Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Genetic Assimilation and Canalisation in the Baldwin Effect

The Baldwin Effect indicates that individually learned behaviours acquired during an organism’s lifetime can influence the evolutionary path taken by a population, without any direct Lamarckian transfer of traits from phenotype to genotype. Several computational studies modelling this effect have included complications that restrict its applicability. Here we present a simplified model that is used to reveal the essential mechanisms and highlight several conceptual issues that have not been clearly defined in prior literature. In particular, we suggest that canalisation and genetic assimilation, often conflated in previous studies, are separate concepts and the former is actually not required for non-heritable phenotypic variation to guide genetic variation. Additionally, learning, often considered to be essential for the Baldwin Effect, can be replaced with a more general phenotypic plasticity model. These simplifications potentially permit the Baldwin Effect to operate in much more general circumstances

Health literacy levels of British adults: a cross-sectional survey using two domains of the Health Literacy Questionnaire (HLQ)

Background A person’s health literacy determines whether they are able to make appropriate health decisions and are able to follow treatment instructions. This is important because low health literacy is associated with mortality and extra costs to the healthcare system. Our aim was to describe the health literacy levels of British adults using a nationally representative population survey, and show how health literacy levels vary by population characteristics. Methods A population based cross-sectional survey including questions from two domains from the Health Literacy Questionnaire™: 1) Understanding health information well enough to know what to do, and 2) Ability to actively engage with health care providers. Both domains are made up of 5 Likert style questions with 5 levels ranging from ‘cannot do or always difficult’ (1) to ‘always easy’ (5). The survey was conducted by NatCen in Britain (2018) as part of the annual British Social Attitudes survey. We used weighted descriptive analyses and regression to explore the relationship between population characteristics and health literacy. Weighted analyses were used to ensure the sample was representative of the British population. Results A total of 2309 responded to the questionnaire. The mean score for ‘understanding information’ was 3.98 (95% CI: 3.94, 4.02) and for ‘ability to engage’ was 3.83 (95% CI: 3.80, 3.87), where 5 is the highest score. 19.4% had some level of difficulty reading and understanding written health information, and 23.2% discussing health concerns with health care providers. The adjusted logistic regression for ‘understanding information’ showed that those with lower health literacy were more likely to be in the most socially deprived quintile (OR 2.500 95% CI: 1.180, 5.296), have a limiting health condition or disability (OR 4.326 95% CI: 2.494, 7.704), and have no educational qualifications (OR 7.588 95% CI: 3.305, 17.422). This was similar for the ‘ability to engage’ domain. Conclusions This study described the distribution of health literacy levels for the British population in 2018. Interventions to improve health literacy will best be targeted at those with lower levels of education, those living in the most deprived areas, and those with a limiting health condition or disability

On the maximal sum of exponents of runs in a string

A run is an inclusion maximal occurrence in a string (as a subinterval) of a repetition $v$ with a period $p$ such that $2p \le |v|$. The exponent of a run is defined as $|v|/p$ and is $\ge 2$. We show new bounds on the maximal sum of exponents of runs in a string of length $n$. Our upper bound of $4.1n$ is better than the best previously known proven bound of $5.6n$ by Crochemore & Ilie (2008). The lower bound of $2.035n$, obtained using a family of binary words, contradicts the conjecture of Kolpakov & Kucherov (1999) that the maximal sum of exponents of runs in a string of length $n$ is smaller than $2n$Comment: 7 pages, 1 figur

Non-urgent emergency department attendances in children : a retrospective observational analysis

Introduction: A significant proportion of ED attendances in children may be non-urgent attendances (NUAs), which could be better managed elsewhere. This study aimed to quantify NUAs and urgent attendances (UAs) in children to ED and determine which children present in this way and when. Methods: Dataset extracted from the CUREd research database containing linked data on the provision of care in Yorkshire and Humber. Analysis focused on children’s ED attendances (April 2014–March 2017). Summary statistics and odds ratios (OR) comparing NUAs and UAs were examined by: age, mode and time of arrival and deprivation alongside comparing summary statistics for waiting, treatment and total department times. Results: NUAs were more likely in younger children: OR for NUA in children aged 1–4 years, 0.82 (95% CI: 0.80 to 0.83), age 15 years, 0.39 (95% CI: 0.38 to 0.40), when compared with those under 1 year. NUAs were more likely to arrive out of hours (OOHs) compared with in hours: OR 1.19 (95% CI 1.18 to 1.20), and OOHs arrivals were less common in older children compared with those under 1 year: age 1–4 years, 0.87 (95% CI: 0.84 to 0.89) age 15 years, 0.66 (95% CI: 0.63 to 0.69). NUAs also spent less total time in the ED, with a median (IQR) of 98 min (60–147) compared with 127 min (80–185) for UAs. Conclusion: A substantial proportion of ED attendances in children are NUAs. Our data suggest there are particular groups of children for whom targeted interventions would be most beneficial. Children under 5 years would be such a group, particularly in providing accessible, timely care outside of usual community care opening hours

Recruitment, consent and retention of participants in randomised controlled trials : a review of trials published in the National Institute for Health Research (NIHR) Journals Library (1997–2020)

Objectives To review the consent, recruitment and retention rates for randomised controlled trials (RCTs) funded by the UK’s National Institute for Health Research (NIHR) and published in the online NIHR Journals Library between January 1997 and December 2020. Design Comprehensive review. Setting RCTs funded by the NIHR and published in the NIHR Journals Library. Data extraction Information relating to the trial characteristics, sample size, recruitment and retention. Primary and secondary outcome measures The primary outcome was the recruitment rate (number of participants recruited per centre per month). Secondary outcomes were the target sample size and whether it was achieved; consent rates (percentage of eligible participants who consented and were randomised) and retention rates (percentage of randomised participants retained and assessed with valid primary outcome data). Results This review identified 388 individual RCTs from 379 reports in the NIHR Journals Library. The final recruitment target sample size was achieved in 63% (245/388) of the RCTs. The original recruitment target was revised in 30% (118/388) of trials (downwards in 67% (79/118)). The median recruitment rate (participants per centre per month) was found to be 0.95 (IQR: 0.42–2.60); the median consent rate was 72% (IQR: 50%–88%) and the median retention rate was estimated at 88% (IQR: 80%–97%). Conclusions There is considerable variation in the consent, recruitment and retention rates in publicly funded RCTs. Although the majority of (6 out of 10) trials in this review achieved their final target sample; 3 out of 10 trials revised their original target sample size (downwards in 7 out of 10 trials). Investigators should bear this in mind at the planning stage of their study and not be overly optimistic about their recruitment projections

Pretreatment with beta-blockers and the frequency of hypokalemia in patients with acute chest pain

Plasma potassium concentration was measured at admission in 1234 patients who presented with acute chest pain. One hundred and ninety five patients were on P blockers before admission. The potassium concentrations of patients admitted early (within four hours of onsetof symptoms) were compared with those admitted later (4-18 hours after onset of symptoms). There was a transient fall in plasma potassium concentrations in patients not pre-treated with , B blockers. This was not seen in patients who had been on P blockers before admission. Nonselective, B blockers were more effective than cardioselective agents in maintaining concentrationsof plasma potassium. These findings suggest a mechanism for the beneficial effects of ,B blockers on morbidity and mortality in acute myocardial infarction

Open-label, cluster randomised controlled trial and economic evaluation of a brief letter from a GP on unscheduled medical contacts associated with the start of the school year: the PLEASANT trial

BACKGROUND: Asthma is seasonal with peaks in exacerbation rates in school-age children associated with the return to school following the summer vacation. A drop in prescription collection in August is associated with an increase in the number of unscheduled contacts after the school return. OBJECTIVE: To assess whether a public health intervention delivered in general practice reduced unscheduled medical contacts in children with asthma. DESIGN: Cluster randomised trial with trial-based economic evaluation. Randomisation was at general practice level, stratified by size of practice. The intervention group received a letter from their general practitioner (GP) in late July outlining the importance of (re)taking asthma medication before the return to school. The control group was usual care. SETTING: General practices in England and Wales. PARTICIPANTS: 12 179 school-age children in 142 general practices (70 randomised to intervention). MAIN OUTCOME: Proportion of children aged 5-16 years who had an unscheduled contact in September. Secondary endpoints included collection of prescriptions in August and medical contacts over 12 months (September-August). Economic endpoints were quality-adjusted life-years gained and health service costs. RESULTS: There was no evidence of effect (OR 1.09; 95% CI 0.96 to 1.25 against treatment) on unscheduled contacts in September. The intervention increased the proportion of children collecting a prescription in August by 4% (OR 1.43; 95% CI 1.24 to 1.64). The intervention also reduced the total number of medical contacts between September-August by 5% (incidence ratio 0.95; 95% CI 0.91 to 0.99).The mean reduction in medical contacts informed the health economics analyses. The intervention was estimated to save £36.07 per patient, with a high probability (96.3%) of being cost-saving. CONCLUSIONS: The intervention succeeded in increasing children collecting prescriptions. It did not reduce unscheduled care in September (the primary outcome), but in the year following the intervention, it reduced the total number of medical contacts. TRIAL REGISTRATION NUMBER: ISRCTN03000938; Results

Enzymatic activities and functional interdependencies of Bacillus subtilis lipoteichoic acid synthesis enzymes

Lipoteichoic acid (LTA) is an important cell wall polymer in Gram-positive bacteria. The enzyme responsible for polyglycerolphosphate LTA synthesis is LtaS, first described in Staphylococcus aureus. Four LtaS orthologues, LtaSBS, YfnI, YqgS and YvgJ, are present in Bacillus subtilis. Using an in vitro enzyme assay, we determined that all four proteins are Mn2+-dependent metal enzymes that use phosphatidylglycerol as a substrate. We show that LtaSBS, YfnI and YqgS can produce polymers, suggesting that these three proteins are bona-fide LTA synthases while YvgJ functions as an LTA primase, as indicated by the accumulation of a GroP-Glc2-DAG glycolipid. Western blot analysis of LTA produced by ltaSBS, yfnI, yqgS and yvgJ single, triple and the quadruple mutant, showed that LTA production was only abolished in the quadruple and the YvgJ-only expressing mutant. B. subtilis strains expressing YfnI in the absence of LtaSBS produced LTA of retarded mobility, presumably caused by an increase in chain length as suggested by a structural analysis of purified LTA. Taken together, the presented results indicate that the mere presence or absence of LTA cannot account for cell division and sporulation defects observed in the absence of individual enzymes and revealed an unexpected enzymatic interdependency of LtaS-type proteins in B. subtilis