Gene Ontology annotation quality analysis in model eukaryotes

Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers’ ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintained and optimal for the functional processes that are most relevant for their research community. We report the GO Annotation Quality (GAQ) score, a quantitative measure of GO quality that includes breadth of GO annotation, the level of detail of annotation and the type of evidence used to make the annotation. As a case study, we apply the GAQ scoring method to a set of diverse eukaryotes and demonstrate how the GAQ score can be used to track changes in GO annotations over time and to assess the quality of GO annotations available for specific biological processes. The GAQ score also allows researchers to quantitatively assess the functional data available for their experimental systems (arrays or databases)

Who Did the Arthroplasty? Hip Fracture Surgery Reoperation Rates are Not Affected by Type of Training-An Analysis of the HEALTH Database

OBJECTIVES: This study compares outcomes for patients with displaced femoral neck fractures undergoing hemiarthroplasty (HA) or total hip arthroplasty (THA) by surgeons of different fellowship training. DESIGN: Retrospective review of HEALTH trial data. SETTING: Eighty clinical sites across 10 countries. PATIENTS/PARTICIPANTS: One thousand four hundred forty-one patients ≥50 years with low-energy hip fractures requiring surgical intervention. INTERVENTION: Patients were randomized to either HA or THA groups in the initial data set. Surgeons' fellowship training was ascertained retrospectively, and outcomes were compared. MAIN OUTCOME MEASUREMENTS: The main outcome was an unplanned secondary procedure at 24 months. Secondary outcomes included death, serious adverse events, prosthetic joint infection (PJI), dislocation, discharge disposition, an

A Trial of Wound Irrigation in the Initial Management of Open Fracture Wounds

Copyright © 2015 Massachusetts Medical Society. BACKGROUND The management of open fractures requires wound irrigation and dridement to remove contaminants, but the effectiveness of various pressures and solutions for irrigation remains controversial. We investigated the effects of castile soap versus normal saline irrigation delivered by means of high, low, or very low irrigation pressure. METHODS In this study with a 2-by-3 factorial design, conducted at 41 clinical centers, we randomly assigned patients who had an open fracture of an extremity to undergo irrigation with one of three irrigation pressures (high pressure [\u3e20 psi], low pressure [5 to 10 psi], or very low pressure [1 to 2 psi]) and one of two irrigation solutions (castile soap or normal saline). The primary end point was reoperation within 12 months after the index surgery for promotion of wound or bone healing or treatment of a wound infection. RESULTS A total of 2551 patients underwent randomization, of whom 2447 were deemed eligible and included in the final analyses. Reoperation occurred in 109 of 826 patients (13.2%) in the high-pressure group, 103 of 809 (12.7%) in the low-pressure group, and 111 of 812 (13.7%) in the very-low-pressure group. Hazard ratios for the three pairwise comparisons were as follows: for low versus high pressure, 0.92 (95% confidence interval [CI], 0.70 to 1.20; P = 0.53), for high versus very low pressure, 1.02 (95% CI, 0.78 to 1.33; P = 0.89), and for low versus very low pressure, 0.93 (95% CI, 0.71 to 1.23; P = 0.62). Reoperation occurred in 182 of 1229 patients (14.8%) in the soap group and in 141 of 1218 (11.6%) in the saline group (hazard ratio, 1.32, 95% CI, 1.06 to 1.66; P = 0.01). CONCLUSIONS The rates of reoperation were similar regardless of irrigation pressure, a finding that indicates that very low pressure is an acceptable, low-cost alternative for the irrigation of open fractures. The reoperation rate was higher in the soap group than in the saline group. (Funded by the Canadian Institutes of Health Research and others; FLOW ClinicalTrials.gov number, NCT00788398

Characterization of the Morphometry of Impact Craters Hosting Polar Deposits in Mercury's North Polar Region

Earth-based radar images dating back two decades show that the floors of some polar craters on Mercury host radar-bright deposits that have been proposed to consist of frozen volatiles. Several hypotheses have been put forth to explain their source, including volcanic outgassing, chemical sputtering, and deposition of exogenous water ice. Calculations show that volatiles are thermally stable in permanently shadowed areas. An earlier study of the depths of north polar craters determined with photoclinometric techniques applied to Mariner 10 images yielded the conclusion that the mean ratio of crater depth d to rim-crest diameter D for craters hosting polar deposits is two-thirds that of the mean ratio for a comparable population of neighboring craters lacking such deposits. This result could be explained by (though doesn't require) the presence of a thick layer of volatiles within the polar deposit-hosting craters. Here we use altimetric profiles and topographic maps obtained by the Mercury Laser Altimeter (MLA) to revisit this analysis. MLA is an instrument on the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft, which has been orbiting Mercury since March 2011. MLA transmits a 1064-nm laser pulse at 8 Hz during MESSENGER's trajectory over Mercury s surface. The MLA illuminates surface areas averaging between 15 m and 100 m in diameter, spaced approx 400 m apart along the spacecraft ground track. The radial precision of individual measurements is <1 m, and the current accuracy with respect to Mercury s center of mass is better than 20 m. As of mid-December 2011, MLA coverage had reached to 15 S and has yielded a comprehensive map of the topography of Mercury s northern hemisphere. The MLA data are used here to quantify the shapes of craters in the north polar region and to avoid the shadowing bias of photoclinometric techniques

Risk Factors Associated With Infection in Open Fractures of the Upper and Lower Extremities

Introduction: Open fractures are associated with a high risk of infection. The prevention of infection is the single most important goal, influencing perioperative care of patients with open fractures. Using data from 2,500 participants with open fracture wounds enrolled in the Fluid Lavage of Open Wounds trial, we conducted a multivariable analysis to determine the factors that are associated with infections 12 months postfracture. Methods: Eighteen predictor variables were identified for infection a priori from baseline data, fracture characteristics, and surgical data from the Fluid Lavage of Open Wounds trial. Twelve predictor variables were identified for deep infection, which included both surgically and nonoperatively managed infections.We used multivariable Cox proportional hazards regression analyses to identify the factors associated with infection. Irrigation solution and pressure were included as variables in the analysis. The results were reported as adjusted hazard ratios (HRs), 95% confidence intervals (CIs), and associated P values. All tests were two tailed with alpha = 0.05. Results: Factors associated with any infection were fracture location (tibia: HR 5.13 versus upper extremity, 95% CI 3.28 to 8.02; other lower extremity: HR 3.63 versus upper extremity, 95% CI 2.38 to 5.55; overall P\u3c 0.001), low energy injury (HR 1.64, 95% CI 1.08 to 2.46; P = 0.019), degree of wound contamination (severe: HR 2.12 versus mild, 95% CI 1.35 to 3.32; moderate: HR 1.08 versus mild, 95% CI 0.78 to 1.49; overall P = 0.004), and need for flap coverage (HR 1.82, 95% CI 1.11 to 2.99; P = 0.017). Discussion: The results of this study provide a better understanding of which factors are associated with a greater risk of infection in open fractures. In addition, it can allow for surgeons to better counsel patients regarding prognosis, helping patients to understand their individual risk of infection

Risk Factors Associated With Infection in Open Fractures of the Upper and Lower Extremities

Introduction: Open fractures are associated with a high risk of infection. The prevention of infection is the single most important goal, influencing perioperative care of patients with open fractures. Using data from 2,500 participants with open fracture wounds enrolled in the Fluid Lavage of Open Wounds trial, we conducted a multivariable analysis to determine the factors that are associated with infections 12 months postfracture. Methods: Eighteen predictor variables were identified for infection a priori from baseline data, fracture characteristics, and surgical data from the Fluid Lavage of Open Wounds trial. Twelve predictor variables were identified for deep infection, which included both surgically and nonoperatively managed infections.We used multivariable Cox proportional hazards regression analyses to identify the factors associated with infection. Irrigation solution and pressure were included as variables in the analysis. The results were reported as adjusted hazard ratios (HRs), 95% confidence intervals (CIs), and associated P values. All tests were two tailed with alpha = 0.05. Results: Factors associated with any infection were fracture location (tibia: HR 5.13 versus upper extremity, 95% CI 3.28 to 8.02; other lower extremity: HR 3.63 versus upper extremity, 95% CI 2.38 to 5.55; overall P\u3c 0.001), low energy injury (HR 1.64, 95% CI 1.08 to 2.46; P = 0.019), degree of wound contamination (severe: HR 2.12 versus mild, 95% CI 1.35 to 3.32; moderate: HR 1.08 versus mild, 95% CI 0.78 to 1.49; overall P = 0.004), and need for flap coverage (HR 1.82, 95% CI 1.11 to 2.99; P = 0.017). Discussion: The results of this study provide a better understanding of which factors are associated with a greater risk of infection in open fractures. In addition, it can allow for surgeons to better counsel patients regarding prognosis, helping patients to understand their individual risk of infection

Are large clinical trials in orthopaedic trauma justified?

© 2018 The Author(s). Background: The objective of this analysis is to evaluate the necessity of large clinical trials using FLOW trial data. Methods: The FLOW pilot study and definitive trial were factorial trials evaluating the effect of different irrigation solutions and pressures on re-operation. To explore treatment effects over time, we analyzed data from the pilot and definitive trial in increments of 250 patients until the final sample size of 2447 patients was reached. At each increment we calculated the relative risk (RR) and associated 95% confidence interval (CI) for the treatment effect, and compared the results that would have been reported at the smaller enrolments with those seen in the final, adequately powered study. Results: The pilot study analysis of 89 patients and initial incremental enrolments in the FLOW definitive trial favored low pressure compared to high pressure (RR: 1.50, 95% CI: 0.75-3.04; RR: 1.39, 95% CI: 0.60-3.23, respectively), which is in contradiction to the final enrolment, which found no difference between high and low pressure (RR: 1.04, 95% CI: 0.81-1.33). In the soap versus saline comparison, the FLOW pilot study suggested that re-operation rate was similar in both the soap and saline groups (RR: 0.98, 95% CI: 0.50-1.92), whereas the FLOW definitive trial found that the re-operation rate was higher in the soap treatment arm (RR: 1.28, 95% CI: 1.04-1.57). Conclusions: Our findings suggest that studies with smaller sample sizes would have led to erroneous conclusions in the management of open fracture wounds. Trial registration: NCT01069315 (FLOW Pilot Study) Date of Registration: February 17, 2010, NCT00788398 (FLOW Definitive Trial) Date of Registration: November 10, 2008

Fixation Using Alternative Implants for the Treatment of Hip Fractures

Objectives: To conduct a pilot trial for the Fixation using Alternative Implants for the Treatment of Hip Fractures (FAITH-2) protocol to assess feasibility of a definitive trial. Design: Pilot trial. Setting: Twenty-five clinical sites across North America and Australia were initiated, but enrolment occurred in only 15 North American sites. Patients/participants: Ninety-one randomized adults aged 18 to 60 years with a femoral neck fracture requiring surgical fixation. Intervention: Eligible patients were randomized to receive surgical treatment (sliding hip screw or cancellous screws) AND nutritional supplementation (4000 IU of vitamin D or placebo) for 6 months postfracture. Main outcome measurements: Feasibility outcomes included: clinical site initiation, participant enrolment rate, proportion of participants with complete 12-month follow-up, level of data quality, and rate of protocol adherence (number of randomization errors, crossovers between treatment groups, and daily supplementation adherence). Results: Eighty-six of 91 participants randomized into the pilot trial from 15 North American hospitals were deemed eligible. Four of five primary feasibility criteria were not achieved as we were unable to initiate clinical sites outside of North America and Australia due to feasibility constraints, slow participant enrolment (60 participants recruited over 36 mo), low adherence with daily nutritional supplementation at the 6-week (72.1%), 3-month (60.5%), and 6-month (54.7%) follow-up visits, and a high loss to follow-up rate of 22.1% at 12 months. Conclusions: Despite not meeting key feasibility criteria, we increased our knowledge on the logistics and anticipated barriers when conducting vitamin D supplementation trials in this trauma population, which can be used to inform the design and conduct of future trials on this topic

Fixation Using Alternative Implants for the Treatment of Hip Fractures (FAITH-2): The Clinical Outcomes of a Multicenter 2 × 2 Factorial Randomized Controlled Pilot Trial in Young Femoral Neck Fracture Patients

Objective: To assess whether the fixation method and vitamin D supplementation affect the risk of patient-important outcomes within 12 months of injury in nongeriatric femoral neck fracture patients. Design: A pilot factorial randomized controlled trial. Setting: Fifteen North American clinical sites. Participants: Ninety-one adults 18–60 years of age with a femoral neck fracture requiring surgical fixation. Intervention: Participants were randomized to a surgical intervention (sliding hip screw or cancellous screws) and a vitamin D intervention (vitamin D3 4000 IU daily vs. placebo for 6 months). Main Outcome Measurements: The primary clinical outcome was a composite of patient-important complications (reoperation, femoral head osteonecrosis, severe femoral neck malunion, and nonunion). Secondary outcomes included fracture-healing complications and radiographic fracture healing. Results: Eighty-six participants with a mean age of 41 years were included. We found no statistically significant difference in the risk of patient-important outcomes between the surgical treatment arms (hazard ratio 0.90, 95% confidence interval 0.40–2.02, P = 0.80) and vitamin D supplementation treatment arms (hazard ratio 0.96, 95% confidence interval 0.42–2.18, P = 0.92). Conclusions: These pilot trial results continue to describe the results of current fixation implants, inform the challenges of improving outcomes in this fracture population, and may guide future vitamin D trials to improve healing outcomes in young fracture populations. Although the pilot trial was not adequately powered to detect treatment effects, publishing these results may facilitate future meta-analyses on this topic. Level of Evidence: Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence

Checkpoints in a Yeast Differentiation Pathway Coordinate Signaling during Hyperosmotic Stress

All eukaryotes have the ability to detect and respond to environmental and hormonal signals. In many cases these signals evoke cellular changes that are incompatible and must therefore be orchestrated by the responding cell. In the yeast Saccharomyces cerevisiae, hyperosmotic stress and mating pheromones initiate signaling cascades that each terminate with a MAP kinase, Hog1 and Fus3, respectively. Despite sharing components, these pathways are initiated by distinct inputs and produce distinct cellular behaviors. To understand how these responses are coordinated, we monitored the pheromone response during hyperosmotic conditions. We show that hyperosmotic stress limits pheromone signaling in at least three ways. First, stress delays the expression of pheromone-induced genes. Second, stress promotes the phosphorylation of a protein kinase, Rck2, and thereby inhibits pheromone-induced protein translation. Third, stress promotes the phosphorylation of a shared pathway component, Ste50, and thereby dampens pheromone-induced MAPK activation. Whereas all three mechanisms are dependent on an increase in osmolarity, only the phosphorylation events require Hog1. These findings reveal how an environmental stress signal is able to postpone responsiveness to a competing differentiation signal, by acting on multiple pathway components, in a coordinated manner