a quantitative online survey assessing anticipated acceptability of the proposed text messages (n = 59) and a 12-week proof-of-concept mixed methods study assessing experienced acceptability while receiving the text messages (n = 48). Both quantitative ratings by return text message, and qualitative data from participant interviews were collected during the proof-of-concept study. RESULTS: The quantitative analysis showed anticipated and experienced acceptability were significantly positively correlated (rs > .4). The qualitative analysis identified four of the seven constructs of the TFA as themes (burden, intervention coherence, affective attitude and perceived effectiveness). An additional two themes were identified as having an important impact on the TFA constructs (perceptions of appropriateness and participants' role). Three suggestions are given related to the importance of appropriateness, what may affect ratings of acceptability and what to consider when measuring acceptability. CONCLUSIONS: The high correlation between anticipated and experienced acceptability was a surprising finding and could indicate that, in some cases, acceptability of an intervention can be gauged adequately from an anticipated acceptability study, prior to an expensive pilot or feasibility study. Directly exploring perceptions of appropriateness and understanding whether the acceptability described by participants is related to the intervention or the research - and is for themselves or others - is important in interpreting the results and using them to further develop interventions and predict future use.

The genome of cowpea (Vigna unguiculata [L.] Walp.).

Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.

Identifying routine clinical predictors of non-adherence to second-line therapies in type 2 diabetes: A retrospective cohort analysis in a large primary care database.

AIMS: To investigate whether combinations of routinely available clinical features can predict which patients are likely to be non-adherent to diabetes medication. MATERIALS AND METHODS: A total of 67 882 patients with prescription records for their first and second oral glucose-lowering therapies were identified from electronic healthcare records (Clinical Practice Research Datalink). Non-adherence was defined as a medical possession ratio (MPR) ≤80%. Potential predictors were examined, including age at diagnosis, sex, body mass index, duration of diabetes, glycated haemoglobin, Charlson index and other recent prescriptions. RESULTS: Routine clinical features were poor at predicting non-adherence to the first diabetes therapy (c-statistic = 0.601 for all in combined model). Non-adherence to the second drug was better predicted for all combined factors (c-statistic =0.715) but this improvement was predominantly a result of including adherence to the first drug (c-statistic =0.695 for this alone). Patients with an MPR ≤80% for their first drug were 3.6 times (95% confidence interval 3.3,3.8) more likely to be non-adherent to their second drug (32% vs. 9%). CONCLUSIONS: Although certain clinical features were associated with poor adherence, their performance for predicting who is likely to be non-adherent, even when combined, was weak. The strongest predictor of adherence to second-line therapy was adherence to the first therapy. Examining previous prescription records could offer a practical way for clinicians to identify potentially non-adherent patients and is an area warranting further research.

Economic Evaluation of Factorial Trials: Cost-Utility Analysis of the Atorvastatin in Factorial With Omega EE90 Risk Reduction in Diabetes 2 × 2 × 2 Factorial Trial of Atorvastatin, Omega-3 Fish Oil, and Action Planning.

OBJECTIVES: We applied principles for conducting economic evaluations of factorial trials to a trial-based economic evaluation of a cluster-randomized 2 × 2 × 2 factorial trial. We assessed the cost-effectiveness of atorvastatin, omega-3 fish oil, and an action-planning leaflet, alone and in combination, from a UK National Health Service perspective. METHODS: The Atorvastatin in Factorial With Omega EE90 Risk Reduction in Diabetes (AFORRD) Trial randomized 800 patients with type 2 diabetes to atorvastatin, omega-3, or their respective placebos and randomized general practices to receive a leaflet-based action-planning intervention designed to improve compliance or standard care. The trial was conducted at 59 UK general practices. Sixteen-week outcomes for each trial participant were extrapolated for 70 years using the United Kingdom Prospective Diabetes Study Outcomes Model v2.01. We analyzed the trial as a 2 × 2 factorial trial (ignoring interactions between action-planning leaflet and medication), as a 2 × 2 × 2 factorial trial (considering all interactions), and ignoring all interactions. RESULTS: We observed several qualitative interactions for costs and quality-adjusted life-years (QALYs) that changed treatment rankings. However, different approaches to analyzing the factorial design did not change the conclusions. There was a ≥99% chance that atorvastatin is cost-effective and omega-3 is not, at a £20 000/QALY threshold. CONCLUSIONS: Atorvastatin monotherapy was the most cost-effective combination of the 3 trial interventions at a £20 000/QALY threshold. Omega-3 fish oil was not cost-effective, while there was insufficient evidence to draw firm conclusions about action planning. Recently-developed methods for analyzing factorial trials and combining parameter and sampling uncertainty were extended to estimate cost-effectiveness acceptability curves within a 2x2x2 factorial design with model-based extrapolation.