Peptide vocabulary analysis reveals ultra-conservation and homonymity in protein sequences

A new algorithm is presented for vocabulary analysis (word detection) in texts of human origin. It performs at 60%–70% overall accuracy and greater than 80% accuracy for longer words, and approximately 85% sensitivity on Alice in Wonderland, a considerable improvement on previous methods. When applied to protein sequences, it detects short sequences analogous to words in human texts, i.e. intolerant to changes in spelling (mutation), and relatively contextindependent in their meaning (function). Some of these are homonyms of up to 7 amino acids, which can assume different structures in different proteins. Others are ultra-conserved stretches of up to 18 amino acids within proteins of less than 40% overall identity, reflecting extreme constraint or convergent evolution. Different species are found to have qualitatively different major peptide vocabularies, e.g. some are dominated by large gene families, while others are rich in simple repeats or dominated by internally repetitive proteins. This suggests the possibility of a peptide vocabulary signature, analogous to genome signatures in DNA. Homonyms may be useful in detecting convergent evolution and positive selection in protein evolution. Ultra-conserved words may be useful in identifying structures intolerant to substitution over long periods of evolutionary time

Comparison of Eurovision Song Contest simulation with actual results reveals shifting patterns of collusive voting alliances.

The voting patterns in the Eurovision Song Contest have attracted attention from various researchers, spawning a small cross-disciplinary field of what might be called 'eurovisiopsephology' incorporating insights from politics, sociology and computer science. Although the outcome of the contest is decided using a simple electoral system, its single parameter - the number of countries casting a vote - varies from year to year. Analytical identification of statistically significant trends in voting patterns over a period of several years is therefore mathematically complex. Simulation provides a method for reconstructing the contest's history using Monte Carlo methods. Comparison of simulated histories with the actual history of the contest allows the identification of statistically significant changes in patterns of voting behaviour, without requiring a full mathematical solution. In particular, the period since the mid-90s has seen the emergence of large geographical voting blocs from previously small voting partnerships, which initially appeared in the early 90s. On at least two occasions, the outcome of the contest has been crucially affected by voting blocs. The structure of these blocs implies that a handful of centrally placed countries have a higher probability of being future winners

Phylogenetic differences in content and intensity of periodic proteins

Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-square-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 species reveals striking differences in the proportion of periodic proteins and the intensity of the most significant periodicities. Eukaryotes tend to have a higher proportion of periodic proteins than eubacteria, which in turn tend to have more than archaea. The intensity of periodicity in the most periodic proteins is also greatest in eukaryotes. By contrast, the relatively small group of periodic proteins in archaea also tend to be weakly periodic compared to those of eukaryotes and eubacteria. Exceptions to this general rule are found in those prokaryotes with multicellular life-cycle phases, e.g. Methanosarcina sps. or Anabaena sps., which have more periodicities than prokaryotes in general, and in unicellular eukaryotes, which have fewer than multicellular eukaryotes. The distribution of significantly periodic proteins in eukaryotes is over a wide range of period lengths, whereas prokaryotic proteins typically have a more limited set of period lengths. This is further investigated by repeating the analysis on the NRL-3D database of proteins of solved structure. Some short range periodicities are explicable in terms of basic secondary structure, e.g. alpha helices, while middle range periodicities are frequently found to consist of known short Pfam domains, e.g. leucine-rich repeats, tetratricopeptides or armadillo domains. However, not all can be explained in this way

Viral forensic genomics reveals the relatedness of classic herpes simplex virus strains KOS, KOS63, and KOS79

Herpes simplex virus 1 (HSV-1) is a widespread global pathogen, of which the strain KOS is one of the most extensively studied. Previous sequence studies revealed that KOS does not cluster with other strains of North American geographic origin, but instead clustered with Asian strains. We sequenced a historical isolate of the original KOS strain, called KOS63, along with a separately isolated strain attributed to the same source individual, termed KOS79. Genomic analyses revealed that KOS63 closely resembled other recently sequenced isolates of KOS and was of Asian origin, but that KOS79 was a genetically unrelated strain that clustered in genetic distance analyses with HSV-1 strains of North American/European origin. These data suggest that the human source of KOS63 and KOS79 could have been infected with two genetically unrelated strains of disparate geographic origins. A PCR RFLP test was developed for rapid identification of these strains

The Victorian anti-vaccination discourse corpus (VicVaDis): construction and exploration

This article introduces and explores the 3.5-million-word Victorian Anti-Vaccination Discourse Corpus (VicVaDis). The corpus is intended to provide a (freely accessible) historical resource for the investigation of the earliest public concerns and arguments against vaccination in England, which revolved around compulsory vaccination against smallpox in the second half of the 19th century. It consists of 133 anti-vaccination pamphlets and publications gathered from 1854 to 1906, a span of 53 years that loosely coincides with the Victorian era (1837–1901). This timeframe was chosen to capture the period between the 1853 Vaccination Act, which made smallpox vaccination for babies compulsory, and the 1907 Act that effectively ended the mandatory nature of vaccination. After an overview of the historical background, this article describes the rationale, design and construction of the corpus, and then demonstrates how it can be exploited to investigate the main arguments against compulsory vaccination by means of widely accessible corpus linguistic tools. Where appropriate, parallels are drawn between Victorian and 21st-century vaccine-hesitant attitudes and arguments. Overall, this article demonstrates the potential of corpus analysis to add to our understanding of historical concerns about vaccination

Age-related differences in the neck strength of adolescent rugby players: A cross-sectional cohort study of Scottish schoolchildren

ObjectivesTo evaluate the neck strength of school-aged rugby players, and to define the relationship with proxy physical measures with a view to predicting neck strength.MethodsCross-sectional cohort study involving 382 rugby playing schoolchildren at three Scottish schools (all male, aged between 12 and 18 years). Outcome measures included maximal isometric neck extension, weight, height, grip strength, cervical range of movement and neck circumference.ResultsMean neck extension strength increased with age (p = 0.001), although a wide inter-age range variation was evident, with the result that some of the oldest children presented with the same neck strength as the mean of the youngest group. Grip strength explained the most variation in neck strength (R2 = 0.53), while cervical range of movement and neck girth demonstrated no relationship. Multivariable analysis demonstrated the independent effects of age, weight and grip strength, and the resultant model explained 62.1% of the variance in neck strength. This model predicted actual neck strength well for the majority of players, although there was a tendency towards overestimation at the lowest range and underestimation at the highest.ConclusionA wide variation was evident in neck strength across the range of the schoolchild-playing population, with a surprisingly large number of senior players demonstrating the same mean strength as the 12-year-old mean value. This may suggest that current training regimes address limb strength but not neck strength, which may be significant for future neck injury prevention strategies. Age, weight and grip strength can predict around two thirds of the variation in neck strength, however specific assessment is required if precise data is sought

Media events and cosmopolitan fandom:"Playful nationalism' in the Eurovision Song Contest

Academic literature on media events is increasingly concerned with their global dimensions and the applicability of Dayan and Katz's (1992) theoretical concept in a post-national context. This paper contributes to this debate by exploring the Eurovision Song Contest as a global media event. In particular, we employ a perspective from 'inside the media event', drawing upon empirical material collected during the 2014 Eurovision final in Copenhagen and focusing on the experiences of fans attending the contest. We argue that the ESC as a media event is experienced by its fans as a cosmopolitan space, open and diverse, whereas national belonging is expressed in a playful way tied to the overall visual aesthetics of the contest. However, the bounded and narrow character of participation render this cosmopolitan space rather limited

Comparative cervical profiles of adult and under-18 front-row rugby players: implications for playing policy

Objective To compare the cervical isometric strength, fatigue endurance and range of motion of adult and under-18 age-grade front-row rugby players to inform the development of a safe age group policy with particular reference to scrummaging.Design Cross-sectional cohort study.Setting ‘Field testing’ at Murrayfield stadium.Participants 30 high-performance under-18 players and 22 adult front-row rugby players.Outcome measures Isometric neck strength, height, weight and grip strength.Results Youth players demonstrated the same height and grip strength as the adult players; however, the adults were significantly heavier and demonstrated substantially greater isometric strength (p<0.001). Only two of the ‘elite’ younger players could match the adult mean cervical isometric strength value. In contrast to school age players in general, grip strength was poorly associated with neck strength (r=0.2) in front-row players; instead, player weight (r=0.4) and the number of years’ experience of playing in the front row (r=0.5) were the only relevant factors in multivariate modelling of cervical strength (R2=0.3).Conclusions Extreme forces are generated between opposing front rows in the scrum and avoidance of mismatch is important if the risk of injury is to be minimised. Although elite youth front-row rugby players demonstrate the same peripheral strength as their adult counterparts on grip testing, the adults demonstrate significantly greater cervical strength. If older youths and adults are to play together, such findings have to be noted in the development of age group policies with particular reference to the scrum