Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process

Breakage-Fusion-Bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then 'unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. The process has parallels with paper folding sequences that arise when a piece of paper is folded several times and then unfolded. Here we adapt such methods to study the breakage-fusion-bridge structures in detail. We firstly consider discrete representations of this space with 2-d trees to demonstrate that there are 2^(n(n-1)/2) qualitatively distinct evolutions involving n breakage-fusion-bridge cycles. Secondly we consider the stochastic nature of the fold positions, to determine evolution likelihoods, and also describe how amplicons become localised. Finally we highlight these methods by inferring the evolution of breakage-fusion-bridge cycles with data from primary tissue cancer samples

What can polysemy tell us about theories of explanation?

Philosophical accounts of scientific explanation are broadly divided into ontic and epistemic views. This paper explores the idea that the lexical ambiguity of the verb to explain and its nominalisation supports an ontic conception of explanation. I analyse one argument which challenges this strategy by criticising the claim that explanatory talk is lexically ambiguous, 375–394, 2012). I propose that the linguistic mechanism of transfer of meaning, 109–132, 1995) provides a better account of the lexical alternations that figure in the systematic polysemy of explanatory talk, and evaluate the implications of this proposal for the debate between ontic and epistemic conceptions of scientific explanation

Glucose enhancement of memory is modulated by trait anxiety in healthy adolescent males

Glucose administration is associated with memory enhancement in healthy young individuals under conditions of divided attention at encoding. While the specific neurocognitive mechanisms underlying this ‘glucose memory facilitation effect’ are currently uncertain, it is thought that individual differences in glucoregulatory efficiency may alter an individual’s sensitivity to the glucose memory facilitation effect. In the present study, we sought to investigate whether basal hypothalamic–pituitary–adrenal axis function (itself a modulator of glucoregulatory efficiency), baseline self-reported stress and trait anxiety influence the glucose memory facilitation effect. Adolescent males (age range = 14–17 years) were administered glucose and placebo prior to completing a verbal episodic memory task on two separate testing days in a counter-balanced, within-subjects design. Glucose ingestion improved verbal episodic memory performance when memory recall was tested (i) within an hour of glucose ingestion and encoding, and (ii) one week subsequent to glucose ingestion and encoding. Basal hypothalamic–pituitary–adrenal axis function did not appear to influence the glucose memory facilitation effect; however, glucose ingestion only improved memory in participants reporting relatively higher trait anxiety. These findings suggest that the glucose memory facilitation effect may be mediated by biological mechanisms associated with trait anxiety

Cross-protection against European swine influenza viruses in the context of infection immunity against the 2009 pandemic H1N1 virus : studies in the pig model of influenza

Pigs are natural hosts for the same influenza virus subtypes as humans and are a valuable model for cross-protection studies with influenza. In this study, we have used the pig model to examine the extent of virological protection between a) the 2009 pandemic H1N1 (pH1N1) virus and three different European H1 swine influenza virus (SIV) lineages, and b) these H1 viruses and a European H3N2 SIV. Pigs were inoculated intranasally with representative strains of each virus lineage with 6- and 17-week intervals between H1 inoculations and between H1 and H3 inoculations, respectively. Virus titers in nasal swabs and/or tissues of the respiratory tract were determined after each inoculation. There was substantial though differing cross-protection between pH1N1 and other H1 viruses, which was directly correlated with the relatedness in the viral hemagglutinin (HA) and neuraminidase (NA) proteins. Cross-protection against H3N2 was almost complete in pigs with immunity against H1N2, but was weak in H1N1/pH1N1-immune pigs. In conclusion, infection with a live, wild type influenza virus may offer substantial cross-lineage protection against viruses of the same HA and/or NA subtype. True heterosubtypic protection, in contrast, appears to be minimal in natural influenza virus hosts. We discuss our findings in the light of the zoonotic and pandemic risks of SIVs

Анализ механических состояний силовых систем. Сообщение 1. Предельное состояние

Изложены основы теории предельных состояний силовых систем, которые работают в условиях сложного нагружения (механическая усталость, трение и изнашивание, температура, электрохимическая коррозия). Получен энергетический критерий предельного состояния и описаны методы определения его параметров. Записаны условия прочности с учетом как циклической, так и контактной нагрузок.Викладено основи теорії граничних станів силових систем, що працюють в умовах складного навантаження (механічна утома, тертя та спрацьовування, температура, електрохімічна корозія). Отримано енергетичний критерій граничного стану та описано методи визначення його параметрів. Записано рівняння міцності з урахуванням як циклічного, так і контактного навантажень.Fundamentals of the theory of ultimate states in force systems operating under complex loading (mechanical fatigue, friction and wear, temperature, and electrochemical corrosion) have been described. Energy criterion of an ultimate state has been obtained and methods for calculating its parameters are given. Strength conditions taking into account both cyclic and contact loads are described

A complete characterization of plateaued Boolean functions in terms of their Cayley graphs

In this paper we find a complete characterization of plateaued Boolean functions in terms of the associated Cayley graphs. Precisely, we show that a Boolean function $f$ is $s$-plateaued (of weight $=2^{(n+s-2)/2}$) if and only if the associated Cayley graph is a complete bipartite graph between the support of $f$ and its complement (hence the graph is strongly regular of parameters $e=0,d=2^{(n+s-2)/2}$). Moreover, a Boolean function $f$ is $s$-plateaued (of weight $\neq 2^{(n+s-2)/2}$) if and only if the associated Cayley graph is strongly $3$-walk-regular (and also strongly $\ell$-walk-regular, for all odd $\ell\geq 3$) with some explicitly given parameters.Comment: 7 pages, 1 figure, Proceedings of Africacrypt 201

Generic prognostic factors for musculoskeletal pain in primary care: a systematic review.

OBJECTIVES: To summarise the evidence for generic prognostic factors across a range of musculoskeletal (MSK) conditions. SETTING: primary care. METHODS AND OUTCOMES: Comprehensive systematic literature review. MEDLINE, CINAHL, PsychINFO and EMBASE were searched for prospective cohort studies, based in primary care (search period-inception to December 2015). Studies were included if they reported on adults consulting with MSK conditions and provided data on associations between baseline characteristics (prognostic factors) and outcome. A prognostic factor was identified as generic when significantly associated with any outcome for 2 or more different MSK conditions. Evidence synthesis focused on consistency of findings and study quality. RESULTS: 14 682 citations were identified and 78 studies were included (involving more than 48 000 participants with 18 different outcome domains). 51 studies were on spinal pain/back pain/low back pain, 12 on neck/shoulder/arm pain, 3 on knee pain, 3 on hip pain and 9 on multisite pain/widespread pain. Total quality scores ranged from 5 to 14 (mean 11) and 65 studies (83%) scored 9 or more. Out of a total of 78 different prognostic factors for which data were provided, the following factors are considered to be generic prognostic factors for MSK conditions: widespread pain, high functional disability, somatisation, high pain intensity and presence of previous pain episodes. In addition, consistent evidence was found for use of pain medications not to be associated with outcome, suggesting that this factor is not a generic prognostic factor for MSK conditions. CONCLUSIONS: This large review provides new evidence for generic prognostic factors for MSK conditions in primary care. Such factors include pain intensity, widespread pain, high functional disability, somatisation and movement restriction. This information can be used to screen and select patients for targeted treatment in clinical research as well as to inform the management of MSK conditions in primary care

Radiocarbon Chronologies and Extinction Dynamics of the Late Quaternary Mammalian Megafauna of the Taimyr Peninsula, Russian Federation

This paper presents 75 new radiocarbon dates based on late Quaternary mammal remains recovered from eastern Taimyr Peninsula and adjacent parts of the northern Siberian lowlands, Russian Federation, including specimens of woolly mammoth (Mammuthus primigenius), steppe bison (Bison priscus), muskox (Ovibos moschatus), moose (Alces alces), reindeer (Rangifer tarandus), horse (Equus caballus) and wolf (Canis lupus). New evidence permits reanalysis of megafaunal extinction dynamics in the Asian high Arctic periphery. Increasingly, radiometric records of individual species show evidence of a gap at or near the Pleistocene/Holocene boundary (PHB). In the past, the PHB gap was regarded as significant only when actually terminal, i.e., when it marked the apparent ‘‘last’’ occurrence of a species (e.g., current ‘‘last’’ occurrence date for woolly mammoth in mainland Eurasia is 9600 yr BP). However, for high Arctic populations of horses and muskoxen the gap marks an interruption rather than extinction, because their radiocarbon records resume, nearly simultaneously, much later in the Holocene. Taphonomic effects, ΔC14 flux, and biased sampling are unlikely explanations for these hiatuses. A possible explanation is that the gap is the signature of an event, of unknown nature, that prompted the nearly simultaneous crash of many megafaunal populations in the high Arctic and possibly elsewhere in Eurasia.

Cirsium species show disparity in patterns of genetic variation at their range-edge, despite similar patterns of reproduction and isolation

Genetic variation was assessed across the UK geographical range of Cirsium acaule and Cirsium heterophyllum. A decline in genetic diversity and increase in population divergence approaching the range edge of these species was predicted based on parallel declines in population density and seed production reported seperately. Patterns were compared with UK populations of the widespread Cirsium arvense.Populations were sampled along a latitudinal transect in the UK and genetic variation assessed using microsatellite markers. Cirsium acaule shows strong isolation by distance, a significant decline in diversity and an increase in divergence among range-edge populations. Geographical structure is also evident in C. arvense, whereas no such patterns are seen in C.heterophyllum. There is a major disparity between patterns of genetic variation in C. acaule and C. heterophyllum despite very similar patterns in seed production and population isolation in these species. This suggests it may be misleading to make assumptions about the geographical structure of genetic variation within species based solely on the present-day reproduction and distribution of populations