Genome-wide profiling of uncapped mRNA

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale

Vacuolating cytotoxin and variants in Atg16L1 that disrupt autophagy promote Helicobacter pylori infection in humans

Peer reviewedPreprin

Comfort from the perspective of families of people hospitalized in the intensive care unit

This study aimed at understanding the meaning of comfort to the families of people in intensive care units. It consists of a qualitative study carried out in the intensive care unit of a hospital in Salvador-Bahia. Fourteen family members were interviewed. The authors utilized the theoretical principles of symbolic interactionism and the technique of qualitative data analysis. Results indicated that the categories Safety, Receptiveness, Information, Proximity, Social and Spiritual Support, Convenience and Integration expressed the meaning of comfort, which was comprised of reliability in terms of technical-scientific competence and a supportive and sensitive attitude of the team, chance of recovery, access to information and the opportunity to be close to the patient, support of people in their social life, spiritual sources and the environmental structure of the hospital, preservation of self-care and routine activities. It was concluded that the family is important as objects and subjects of the actions in healthcare and must be the focus in public health policies and programs in Brazil

The Palomar Testbed Interferometer Calibrator Catalog

The Palomar Testbed Interferometer (PTI) archive of observations between 1998 and 2005 is examined for objects appropriate for calibration of optical long-baseline interferometer observations - stars that are predictably point-like and single. Approximately 1,400 nights of data on 1,800 objects were examined for this investigation. We compare those observations to an intensively studied object that is a suitable calibrator, HD217014, and statistically compare each candidate calibrator to that object by computing both a Mahalanobis distance and a Principal Component Analysis. Our hypothesis is that the frequency distribution of visibility data associated with calibrator stars differs from non-calibrator stars such as binary stars. Spectroscopic binaries resolved by PTI, objects known to be unsuitable for calibrator use, are similarly tested to establish detection limits of this approach. From this investigation, we find more than 350 observed stars suitable for use as calibrators (with an additional $\approx 140$ being rejected), corresponding to $\gtrsim 95$ sky coverage for PTI. This approach is noteworthy in that it rigorously establishes calibration sources through a traceable, empirical methodology, leveraging the predictions of spectral energy distribution modeling but also verifying it with the rich body of PTI's on-sky observations.Comment: 100 pages, 7 figures, 7 tables; to appear in the May 2008ApJS, v176n

Two-year outcomes in de novo renal transplant recipients receiving everolimus-facilitated calcineurin inhibitor reduction regimen from TRANSFORM study

TRANSFORM was a 24-month, prospective, open-label trial in 2037 de novo renal transplant recipients (RTxRs) randomized (1:1) within 24 hours of transplantation to receive everolimus (EVR) with reduced-exposure calcineurin inhibitor (EVR+rCNI) or mycophenolate with standard-exposure CNI (MPA+sCNI). Consistent with previously reported 12-month findings, noninferiority of the EVR+rCNI regimen for the primary endpoint of treated biopsy-proven acute rejection (tBPAR) or estimated glomerular filtration rate (eGFR) <50 mL/min/1.73 m2 was achieved at Month 24 (47.9% vs 43.7%; difference = 4.2%; 95% confidence interval [CI] = -0.3, 8.7; P = 0.006). Mean eGFR was stable up to Month 24 (52.6 vs 54.9 mL/min/1.73m2 ) in both arms. The incidence of de novo donor-specific antibodies (dnDSA) was lower in the EVR+rCNI arm (12.3% vs 17.6%) among on-treatment patients. Although discontinuation rates due to adverse events were higher with EVR+rCNI (27.2% vs 15.0%), rates of cytomegalovirus (2.8% vs 13.5%) and BK virus (5.8% vs 10.3%) infections were lower. Cytomegalovirus infection rates were significantly lower with EVR+rCNI even in the D+/R- high-risk group (P<0.0001). In conclusion, the EVR+rCNI regimen offers comparable efficacy and graft function with low tBPAR and dnDSA rates and significantly lower incidence of viral infections relative to standard-of-care up to 24 months. This article is protected by copyright. All rights reserved

Difficulties when Assessing Birdsong Learning Programmes under Field Conditions: A Re-Evaluation of Song Repertoire Flexibility in the Great Tit

There is a remarkable diversity of song-learning strategies in songbirds. Establishing whether a species is closed- or open-ended is important to be able to interpret functional and evolutionary consequences of variation in repertoire size. Most of our knowledge regarding the timing of vocal learning is based on laboratory studies, despite the fact that these may not always replicate the complex ecological and social interactions experienced by birds in the wild. Given that field studies cannot provide the experimental control of laboratory studies, it may not be surprising that species such as the great tit that were initially assumed to be closed-ended learners have later been suggested to be open-ended learners. By using an established colour-ringed population, by following a standardized recording protocol, and by taking into account the species' song ecology (using only recordings obtained during peak of singing at dawn), we replicated two previous studies to assess song repertoire learning and flexibility in adult wild great tits elicited by social interactions. First, we performed a playback experiment to test repertoire plasticity elicited by novel versus own songs. Additionally, in a longitudinal study, we followed 30 males in two consecutive years and analysed whether new neighbours influenced any change in the repertoire. Contrary to the previous studies, song repertoire size and composition were found to be highly repeatable both between years and after confrontation with a novel song. Our results suggest that great tits are closed-ended learners and that their song repertoire probably does not change during adulthood. Methodological differences that may have led to an underestimation of the repertoires or population differences may explain the discrepancy in results with previous studies. We argue that a rigorous and standardized assessment of the repertoire is essential when studying age- or playback-induced changes in repertoire size and composition under field conditions

Measurement of the Bs0→J/ψηB_{s}^{0} \rightarrow J/\psi \eta lifetime

Using a data set corresponding to an integrated luminosity of $3 fb^{-1}$, collected by the LHCb experiment in $pp$ collisions at centre-of-mass energies of 7 and 8 TeV, the effective lifetime in the $B^0_s \rightarrow J/\psi \eta$ decay mode, $\tau_{\textrm{eff}}$, is measured to be $\tau_{\textrm{eff}} = 1.479 \pm 0.034~\textrm{(stat)} \pm 0.011 ~\textrm{(syst)}$ ps. Assuming $CP$ conservation, $\tau_{\textrm{eff}}$ corresponds to the lifetime of the light $B_s^0$ mass eigenstate. This is the first measurement of the effective lifetime in this decay mode.Comment: All figures and tables, along with any supplementary material and additional information, are available at https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2016-017.htm

Performance assessment of the database downscaled ocean waves (DOW) on Santa Catarina coast, South Brazil

ABSTRACT: This work presents a validation of wave parameters from the new sixty years Downscaled Ocean Waves (DOW) reanalysis database. This study compares quantiles of the Gumbel distribution of Hs (significant wave height) and Tp (peak period) from simulated data with an 11 months' time series obtained from a buoy moored seaward on the Santa Catarina coast. Analysis by means of Gumbel distribution quantiles allows more weight to be given to the highest values of the time series, which are especially important in design projects. The statistical parameters used to verify the fit between the measured and the modeled data included: RMSE, BIAS, Scatter Index and Pearson Correlation Coefficient. Mean direction (9m) validation was conducted qualitatively. The database showed good fit of the mean conditions, especially Hs which was well Reproduced by the wave model. Underestimation of Tp, related mainly to the low spatial and temporal resolution of wind data used to generate waves, highlights this general modeling problem. Based on calculated statistical parameters, DOW data were considered comparable to the values obtained by measurements; however, such data must be cautiously used for extreme events analysis and in areas of bimodal sea conditions, where major deficiencies in the database were observed.The authors are also thankful to the Brazilian government through the Ministério do Meio Ambiente (MMA) and the Agência Brasileira de Cooperação (ABC) for the financial support of this research (within the project Transference of Methodologies and Tools to Support the Brazilian Coastal Management)