Variation in the strength of selected codon usage bias among bacteria

Among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. However, in other species selection appears to have been ineffective. Here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. The approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. The strength of selected codon usage bias, S, is found to vary substantially among species; in 30% of the genomes examined, there was no significant evidence that selection had been effective. Values of S are highly positively correlated with both the number of rRNA operons and the number of tRNA genes. These results are consistent with the hypothesis that species exposed to selection for rapid growth have more rRNA operons, more tRNA genes and more strongly selected codon usage bias. For example, Clostridium perfringens, the species with the highest value of S, can have a generation time as short as 7 min

Full-length sequence analysis of SIVmus in wild populations of mustached monkeys (Cercopithecus cephus) from Cameroon provides evidence for two co-circulating SIVmus lineages

AbstractMustached monkeys (Cercopithecus cephus), which form a significant component of primate bushmeat in west central Africa, are infected with simian immunodeficiency virus (SIVmus). We identified and genetically characterized five new SIVmus strains infecting wild living mustached monkeys from Cameroon. Phylogenetic analysis of partial pol sequences revealed that SIVmus strains form two distinct groups within the clade comprised of lentiviruses isolated from Cercopithecus nictitans (SIVgsn), Cercopithecus mona (SIVmon) and C. cephus (SIVmus). Characterisation of three full-length SIVmus genomes confirmed the presence of two distinct lineages infecting mustached monkeys. These two variants of SIVmus, here designated SIVmus-1 and SIVmus-2, were isolated from animals sharing habitats within the same geographic region. Phylogenetic analyses showed that the diversification of SIVmus, SIVgsn and SIVmon involved inter-lineage recombination, and suggested that one of the SIVmus lineages likely resulted from cross-species transmission and recombination involving SIVmus and an as yet uncharacterized SIV. These results indicate that cross-species transmission and recombination play a major role in the evolution of primate lentiviruses among sympatric primate species

High-Q Si3N4 Ring Resonators for Locking 780nm GaAs-Based Distributed Feedback Laser

High-Q microring resonators have applications in gyroscopes, frequency comb generation, and feedback systems to control narrow linewidth integrated lasers [1–3]. This paper demonstrates the highest Q values measured for microring resonators at 780 nm wavelength. These sub mm integrated cavities can be used to provide an error signal for locking a distributed feedback laser (DFB), Fig. 1(a), using the Pound-Drever-Hall (PDH) method. High stability DFBs can also be achieved using a micro-electro-mechanical system (MEMS) cell containing 87 Rb vapour and taking advantage of the absorption line at 780.24 nm. This provides an absolute reference for locking the laser but only to the 87 Rb transition wavelengths. The microring resonator can be tailor made for any wavelength but is susceptible to thermal effects; this could in part be overcome using a top cladding with a thermo-optic coefficient that counteracts that of the waveguide core

Convergence of decreasing male and increasing female incidence rates in major tobacco-related cancers in Europe in 1988-2010

Introduction: Smoking prevalence has been declining in men all over Europe, while the trend varies in European regions among women. To study the impact of past smoking prevalence, we present a comprehensive overview of the most recent trends in incidence, during 1988-2010, in 26 countries, of four of the major cancers in the respiratory and upper gastro-intestinal tract associated with tobacco smoking. Methods: Data from 47 population-based cancer registries for lung, laryngeal, oral cavity and pharyngeal, and oesophageal cancer cases were obtained from the newly developed data repository within the European Cancer Observatory (http://eco.iarc.fr/). Truncated age-standardised incidence rates (35-74 years) by calendar year, average annual percentage change in incidence over 1998-2007 were calculated. Smoking prevalence in selected countries was extracted from the Organisation for Economic Co-operation and Development and the World Health Organization databases. Results:

The Primordial Inflation Polarization Explorer (PIPER)

The Primordial Inflation Polarization Explorer (PIPER) is a balloon-borne cosmic microwave background (CMB) polarimeter designed to search for evidence of inflation by measuring the large-angular scale CMB polarization signal. BICEP2 recently reported a detection of B-mode power corresponding to the tensor-to-scalar ratio r = 0.2 on ~2 degree scales. If the BICEP2 signal is caused by inflationary gravitational waves (IGWs), then there should be a corresponding increase in B-mode power on angular scales larger than 18 degrees. PIPER is currently the only suborbital instrument capable of fully testing and extending the BICEP2 results by measuring the B-mode power spectrum on angular scales $\theta$ = ~0.6 deg to 90 deg, covering both the reionization bump and recombination peak, with sensitivity to measure the tensor-to-scalar ratio down to r = 0.007, and four frequency bands to distinguish foregrounds. PIPER will accomplish this by mapping 85% of the sky in four frequency bands (200, 270, 350, 600 GHz) over a series of 8 conventional balloon flights from the northern and southern hemispheres. The instrument has background-limited sensitivity provided by fully cryogenic (1.5 K) optics focusing the sky signal onto four 32x40-pixel arrays of time-domain multiplexed Transition-Edge Sensor (TES) bolometers held at 140 mK. Polarization sensitivity and systematic control are provided by front-end Variable-delay Polarization Modulators (VPMs), which rapidly modulate only the polarized sky signal at 3 Hz and allow PIPER to instantaneously measure the full Stokes vector (I, Q, U, V) for each pointing. We describe the PIPER instrument and progress towards its first flight.Comment: 11 pages, 7 figures. To be published in Proceedings of SPIE Volume 9153. Presented at SPIE Astronomical Telescopes + Instrumentation 2014, conference 915

Effectiveness and cost-effectiveness of the GoActive intervention to increase physical activity among UK adolescents: A cluster randomised controlled trial

Background: Less than 20% of adolescents globally meet recommended levels of physical activity, and not meeting these recommended levels is associated with social disadvantage and rising disease risk. The determinants of physical activity in adolescents are multilevel and poorly understood, but the school’s social environment likely plays an important role. We conducted a cluster randomised controlled trial to assess the effectiveness of a school-based programme (GoActive) to increase moderate-to-vigorous physical activity (MVPA) among adolescents. Methods and findings: Non-fee-paying, co-educational schools including Year 9 students in the UK counties of Cambridgeshire and Essex were eligible for inclusion. Within participating schools (n = 16), all Year 9 students were eligible and invited to participate. Participants were 2,862 13- to 14-year-olds (84% of eligible students). After baseline assessment, schools were computer-randomised, stratified by school-level pupil premium funding (below/above county-specific median) and county (control: 8 schools, 1,319 participants, mean [SD] participants per school n = 165 [62]; intervention: 8 schools, 1,543 participants, n = 193 [43]). Measurement staff were blinded to allocation. The iteratively developed, feasibility-tested 12-week intervention, aligned with self-determination theory, trained older adolescent mentors and in-class peer-leaders to encourage classes to conduct 2 new weekly activities. Students and classes gained points and rewards for engaging in any activity in or out of school. The primary outcome was average daily minutes of accelerometer-assessed MVPA at 10-month follow-up; a mixed-methods process evaluation evaluated implementation. Of 2,862 recruited participants (52.1% male), 2,167 (76%) attended 10-month follow-up measurements; we analysed the primary outcome for 1,874 participants (65.5%). At 10 months, there was a mean (SD) decrease in MVPA of 8.3 (19.3) minutes in the control group and 10.4 (22.7) minutes in the intervention group (baseline-adjusted difference [95% confidence interval] −1.91 minutes [−5.53 to 1.70], p = 0.316). The programme cost £13 per student compared with control; it was not cost-effective. Overall, 62.9% of students and 87.3% of mentors reported that GoActive was fun. Teachers and mentors commented that their roles in programme delivery were unclear. Implementation fidelity was low. The main methodological limitation of this study was the relatively affluent and ethnically homogeneous sample. Conclusions: In this study, we observed that a rigorously developed school-based intervention was no more effective than standard school practice at preventing declines in adolescent physical activity. Interdisciplinary research is required to understand educational-setting-specific implementation challenges. School leaders and authorities should be realistic about expectations of the effect of school-based physical activity promotion strategies implemented at scale. Trial registration: ISRCTN Registry ISRCTN31583496

Про маловідомі математичні таблиці Якова Пилипа Кулика

У статті описано маловідомі математичні таблиці професора Пражського університету Якова Пилипа Кулика. Виконано короткий аналіз складу та структури таблиць, що не тільки широко використовувались в арифметиці, алгебрі, теорії чисел і в теорії алгебраїчних рівнянь, але й мали широке практичне застосування.В статье описаны малоизвестные математические таблицы профессора Пражского университета Якова Филиппа Кулика. Произведен короткий анализ содержания и структуры таблиц, которые не только широко использовались в арифметике, алгебре, теории чисел и в теории алгебраических уравнений, но и имели широкое практическое применение.The unknown mathematical tables by Jakob Pilip Kulik – the professor of Prague University, are described in this article. The analysis of the content and structure of tables was conducted, they were not only used widely in arithmetic, algebra, the theory of numbers and in the Theory of equalizations of algebra, but They had a wide practical application

Alginate inhibits iron absorption from ferrous gluconate in a randomized controlled trial and reduces iron uptake into Caco-2 cells

Previous in vitro results indicated that alginate beads might be a useful vehicle for food iron fortification. A human study was undertaken to test the hypothesis that alginate enhances iron absorption. A randomised, single blinded, cross-over trial was carried out in which iron absorption was measured from serum iron appearance after a test meal. Overnight-fasted volunteers (n=15) were given a test meal of 200g cola-flavoured jelly plus 21 mg iron as ferrous gluconate, either in alginate beads mixed into the jelly or in a capsule. Iron absorption was lower from the alginate beads than from ferrous gluconate (8.5% and 12.6% respectively, p=0.003). Sub-group B (n=9) consumed the test meals together with 600 mg calcium to determine whether alginate modified the inhibitory effect of calcium. Calcium reduced iron absorption from ferrous gluconate by 51%, from 11.5% to 5.6% (p=0.014), and from alginate beads by 37%, from 8.3% to 5.2% (p=0.009). In vitro studies using Caco-2 cells were designed to explore the reasons for the difference between the previous in vitro findings and the human study; confirmed the inhibitory effect of alginate. Beads similar to those used in the human study were subjected to simulated gastrointestinal digestion, with and without cola jelly, and the digestate applied to Caco-2 cells. Both alginate and cola jelly significantly reduced iron uptake into the cells, by 34% (p=0.009) and 35% (p=0.003) respectively. The combination of cola jelly and calcium produced a very low ferritin response, 16.5% (p<0.001) of that observed with ferrous gluconate alone. The results of these studies demonstrate that alginate beads are not a useful delivery system for soluble salts of iron for the purpose of food fortification