Safely Filling Gaps with Partial Solutions Common to All Solutions

Gap filling has emerged as a natural sub-problem of many de novo genome assembly projects. The gap filling problem generally asks for an s-t path in an assembly graph whose length matches the gap length estimate. Several methods have addressed it, but only few have focused on strategies for dealing with multiple gap filling solutions and for guaranteeing reliable results. Such strategies include reporting only unique solutions, or exhaustively enumerating all filling solutions and heuristically creating their consensus. Our main contribution is a new method for reliable gap filling: filling gaps with those sub-paths common to all gap filling solutions. We call these partial solutions safe, following the framework of (Tomescu and Medvedev, RECOMB 2016). We give an efficient safe algorithm running in O(dm) time and space, where d is the gap length estimate and m is the number of edges of the assembly graph. To show the benefits of this method, we implemented this algorithm for the problem of filling gaps in scaffolds. Our experimental results on bacterial and on conservative human assemblies show that, on average, our method can retrieve over 73 percent more safe and correct bases as compared to previous methods, with a similar precision.Peer reviewe

Pianonsoiton alkeet alakoulussa:luokanopettaja ryhmäsoittoa mahdollistamassa

Tiivistelmä. Tutkielman tavoite on perehtyä luokanopettajan mahdollisuuksiin pianonsoiton alkeiden hyödyntämisestä peruskoulun musiikintunneilla. Tutkielmassani selvitän siis sitä, mitä pianonsoiton alkeet pitävät sisällään, kuinka luokanopettaja voi toteuttaa niiden opettamista peruskoulun musiikintunneilla ja mitä laajempia hyötyjä tästä voi olla oppilaalle muuhunkin koulunkäyntiin liittyen. Piano instrumenttina on visuaalisesti selkeä väline musiikinteorian esittämiseen ja sen harjoittaminen kehittää molempien käsien hienomotorisia taitoja. Piano löytyy valmiiksi useista kodeista ja sen perusteiden hallinnasta voi olla iloa koko elämän ajan. Tutkimusmenetelmä on systemaattinen kirjallisuuskatsaus. Olen perehtynyt aiheeseen liittyvään kirjallisuuteen ja pyrkinyt esittämään löydettyjä tutkimuksia ja havaintoja tiivistetyssä muodossa. Tutkielmassani pyrin luomaan yhteyksiä tutkimusten välille ja vetämään johtopäätöksiä siitä, onko luokanopettajan mahdollista hyödyntää pianonsoiton ryhmäopetuksen menetelmiä työssään ja miksi sitä ylipäätään kannattaisi toteuttaa peruskoulussa. Luokanopettajakoulutuksesta valmistuneella on pätevyys opettaa musiikkia peruskoulussa, mutta tutkimukset osoittavat halukkuuden musiikintuntien pitämiseen olevan nihkeää. Tutkimuksellani haluan korostaa musiikin opettamisen merkitystä ja antaa perustellun idean musiikintuntien sisältöön. Pianonsoitolla on luokanopettajan roolissa pitkät perinteet ja olisikin sääli, jos tämä taito kuihtuisi hiljalleen olemattomiin. Esittelemällä instrumentin hallinnan perusteita alakoulussa voidaan herättää kipinä soitinta kohtaan tuleville sukupolville ja näin turvata sen säilyminen yhtenä soitetuimmista instrumenteista

Gap Filling as Exact Path Length Problem

Peer reviewe

Developmental trajectories of emotional disengagement from schoolwork and their longitudinal associations in England

This study identified the varied ways in which emotional disengagement from schoolwork typically developed between 14 and 16 years of age, in the Longitudinal Study of Young People in England. Using growth mixture modelling we found eight main trajectories of (dis)engagement, with four trajectories of either increasing or stable emotional disengagement with schoolwork (41% of the sample). Using propensity score matching to create groups balanced on a wide range of covariates at Wave 1, we compared disengaged students to their engaged counterparts to identify the longitudinal effects of disengagement-trajectory membership on behavioural engagement, psychological wellbeing, substance use, career pathways and achievement. Using linear and binary logistic regressions, we established that students in disengagement trajectories developed lower achievement across compulsory secondary school, and participated less in education and more in employment at age 17 years. In young adulthood (age 19–20 years) they were less likely to attend university and more likely to be unemployed. During secondary schooling, they developed higher levels of substance use and poorer psychological wellbeing, which persisted in the year after compulsory school. However, in young adulthood, the differences in substance use dissipated and students in most of the disengagement trajectories had relatively similar life satisfaction to their counterparts. These findings suggest that students (except perhaps those who became unemployed) were able to develop healthily and happily after leaving the schoolwork environments from which they were emotionally disengaged

Adolescent survey non-response and later risk of death. A prospective cohort study of 78 609 persons with 11-year follow-up

<p>Abstract</p> <p>Background</p> <p>Non-response in survey studies is a growing problem and, being usually selective, it leads to under- or overestimation of health outcomes in the follow-up. We followed both respondents and non-respondents by registry linkage to determine whether there is a risk of death, related to non-response at baseline.</p> <p>Methods</p> <p>Sample data of biennial surveys to 12-18-year-old Finns in 1979–1997 were linked with national death registry up to 2001. The number of respondents was 62 528 (79.6%) and non-respondents 16 081 (20.4%). The average follow-up was 11.1 years, totalling 876 400 person-years. The risk of death between non-respondents and respondents was estimated by hazard ratios (HR).</p> <p>Results</p> <p>The number of deaths per 100 000 person-years were 229 in non-respondents and 447 in respondents (HR 2.0, 95% CI: 1.5–2.6). The hazard ratios of death were for intoxication 3.2 (95% CI: 1.9–5.4), for disease 3.1 (95% CI: 2.2–4.1), for violence-related injury 2.0 (95% CI: 1.5–2.6) and for unintentional injury 1.8 (95% CI: 1.3–2.4) in non-respondents vs. respondents. The association between non-response and death increased with age at baseline, and the increase persisted after the age of 25.</p> <p>Conclusion</p> <p>Our study demonstrated significantly increased rates of death among adolescent non-respondents in a follow-up. The highest hazard ratios were seen in disease- and violence-related deaths. The death rate varied between respondents and non-respondents by death type. Increased rates of death persisted beyond the age of 25.</p

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

During the last few years, DNA and RNA sequencing have started to play an increasingly important role in biological and medical applications, especially due to the greater amount of sequencing data yielded from the new sequencing machines and the enormous decrease in sequencing costs. Particularly, Illumina/Solexa sequencing has had an increasing impact on gathering data from model and non-model organisms. However, accurate and easy to use tools for quality filtering have not yet been established. We present ConDeTri, a method for content dependent read trimming for next generation sequencing data using quality scores of each individual base. The main focus of the method is to remove sequencing errors from reads so that sequencing reads can be standardized. Another aspect of the method is to incorporate read trimming in next-generation sequencing data processing and analysis pipelines. It can process single-end and paired-end sequence data of arbitrary length and it is independent from sequencing coverage and user interaction. ConDeTri is able to trim and remove reads with low quality scores to save computational time and memory usage during de novo assemblies. Low coverage or large genome sequencing projects will especially gain from trimming reads. The method can easily be incorporated into preprocessing and analysis pipelines for Illumina data

Bricoleurs Extraordinaire: Sports Coaches in Inter War Britain

In Inter War Britain, individuals exploited their athletic skills by pursuing professional careers, or adopting amateur roles, as instructors, trainers and coaches, invariably drawing from, and elaborating on, existing practices. The coach was the master of a body of specialist craft knowledge, the tacit nature of which was transmitted through ‘stealing with the eyes’ as the apprentice watched the master in action (Gamble, 2001). Professional coaches saw themselves as practical men whose experiential knowledge concerning diet, physiological and psychological preparation, stimulants, massaging, medical treatments, talent identification, and so on provided critical components in their coaching ‘toolbox’ (Nelson, 1924, 25-26). Craft knowledge was never static. Coaching expertise is a fluid, cyclical process with practitioners continuously redeveloping their competencies (Turner, Nelson and Potrac, 2012, 323), and part of traditional craft expertise was the ability to react positively to shifting circumstances. Coaches were constantly stimulated to experiment by competitors, commercialisation, and emerging technologies (Clegg, 1977, 244), and they exemplified the notion of the ‘Bricoleur’ in constantly trialling emerging knowledge, intuitively accepting or rejecting appropriate material. This paper explores the ways in which practitioners developed their coaching ‘toolbox’ in Inter War Britain by drawing on examples from newspaper reports, personal and public archives, and instructional texts (eg. Tilden, 1920; Gent, 1922; Nelson, 1924; Mussabini, 1926; Lowe and Porritt, 1929; Abrahams and Abrahams, 1936). The author highlights the range of knowledge that coaches had at their command, well before the emergence of sports science and coaching certification programmes, and questions assumptions that coaches can no longer rely solely on ‘learning the trade’ through experience (Evans and Light, 2007). As Winchester et al. (2013) have emphasised, knowledge, skills, attitudes, and insights are developed from daily experiences in sport, work and at home, as well as through exposure to the coaching environment, and contemporary coaches still employ a largely implicit form of knowledge, closely connected to past experiences, which shares similarities with Inter War craft knowledge (Smith and Cushion, 2006, 363; Jones, Armour and Potrac, 2003), while identifying experimentation and experience as key reference points (Irwin, Hanton and Kerwin, 2004, 436, 439; Potrac, Jones and Cushion, 2007)

Incidence and trends of low back pain hospitalisation during military service – An analysis of 387,070 Finnish young males

<p>Abstract</p> <p>Background</p> <p>There is evidence that low back pain (LBP) during young adulthood and military service predicts LBP later in life. The purpose of this study was to investigate the incidence and trends of LBP hospitalisation among Finnish military conscripts.</p> <p>Methods</p> <p>All male conscripts performing their compulsory military service during 1990–2002 were included in the study population. Altogether 387,070 military conscripts were followed throughout their six-to-twelve-month service period. Data on LBP hospitalisations were obtained from the National Hospital Discharge Register.</p> <p>Results</p> <p>Altogether 7,240 LBP hospitalisations were identified among 5,061 (1.3%) male conscripts during the study period. The event-based incidence of LBP hospitalisation was 27.0 (95% confidence interval (CI): 25.7–28.2). In most cases, the diagnosis was unspecified LBP (<it>n </it>= 5,141, 71%) followed by lumbar disc disorders (<it>n </it>= 2,069, 29%). Hospitalisation incidence due to unspecified LBP was 19.1 per 1,000 person-years (95% CI: 18.3 to 20.4), and 7.8 per 1,000 person-years (95% CI: 6.7 to 8.3) due to lumbar disc disorders. The incidence of unspecified LBP remained unaltered, while hospitalisation due to lumbar disc disorders declined from 1993 onwards.</p> <p>Conclusion</p> <p>Although conscripts accepted into military training pass physician-performed examinations as healthy, young adults, LBP hospitalisation causes significant morbidity during military service.</p