Precise detection of rearrangement breakpoints in mammalian chromosomes

<p>Abstract</p> <p>Background</p> <p>Genomes undergo large structural changes that alter their organisation. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. We developed a method to precisely delimit rearrangement breakpoints on a genome by comparison with the genome of a related species. Contrary to current methods which search for synteny blocks and simply return what remains in the genome as breakpoints, we propose to go further and to investigate the breakpoints themselves in order to refine them.</p> <p>Results</p> <p>Given some reliable and non overlapping synteny blocks, the core of the method consists in refining the regions that are not contained in them. By aligning each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Since this method requires as input synteny blocks with some properties which, though they appear natural, are not verified by current methods for detecting such blocks, we further give a formal definition and provide an algorithm to compute them.</p> <p>The whole method is applied to delimit breakpoints on the human genome when compared to the mouse and dog genomes. Among the 355 human-mouse and 240 human-dog breakpoints, 168 and 146 respectively span less than 50 Kb. We compared the resulting breakpoints with some publicly available ones and show that we achieve a better resolution. Furthermore, we suggest that breakpoints are rarely reduced to a point, and instead consist in often large regions that can be distinguished from the sequences around in terms of segmental duplications, similarity with related species, and transposable elements.</p> <p>Conclusion</p> <p>Our method leads to smaller breakpoints than already published ones and allows for a better description of their internal structure. In the majority of cases, our refined regions of breakpoint exhibit specific biological properties (no similarity, presence of segmental duplications and of transposable elements). We hope that this new result may provide some insight into the mechanism and evolutionary properties of chromosomal rearrangements.</p

Differences in Brain Function and Changes with Intervention in Children with Poor Spelling and Reading Abilities

Previous fMRI studies in English-speaking samples suggested that specific interventions may alter brain function in language-relevant networks in children with reading and spelling difficulties, but this research strongly focused on reading impaired individuals. Only few studies so far investigated characteristics of brain activation associated with poor spelling ability and whether a specific spelling intervention may also be associated with distinct changes in brain activity patterns. We here investigated such effects of a morpheme-based spelling intervention on brain function in 20 children with comparatively poor spelling and reading abilities using repeated fMRI. Relative to 10 matched controls, children with comparatively poor spelling and reading abilities showed increased activation in frontal medial and right hemispheric regions and decreased activation in left occipito-temporal regions prior to the intervention, during processing of a lexical decision task. After five weeks of intervention, spelling and reading comprehension significantly improved in the training group, along with increased activation in the left temporal, parahippocampal and hippocampal regions. Conversely, the waiting group showed increases in right posterior regions. Our findings could indicate an increased left temporal activation associated with the recollection of the new learnt morpheme-based strategy related to successful training

The @RISK Study: Risk communication for patients with type 2 diabetes: design of a randomised controlled trial

<p>Abstract</p> <p>Background</p> <p>Patients with type 2 diabetes mellitus (T2DM) have an increased risk to develop severe diabetes related complications, especially cardiovascular disease (CVD). The risk to develop CVD can be estimated by means of risk formulas. However, patients have difficulties to understand the outcomes of these formulas. As a result, they may not recognize the importance of changing lifestyle and taking medication in time. Therefore, it is important to develop risk communication methods, that will improve the patients' understanding of risks associated with having diabetes, which enables them to make informed choices about their diabetes care.</p> <p>The aim of this study is to investigate the effects of an intervention focussed on the communication of the absolute 10-year risk to develop CVD on risk perception, attitude and intention to change lifestyle behaviour in patients with T2DM. The conceptual framework of the intervention is based on the Theory of Planned Behaviour and the Self-regulation Theory.</p> <p>Methods</p> <p>A randomised controlled trial will be performed in the Diabetes Care System West-Friesland (DCS), a managed care system. Newly referred T2DM patients of the DCS, younger than 75 years will be eligible for the study. The intervention group will be exposed to risk communication on CVD, on top of standard managed care of the DCS. This intervention consists of a simple explanation on the causes and consequences of CVD, and possibilities for prevention. The probabilities of CVD in 10 year will be explained in natural frequencies and visualised by a population diagram. The control group will receive standard managed care. The primary outcome is appropriateness of risk perception. Secondary outcomes are attitude and intention to change lifestyle behaviour and illness perception. Differences between baseline and follow-up (2 and 12 weeks) between groups will be analysed according to the intention-to-treat principle. The study was powered on 120 patients in each group.</p> <p>Discussion</p> <p>This innovative risk communication method based on two behavioural theories might improve patient's appropriateness of risk perception and attitude concerning lifestyle change. With a better understanding of their CVD risk, patients will be able to make informed choices concerning diabetes care.</p> <p>Trail registration</p> <p>The trial is registered as NTR1556 in the Dutch Trial Register.</p

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome

Effects of feeding low protein diets to piglets on plasma urea nitrogen, faecal ammonia nitrogen, the incidence of diarrhoea and performance after weaning

This study evaluated the effects of feeding pigs low protein (LP) diets for different lengths of time after weaning on indices of protein fermentation, the incidence of post-weaning diarrhoea (PWD), growth performance, and total-tract apparent digestibility. Sixty weaner pigs weighing 6.1 ± 0.13 kg (mean ± SEM) were used in a completely randomised design having five treatments: (i) a high protein diet (HP, 243 g/kg CP) fed for 14 d after weaning (HP14); (ii) a low protein diet (LP, 173 g CP/kg) fed for 5 d after weaning (LP5); (iii) LP diet fed for 7 d after weaning (LP7); (iv) LP diet fed for 10 d after weaning (LP10), and (v) LP diet fed for 14 d after weaning (LP14). All diets were supplemented with lysine, methionine, tryptophan and threonine, with all LP diets additionally fortified with crystalline isoleucine and valine to conform to a proposed ideal amino acid (AA) pattern. A second-stage diet (215 g CP/kg) was fed to pigs at the conclusion of each treatment. None of the diets contained antimicrobial compounds. Feeding a LP diet, regardless of duration of feeding, decreased plasma urea nitrogen (p \u3c 0.001) and faecal ammonia-nitrogen (p \u3c 0.001) contents. Feeding a LP diet, irrespective of feeding duration, decreased the incidence of PWD at day 8 after weaning (p = 0.044), and pigs fed diets LP7, LP10 and LP14 had firmer faeces (p = 0.030, p = 0.047 and p = 0.007, respectively) between days 10 and 12 after weaning. Treatments LP5, LP7, LP10 and LP14 did not reduce (p \u3e 0.05) growth performance up to 106 days after weaning compared to pigs fed the HP diet. Total-tract apparent digestibility of dry matter, energy and crude protein were similar (p \u3e 0.05) between treatments. Our data suggest that feeding a LP diet, supplemented with AA to conform to an ideal AA pattern, for 7–10 days after weaning can reduce PWD in pigs fed antibiotic-free diets without compromising production

Piglet growth before and after weaning in relation to a qualitative estimate of solid (creep) feed intake during lactation: A pilot study

The experimental objectives were to verify whether a qualitative measure of creep feed consumption using a dye was related to performance, and associate this with teat order. Indigo carmine (5 g/kg) was added to a starter diet between days 12 and 31 (weaning) of lactation. On days 19, 23, 27 and 31, faeces from each piglet were assessed for colouration. Each piglet was categorized as a ‘good’, ‘moderate’ or ‘small/non’ eater of feed. There were no differences in pre-weaning growth rate between categories. Piglets classed as ‘good’ or ‘moderate’ eaters in lactation grew fastest (p = 0.009) in the first three days after weaning, but between days 4 and 7, the highest growth rate occurred in ‘moderate’ eaters. ‘Small/non\u27 eaters grew slower (p \u3c 0.01) between weaning and 28 days after weaning. Piglets drinking milk from anterior teats were heavier at weaning (p \u3c 0.001) and for the first 14 days after weaning (p = 0.104) compared to piglets sucking posterior teats. Data from this study demonstrated that creep feed intake of piglets could qualitatively be assessed using indigo carmine, and that this categorization was related to performance in the immediate post-weaning period

Using network properties to predict disease dynamics on human contact networks

Recent studies have increasingly turned to graph theory to model more realistic contact structures that characterize disease spread. Because of the computational demands of these methods, many researchers have sought to use measures of network structure to modify analytically tractable differential equation models. Several of these studies have focused on the degree distribution of the contact network as the basis for their modifications. We show that although degree distribution is sufficient to predict disease behaviour on very sparse or very dense human contact networks, for intermediate density networks we must include information on clustering and path length to accurately predict disease behaviour. Using these three metrics, we were able to explain more than 98 per cent of the variation in endemic disease levels in our stochastic simulations