PRECIS: Protein reports engineered from concise information in SWISS-PROT

Motivation: There have been several endeavours to address the problem of annotating sequence data computationally, but the task is non-trivial and few tools have emerged that gather useful information on a given sequence, or set of sequences, in a simple and convenient manner. As more genome projects bear fruit, the mass of uncharacterized sequence data accumulating in public repositories grows ever larger. There is thus a pressing need for tools to support the process of automatic analysis and annotation of newly determined sequences. With this in mind, we have developed PRECIS, which automatically creates protein reports from sets of SWISS-PROT entries, collating results into structured reports, detailing known biological and medical information, literature and database cross-references, and relevant keywords. Availability: The software is accessible online at: http://www.bioinf.man.ac.uk/cgi-bin/dbbrowser/precis/blast_precis.cg

Protocol-directed sedation versus non-protocol-directed sedation to reduce duration of mechanical ventilation in mechanically ventilated intensive care patients

Background The sedation needs of critically ill patients have been recognized as a core component of critical care and meeting these is vital to assist recovery and ensure humane treatment. There is growing evidence to suggest that sedation requirements are not always optimally managed. Sub-optimal sedation incorporates both under- and over-sedation and has been linked to both short-term (e.g. length of stay) and long-term (e.g. psychological recovery) outcomes. Various strategies have been proposed to improve sedation management and address aspects of assessment as well as delivery of sedation. Objectives To assess the effects of protocol-directed sedation management on the duration of mechanical ventilation and other relevant patient outcomes in mechanically ventilated intensive care unit (ICU) patients. We looked at various outcomes and examined the role of bias in order to examine the level of evidence for this intervention. Search methods We searched the Cochrane Central Register of Controlled trials (CENTRAL) (2013; Issue 11), MEDLINE (OvidSP) (1990 to November 2013), EMBASE (OvidSP) (1990 to November 2013), CINAHL (BIREME host) (1990 to November 2013), Database of Abstracts of Reviews of Effects (DARE) (1990 to November 2013), LILACS (1990 to November 2013), Current Controlled Trials and US National Institutes of Health Clinical Research Studies (1990 to November 2013), and reference lists of articles. We re-ran the search in October 2014. We will deal with any studies of interest when we update the review. Selection criteria We included randomized controlled trials (RCTs) conducted in adult ICUs comparing management with and without protocol-directed sedation. Data collection and analysis Two authors screened the titles and abstracts and then the full-text reports identified from our electronic search. We assessed seven domains of potential risk of bias for the included studies. We examined the clinical, methodological and statistical heterogeneity and used the random-effects model for meta-analysis where we considered it appropriate. We calculated the mean difference (MD) for duration of mechanical ventilation and risk ratio (RR) for mortality across studies, with 95% confidence intervals (CI). Main results We identified two eligible studies with 633 participants. Both included studies compared the use of protocol-directed sedation, specifically protocols delivered by nurses, with usual care. We rated the risk of selection bias due to random sequence generation low for one study and unclear for one study. The risk of selection bias related to allocation concealment was low for both studies. We also assessed detection and attrition bias as low for both studies while we considered performance bias high due to the inability to blind participants and clinicians in both studies. Risk due to other sources of bias, such as potential for contamination between groups and reporting bias, was considered unclear. There was no clear evidence of differences in duration of mechanical ventilation (MD -5.74 hours, 95% CI -62.01 to 50.53, low quality evidence), ICU length of stay (MD -0.62 days, 95% CI -2.97 to 1.73) and hospital length of stay (MD -3.78 days, 95% CI -8.54 to 0.97) between people being managed with protocol-directed sedation versus usual care. Similarly, there was no clear evidence of difference in hospital mortality between the two groups (RR 0.96, 95% CI 0.71 to 1.31, low quality evidence). ICU mortality was only reported in one study preventing pooling of data. There was no clear evidence of difference in the incidence of tracheostomy (RR 0.77, 95% CI 0.31 to 1.89). The studies reported few adverse event outcomes; one study reported self extubation while the other study reported re-intubation; given this difference in outcomes, pooling of data was not possible. There was significant heterogeneity between studies for duration of mechanical ventilation (I2 = 86%, P value = 0.008), ICU length of stay (I2 = 82%, P value = 0.02) and incidence of tracheostomy (I2 = 76%, P value = 0.04), with one study finding a reduction in duration of mechanical ventilation and incidence of tracheostomy and the other study finding no difference. Authors' conclusions There is currently insufficient evidence to evaluate the effectiveness of protocol-directed sedation. Results from the two RCTs were conflicting, resulting in the quality of the body of evidence as a whole being assessed as low. Further studies, taking into account contextual and clinician characteristics in different ICU environments, are necessary to inform future practice. Methodological strategies to reduce the risk of bias need to be considered in future studies

Phagosomal acidification Is required to kill Streptococcus pneumoniae in a Zebrafish model

Streptococcus pneumoniae (the pneumococcus) is a major human pathogen causing invasive disease, including community-acquired bacteraemia, and remains a leading cause of global mortality. Understanding the role of phagocytes in killing bacteria is still limited, especially in vivo. In this study, we established a zebrafish model to study the interaction between intravenously administered pneumococci and professional phagocytes such as macrophages and neutrophils, to unravel bacterial killing mechanisms employed by these immune cells. Our model confirmed the key role of polysaccharide capsule in promoting pneumococcal virulence through inhibition of phagocytosis. Conversely, we show pneumococci lacking a capsule are rapidly internalised by macrophages. Low doses of encapsulated S. pneumoniae cause near 100% mortality within 48 hours postinfection (hpi), while 50 times higher doses of unencapsulated pneumococci are easily cleared. Time course analysis of in vivo bacterial numbers reveals that while encapsulated pneumococcus proliferates to levels exceeding 105 CFU at the time of host death, unencapsulated bacteria are unable to grow and are cleared within 20 hpi. Using genetically induced macrophage depletion, we confirmed an essential role for macrophages in bacterial clearance. Additionally, we show that upon phagocytosis by macrophages, phagosomes undergo rapid acidification. Genetic and chemical inhibition of vacuolar ATPase (v-ATPase) prevents intracellular bacterial killing and induces host death indicating a key role of phagosomal acidification in immunity to invading pneumococci. We also show that our model can be used to study the efficacy of antimicrobials against pneumococci in vivo. Collectively, our data confirm that larval zebrafish can be used to dissect killing mechanisms during pneumococcal infection in vivo and highlight key roles for phagosomal acidification in macrophages for pathogen clearance

Protocol-directed sedation versus non-protocol-directed sedation in mechanically ventilated intensive care adults and children

Background The sedation needs of critically ill patients have been recognized as a core component of critical care that is vital to assist recovery and ensure humane treatment. Evidence suggests that sedation requirements are not always optimally managed. Suboptimal sedation, both under‐ and over‐sedation, have been linked to short‐term (e.g. length of stay) and long‐term (e.g. psychological recovery) outcomes. Strategies to improve sedation assessment and management have been proposed. This review was originally published in 2015 and updated in 2018. Objectives To assess the effects of protocol‐directed sedation management compared to usual care on the duration of mechanical ventilation, intensive care unit (ICU) and hospital mortality and other patient outcomes in mechanically ventilated ICU adults and children. Search methods We used the standard search strategy of the Cochrane Anaesthesia, Critical and Emergency Care Group (ACE). We searched the Cochrane Central Register of Controlled trials (CENTRAL) (December 2017), MEDLINE (OvidSP) (2013 to December 2017), Embase (OvidSP) (2013 to December 2017), CINAHL (BIREME host) (2013 to December 2017), LILACS (2013 to December 2017), trial registries and reference lists of articles. (The original search was run in November 2013). Selection criteria We included randomized controlled trials (RCTs) and quasi‐randomized controlled trials conducted in ICUs comparing management with and without protocol‐directed sedation in intensive care adults and children. Data collection and analysis Two authors screened the titles and abstracts and then full‐text reports identified from our electronic search. We assessed seven domains of potential risk of bias for the included studies. We examined clinical, methodological and statistical heterogeneity and used the random‐effects model for meta‐analysis where we considered it appropriate. We calculated the mean difference (MD) for duration of mechanical ventilation and risk ratio (RR) for mortality across studies, with 95% confidence intervals (CIs). Main results We included four studies with a total of 3323 participants (864 adults and 2459 paediatrics) in this update. Three studies were single‐centre, patient‐level RCTs and one study was a multicentre cluster‐RCT. The settings were in metropolitan centres and included general, mixed medical‐surgical, medical only and a range of paediatric units. All four included studies compared the use of protocol‐directed sedation, specifically protocols delivered by nurses, with usual care. We rated the risk of selection bias due to random sequence generation low for two studies and unclear for two studies. The risk of bias was highly variable across the domains and studies, with the risk of selection and performance bias generally rated high and the risk of detection and attrition bias generally rated low. When comparing protocol‐directed sedation with usual care, there was no clear evidence of difference in duration of mechanical ventilation in hours for the entire duration of the first ICU stay for each patient (MD ‐28.15 hours, 95% CI ‐69.15 to 12.84; I2 = 85%; 4 studies; adjusted sample 2210 participants; low‐quality evidence). There was no clear evidence of difference in ICU mortality (RR 0.77, 95% CI 0.39 to 1.50; I2 = 67%; 2 studies; 513 participants; low‐quality evidence), or hospital mortality (RR 0.90, 95% CI 0.72 to 1.13; I2 = 10%; 3 studies; adjusted sample 2088 participants; low‐quality evidence). There was no clear evidence of difference in ICU length of stay (MD ‐1.70 days, 95% CI‐3.71 to 0.31; I2 = 82%; 4 studies; adjusted sample of 2123 participants; low‐quality of evidence), however there was evidence of a significant reduction in hospital length of stay (MD ‐3.09 days, 95% CI ‐5.08 to ‐1.10; I2 = 2%; 3 studies; adjusted sample of 1922 participants; moderate‐quality evidence). There was no clear evidence of difference in the incidence of self‐extubation (RR 0.88, 95% CI 0.55 to 1.42; I2 = 0%; 2 studies; adjusted sample of 1687 participants; high‐quality evidence), or incidence of tracheostomy (RR 0.67, 95% CI 0.35 to 1.30; I2 = 66%; 3 studies; adjusted sample of 2008 participants; low‐quality evidence). Only one study examined incidence of reintubation, therefore we could not pool data; there was no clear evidence of difference (RR 0.65, 95% CI 0.35 to 1.24; 1 study; 321 participants; low‐quality evidence). Authors' conclusions There is currently limited evidence from RCTs evaluating the effectiveness of protocol‐directed sedation on patient outcomes. The four included RCTs reported conflicting results and heterogeneity limited the interpretation of results for the primary outcomes of duration of mechanical ventilation and mortality. Further studies, taking into account differing contextual characteristics, are necessary to inform future practice. Methodological strategies to reduce the risk of bias need to be considered in future studies

Cassini multi-instrument assessment of Saturn's polar cap boundary

We present the first systematic investigation of the polar cap boundary in Saturn's high-latitude magnetosphere through a multi-instrument assessment of various Cassini in situ data sets gathered between 2006 and 2009. We identify 48 polar cap crossings where the polar cap boundary can be clearly observed in the step in upper cutoff of auroral hiss emissions from the plasma wave data, a sudden increase in electron density, an anisotropy of energetic electrons along the magnetic field, and an increase in incidence of higher-energy electrons from the low-energy electron spectrometer measurements as we move equatorward from the pole. We determine the average level of coincidence of the polar cap boundary identified in the various in situ data sets to be 0.34° ± 0.05° colatitude. The average location of the boundary in the southern (northern) hemisphere is found to be at 15.6° (13.3°) colatitude. In both hemispheres we identify a consistent equatorward offset between the poleward edge of the auroral upward directed field-aligned current region of ~1.5–1.8° colatitude to the corresponding polar cap boundary. We identify atypical observations in the boundary region, including observations of approximately hourly periodicities in the auroral hiss emissions close to the pole. We suggest that the position of the southern polar cap boundary is somewhat ordered by the southern planetary period oscillation phase but that it cannot account for the boundary's full latitudinal variability. We find no clear evidence of any ordering of the northern polar cap boundary location with the northern planetary period magnetic field oscillation phase

Sedation protocols to reduce duration of mechanical ventilation in the ICU: a Cochrane Systematic Review

Aims: Assess the effects of protocol-directed sedation management on the duration of mechanical ventilation and other relevant patient outcomes in mechanically ventilated intensive care unit patients. Background: Sedation is a core component of critical care. Sub-optimal sedation management incorporates both under-and over-sedation and has been linked to poorer patient outcomes. Design: Cochrane systematic review of randomised controlled trials. Data Sources: Cochrane Central Register of Controlled trials, MEDLINE, EMBASE, CINAHL, Database of Abstracts of Reviews of Effects, LILACS, Current Controlled Trials and US National Institutes of Health Clinical Research Studies (1990 – November 2013), and reference lists of articles were used. Review Methods: Randomised controlled trials conducted in intensive care units comparing management with and without protocol-directed sedation were included. Two authors screened titles, abstracts and full-text reports. Potential risk of bias was assessed. Clinical, methodological and statistical heterogeneity were examined and the random-effects model used for meta-analysis where appropriate. Mean difference for duration of mechanical ventilation and risk ratio for mortality, with 95% confidence intervals, were calculated. Results: Two eligible studies with 633 participants comparing protocol-directed sedation delivered by nurses versus usual care were identified. There was no evidence of differences in duration of mechanical ventilation or hospital mortality. There was significant heterogeneity between studies for duration of mechanical ventilation. Conclusions: There is insufficient evidence to evaluate the effectiveness of protocol-directed sedation as results from the two randomised controlled trials were conflicting

Efeitos da densidade de população de plantas na cultura de couve-flor (Brassica oleracea L. var. botrytis)

An experiment was carried out to study the effects of the following population densities cauliflowers (plants per ha): 20,833 (0.60 m x 0.80 m), 25,641 (0.60 m x 0.65 m), ....37.037 (0.60 m x 0.45 m) , 55.555 (.0.60 m x 0.30 m), and 111,111 (0,60 m x 0,15 m) ; variety Snow ball. It was concluded that the effects of plant population density are greater on curd quality (weight and size) than on production per ha. The best plant population density to produce cauliflowers curd for Brazil market is from 20,000 to 25,000 plants/ha while for mini-curd is above 55,000 plants/ha.O experimento foi instalado na área experimental do Setor de Horticultura da ESALQ. (Piracicaba, SP), em um Latossol Roxo série "Luiz de Queiroz", em março de 1977, considerando as seguintes densidades de população: 20.833 plantas/ha (0,60 m x 0,80m), .. 25.641 plantas/ha (0,60 m x 0,65 m), 37.037 plantas/ha (..0.,60 m x 0,45 ml, 55.550 plantas/ha (,06Q m x 0,30 ,) e 111.111 plantas/ ha (0,60 m x 0,15 m). A partir dos resultados obtidos e para as condições do experimento concluiu-se que a densidade de população sobre a produção de couve-flor afeta mais a qualidade da cabeça (peso e tamanho), enquanto que o rendimento por área é pouco afetado. Para as condições do nosso mercado, a densidade ótima deve estar entre 20.000 a 25.000 plantas por ha e para a produção de mini-couve-flor mais de 55.000 plantas por ha, paraocultivar Bola de Neve

Measurement of Pion Enhancement at Low Transverse Momentum and of the Delta-Resonance Abundance in Si-Nucleus Collisions at AGS Energy

We present measurements of the pion transverse momentum (p_t) spectra in central Si-nucleus collisions in the rapidity range 2.0<y<5.0 for p_t down to and including p_t=0. The data exhibit an enhanced pion yield at low p_t compared to what is expected for a purely thermal spectral shape. This enhancement is used to determine the Delta-resonance abundance at freeze-out. The results are consistent with a direct measurement of the Delta-resonance yield by reconstruction of proton-pion pairs and imply a temperature of the system at freeze-out close to 140 MeV.Comment: 12 pages + 4 figures (uuencoded at end-of-file

Event Reconstruction in the PHENIX Central Arm Spectrometers

The central arm spectrometers for the PHENIX experiment at the Relativistic Heavy Ion Collider have been designed for the optimization of particle identification in relativistic heavy ion collisions. The spectrometers present a challenging environment for event reconstruction due to a very high track multiplicity in a complicated, focusing, magnetic field. In order to meet this challenge, nine distinct detector types are integrated for charged particle tracking, momentum reconstruction, and particle identification. The techniques which have been developed for the task of event reconstruction are described.Comment: Accepted for publication in Nucl. Instrum. A. 34 pages, 23 figure