tRNA functional signatures classify plastids as late-branching cyanobacteria.

BackgroundEukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data.ResultsUsing Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies ("phyloclassifies") cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data.ConclusionsPhylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies

The OPERA trial : a protocol for the process evaluation of a randomised trial of an exercise intervention for older people in residential and nursing accommodation

Background: The OPERA trial is large cluster randomised trial testing a physical activity intervention to address depression amongst people living in nursing and residential homes for older people. A process evaluation was commissioned alongside the trial and we report the protocol for this process evaluation. Challenges included the cognitive and physical ability of the participants, the need to respect the privacy of all home residents, including study non-participants, and the physical structure of the homes. Evaluation activity had to be organised around the structured timetable of homes, leaving limited opportunities for data collection. The aims of this process evaluation are to provide findings that will assist in the interpretation of the clinical trial results, and to inform potential implementation of the physical activity intervention on a wider scale. Methods/design: Quantitative data on recruitment of homes and individuals is being collected. For homes in the intervention arm, data on dose and fidelity of the intervention delivered; including individual rates of participation in exercise classes are collected. In the control homes, uptake and delivery of depression awareness training is monitored. These data will be combined with qualitative data from an in-depth study of a purposive sample of eight homes (six intervention and two control). Discussion: Although process evaluations are increasingly funded alongside trials, it is still rare to see the findings published, and even rarer to see the protocol for such an evaluation published. Process evaluations have the potential to assist in interpreting and understanding trial results as well as informing future roll-outs of interventions. If such evaluations are funded they should also be reported and reviewed in a similar way to the trial outcome evaluation

Efecto de la ablación unilateral del pedúnculo ocular sobre el tiempo de maduración de los ovocitos y fecundidad de Penaeus vannamei

Los estudios de los procesos de maduración tendientes a optimizar el cultivo de P. vannamei, son necesarios para poder planificar adecuadamente la producción y satisfacer la demanda de poslarvas de mejor calidad a escala comercial que exige hoy en día la industria langostinera en el Perú. La inducción a la maduración y desove en P. vannamei por ablación unilateral del pedúnculo ocular ha sido documentada por diferentes investigadores. Hidalgo (1997), reportó que los centros endocrinos que controlan la reproducción, en crustáceos están compuestos, entre otros, por el sistema neurosecretor y el órgano X-glándula sinusal, ambos localizados en el pedúnculo ocular, en donde se desarrollan las Hormonas Inhibidoras de la Gónada (GIH) y la Hormona Estimulante de la Gónada (GSH). Otras áreas como, el cerebro, el ganglio torácico, el órgano mandibular, son reguladores directos de la reproducción al producir hormonas o factores de estimulación o inhibición del desarrollo gonadal (Vaca, 1999; Huberman, 2000; Diwan, 2005)

The R Coronae Borealis stars - carbon abundances from forbidden carbon lines

Spectra of several R Coronae Borealis (RCB) stars at maximum light were examined for the [C I] 9850 A and 8727 A absorption lines. The 9850 A line is variously blended with a Fe II and CN lines but positive identifications of the [C I] line are made for R CrB and SU Tau. The 8727 A line is detected in the spectrum of the five stars observed in this wavelength region. Carbon abundances are derived from the [C I] lines using the model atmospheres and atmospheric parameters used by Asplund et al. (2000). Although the observed strength of a C I line is constant from cool to hot RCB stars, the strength is weaker than predicted by an amount equivalent to a factor of four reduction of a line's gf-value. Asplund et al. dubbed this 'the carbon problem' and discussed possible solutions. The [C I] 9850 A line seen clearly in R CrB and SU Tau confirms the magnitude of the carbon problem revealed by the C I lines. The [C I] 8727 A line measured in five stars shows an enhanced carbon problem. The gf-value required to fit the observed [C I] 8727 A line is a factor of 15 less than the well-determined theoretical gf-value. We suggest that the carbon problem for all lines may be alleviated to some extent by a chromospheric-like temperature rise in these stars. The rise far exceeds that predicted by our non-LTE calculations, and requires a substantial deposition of mechanical energy.Comment: 11 pages (embedded 5 figures and 3 tables), accepted for publication in MNRA

Hooge's Constant of Carbon Nanotube Field Effect Transistors

The 1/f noise in individual semiconducting carbon nanotubes (s-CNT) in a field effect transistor configuration has been measured in ultra-high vacuum and following exposure to air. The amplitude of the normalized current spectral noise density is independent of source-drain current, indicating the noise is due to mobility rather than number fluctuations. Hooge's constant for s-CNT is found to be 9.3 plus minus 0.4x10^-3. The magnitude of the 1/f noise is substantially degreased by exposing the devices to air

Vasilii Belov and the Russian idea

Vasilii Ivanovich Belov (1932-2012) was one of the most wellknown and outspoken of the ‘village writers’ who came to prominence in the Soviet Union in the 1960s, and in the age of ‘glasnost’ and post-Soviet times attracted much attention and even vilification for his nationalist and apparently xenophobic views. In his documentary account of village life and customs published in the journal Nash sovremennik between 1979 and 1982, and subsequently in illustrated book form, Belov provides in great detail and with much personal warmth the history of the northern Russian village, its people, customs and way of life as it has developed over the centuries, showing a place seemingly outside of time and untouched by historical developments. Lad: ocherki o narodnoi estetike may yet prove to be his most enduring contribution to post-Soviet reflections on ‘the Russian idea’, and Russia’s relationship with Europe

Aqueous Angiography with Fluorescein and Indocyanine Green in Bovine Eyes.

PurposeWe characterize aqueous angiography as a real-time aqueous humor outflow imaging (AHO) modality in cow eyes with two tracers of different molecular characteristics.MethodsCow enucleated eyes (n = 31) were obtained and perfused with balanced salt solution via a Lewicky AC maintainer through a 1-mm side-port. Fluorescein (2.5%) or indocyanine green (ICG; 0.4%) were introduced intracamerally at 10 mm Hg individually or sequentially. With an angiographer, infrared and fluorescent images were acquired. Concurrent anterior segment optical coherence tomography (OCT) was performed, and fixable fluorescent dextrans were introduced into the eye for histologic analysis of angiographically positive and negative areas.ResultsAqueous angiography in cow eyes with fluorescein and ICG yielded high-quality images with segmental patterns. Over time, ICG maintained a better intraluminal presence. Angiographically positive, but not negative, areas demonstrated intrascleral lumens with anterior segment OCT. Aqueous angiography with fluorescent dextrans led to their trapping in AHO pathways. Sequential aqueous angiography with ICG followed by fluorescein in cow eyes demonstrated similar patterns.ConclusionsAqueous angiography in model cow eyes demonstrated segmental angiographic outflow patterns with either fluorescein or ICG as a tracer.Translational relevanceFurther characterization of segmental AHO with aqueous angiography may allow for intelligent placement of trabecular bypass minimally invasive glaucoma surgeries for improved surgical results