Quantifying evolutionary constraints on B cell affinity maturation

The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution methods for the analysis of B cell sequence data, and then apply them to a very deep short-read data set of B cell receptors. We find that the substitution process is conserved across individuals but varies significantly across gene segments. We investigate selection on B cell receptors using a novel method that side-steps the difficulties encountered by previous work in differentiating between selection and motif-driven mutation; this is done through stochastic mapping and empirical Bayes estimators that compare the evolution of in-frame and out-of-frame rearrangements. We use this new method to derive a per-residue map of selection, which provides a more nuanced view of the constraints on framework and variable regions.Comment: Previously entitled "Substitution and site-specific selection driving B cell affinity maturation is consistent across individuals

Infected Necrosis in Severe Pancreatitis - Combined Nonsurgical Multi-Drainage with Directed Transabdominal High-Volume Lavage in Critically Ill Patients

Background: Infection of pancreatic necrosis is a life-threatening complication during the course of acute pancreatitis. In critically ill patients, surgical or extended endoscopic interventions are associated with high morbidity and mortality. Minimally invasive procedures on the other hand are often insufficient in patients suffering from large necrotic areas containing solid or purulent material. We present a strategy combining percutaneous and transgastric drainage with continuous high-volume lavage for treatment of extended necroses and liquid collections in a series of patients with severe acute pancreatitis. Patients and Methods: Seven consecutive patients with severe acute pancreatitis and large confluent infected pancreatic necrosis were enrolled. In all cases, the first therapeutic procedure was placement of a CT-guided drainage catheter into the fluid collection surrounding peripancreatic necrosis. Thereafter, a second endosonographically guided drainage was inserted via the gastric or the duodenal wall. After communication between the separate drains had been proven, an external to internal directed high-volume lavage with a daily volume of 500 ml up to 2,000 ml was started. Results: In all patients, pancreatic necrosis/liquid collections could be resolved completely by the presented regime. No patient died in the course of our study. After initiation of the directed high-volume lavage, there was a significant clinical improvement in all patients. Double drainage was performed for a median of 101 days, high-volume lavage for a median of 41 days. Several endoscopic interventions for stent replacement were required (median 8). Complications such as bleeding or perforation could be managed endoscopically, and no subsequent surgical therapy was necessary. All patients could be dismissed from the hospital after a median duration of 78 days. Conclusion: This approach of combined percutaneous/endoscopic drainage with high-volume lavage shows promising results in critically ill patients with extended infected pancreatic necrosis and high risk of surgical intervention. Neither surgical nor endoscopic necrosectomy was necessary in any of our patients. Copyright (C) 2009 S. Karger AG, Basel and IA

Resolution of Clinical Signs of Ventilator-Associated Pneumonia in Trauma Patients

Objectives: The ATS/IDSA Ventilator-Associated Pneumonia (VAP) guidelines suggest that clinical improvement of VAP should be apparent within 3–6 days. This study evaluated resolution of clinical signs of VAP in trauma patients after diagnosis. Methods: Critically injured adults admitted to the trauma intensive care unit (ICU) from June 1, 2006, to December 31, 2007, and subsequently given a diagnosis of VAP were retrospectively assessed. Clinical signs, including derangements of maximum temperature (Tmax), white blood cell (WBC) count, and PaO2/FiO2, were evaluated on days 1–16 after VAP diagnosis. Data are presented as mean ± SD unless otherwise stated. Clinical parameters after VAP were compared using repeated-measures ANOVA with the Tukey test for multiple comparisons. Results: A total of 82 patients were identified. Data for the 34 patients without concurrent infections are presented. Demographic data include: Age 46 ± 17 years; 71% men; 94% blunt trauma; median (IQR) Injury Severity Score 29.5 (24–38); duration of mechanical ventilation 33 ± 27 days; ICU length of stay (LOS) 39 ± 25 days; hospital LOS 53 ± 33 days. Clinical signs following VAP diagnosis: Tmax (°F): Day 1=101.8 ± 1.3, Day 3=101.1 ± 1.1, Day 6=101.1 ± 1.4, Day 16=100.1 ± 3. Compared to Day 1, there was a significant reduction in Tmax at days 10, 11, 12, 13, 14, and 16 (p\u3c0.05 for all). WBC count (cells per microliter): day 1 = 12.9 ± 5, day 3 = 13.7 ± 5, day 6 = 14.4 ± 5, and day 16 = 13.8 ± 6. There was no significant difference in WBC on days 1–16 (p=0.42). PaO2/FiO2: day 1 = 232 ± 108, day 3 = 200 ± 87, day 6 = 218 ± 104, day 16 = 246 ± 126. Differences in PaO2/FiO2 on days 1–16 did not reach statistical significance (p=0.06). Conclusion: Improvement of clinical parameters after a VAP diagnosis is delayed in trauma patients. Alternative methods for determining resolution should be investigated. Published in To be published in Critical Care Medicine’s December 2009 supplement

Resolution of Clinical Signs in Trauma Intensive Care Unit Patients Following Diagnosis of Ventilator-Associated Pneumonia

PURPOSE: The ATS/IDSA Ventilator-Associated Pneumonia (VAP) guidelines suggest that clinical improvement of VAP should be apparent within 3-6 days. Anecdotally, such improvement has not been noted in trauma patients at our institution. The current study was conducted to evaluate resolution of clinical signs of VAP following diagnosis. METHODS: Critically injured adults admitted to the trauma intensive care unit (TICU) from 6/1/06-12/31/07 and subsequently diagnosed with VAP were retrospectively reviewed. Clinical signs, including derangements of maximum temperature (Tmax), white blood cell (WBC) count and Pa02/FiO2, were evaluated on days 1-16 following VAP diagnosis. Data are presented as mean ± SD unless otherwise stated. Clinical parameters following VAP were compared using repeated measures ANOVA with the Tukey test for multiple comparisons. RESULTS: A total of 82 patients were identified. Data for the 34 patients without concurrent infections are presented. Demographic data include: Age 46 ± 17 years; 71% males; 94% blunt trauma; median (IQR) Injury Severity Score 29.5 (24 to 38); duration of mechanical ventilation 33 ± 27 days; ICU length of stay (LOS) 39 ± 25 days; hospital LOS 53 ± 33 days. Clinical signs following VAP diagnosis (Figure): Tmax (°F): Day 1=101.8 ± 1.3, Day 3=101.1 ± 1.1, Day 6=101.1 ± 1.4, Day 16=100.1 ± 3. Compared to Day 1, there was a significant reduction in Tmax at Days 10, 11, 12, 13, 14 and 16 (p \u3c 0.05 for all). WBC count (cells/μL): Day 1=12.9 ± 5, Day 3=13.7 ± 5, Day 6=14.4 ± 5, Day 16=13.8 ± 6. There was no significant difference in WBC count on Days 1-16 (p=0.42). PaO2/FiO2: Day 1=232 ± 108, Day 3=200 ± 87, Day 6=218 ± 104, Day 16=246 ± 126. Differences in PaO2/FiO2 on Days 1-16 did not reach statistical significance (p=0.06). CONCLUSIONS: In trauma patients, improvement of clinical parameters following diagnosis of VAP is delayed beyond the 3-6 day timeframe suggested in the ATS/IDSA guidelines. Alternative methods for determining resolution of VAP in trauma patients should be investigated. METHODS INTRODUCTIO

The bone morphogenetic protein axis is a positive regulator of skeletal muscle mass

Although the canonical transforming growth factor β signaling pathway represses skeletal muscle growth and promotes muscle wasting, a role in muscle for the parallel bone morphogenetic protein (BMP) signaling pathway has not been defined. We report, for the first time, that the BMP pathway is a positive regulator of muscle mass. Increasing the expression of BMP7 or the activity of BMP receptors in muscles induced hypertrophy that was dependent on Smad1/5-mediated activation of mTOR signaling. In agreement, we observed that BMP signaling is augmented in models of muscle growth. Importantly, stimulation of BMP signaling is essential for conservation of muscle mass after disruption of the neuromuscular junction. Inhibiting the phosphorylation of Smad1/5 exacerbated denervation-induced muscle atrophy via an HDAC4-myogenin–dependent process, whereas increased BMP–Smad1/5 activity protected muscles from denervation-induced wasting. Our studies highlight a novel role for the BMP signaling pathway in promoting muscle growth and inhibiting muscle wasting, which may have significant implications for the development of therapeutics for neuromuscular disorders

Low Pathogenic Avian Influenza Isolates from Wild Birds Replicate and Transmit via Contact in Ferrets without Prior Adaptation

Direct transmission of avian influenza viruses to mammals has become an increasingly investigated topic during the past decade; however, isolates that have been primarily investigated are typically ones originating from human or poultry outbreaks. Currently there is minimal comparative information on the behavior of the innumerable viruses that exist in the natural wild bird host. We have previously demonstrated the capacity of numerous North American avian influenza viruses isolated from wild birds to infect and induce lesions in the respiratory tract of mice. In this study, two isolates from shorebirds that were previously examined in mice (H1N9 and H6N1 subtypes) are further examined through experimental inoculations in the ferret with analysis of viral shedding, histopathology, and antigen localization via immunohistochemistry to elucidate pathogenicity and transmission of these viruses. Using sequence analysis and glycan binding analysis, we show that these avian viruses have the typical avian influenza binding pattern, with affinity for cell glycoproteins/glycolipids having terminal sialic acid (SA) residues with α 2,3 linkage [Neu5Ac(α2,3)Gal]. Despite the lack of α2,6 linked SA binding, these AIVs productively infected both the upper and lower respiratory tract of ferrets, resulting in nasal viral shedding and pulmonary lesions with minimal morbidity. Moreover, we show that one of the viruses is able to transmit to ferrets via direct contact, despite its binding affinity for α 2,3 linked SA residues. These results demonstrate that avian influenza viruses, which are endemic in aquatic birds, can potentially infect humans and other mammals without adaptation. Finally this work highlights the need for additional study of the wild bird subset of influenza viruses in regard to surveillance, transmission, and potential for reassortment, as they have zoonotic potential

Web-based alcohol screening and brief intervention for Māori and non-Māori: the New Zealand e-SBINZ trials

BACKGROUND: Hazardous alcohol consumption is a leading modifiable cause of mortality and morbidity among young people. Screening and brief intervention (SBI) is a key strategy to reduce alcohol-related harm in the community, and web-based approaches (e-SBI) have advantages over practitioner-delivered approaches, being cheaper, more acceptable, administrable remotely and infinitely scalable. An efficacy trial in a university population showed a 10-minute intervention could reduce drinking by 11% for 6 months or more among 17-24 year-old undergraduate hazardous drinkers. The e-SBINZ study is designed to examine the effectiveness of e-SBI across a range of universities and among Māori and non-Māori students in New Zealand. METHODS/DESIGN: The e-SBINZ study comprises two parallel, double blind, multi-site, individually randomised controlled trials. This paper outlines the background and design of the trial, which is recruiting 17-24 year-old students from seven of New Zealand's eight universities. Māori and non-Māori students are being sampled separately and are invited by e-mail to complete a web questionnaire including the AUDIT-C. Those who score >4 will be randomly allocated to no further contact until follow-up (control) or to assessment and personalised feedback (intervention) via computer. Follow-up assessment will occur 5 months later in second semester. Recruitment, consent, randomisation, intervention and follow-up are all online. Primary outcomes are (i) total alcohol consumption, (ii) frequency of drinking, (iii) amount consumed per typical drinking occasion, (iv) the proportions exceeding medical guidelines for acute and chronic harm, and (v) scores on an academic problems scale. DISCUSSION: The trial will provide information on the effectiveness of e-SBI in reducing hazardous alcohol consumption across diverse university student populations with separate effect estimates for Māori and non-Māori students. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12610000279022

Avian Influenza Viruses Infect Primary Human Bronchial Epithelial Cells Unconstrained by Sialic Acid α2,3 Residues

Avian influenza viruses (AIV) are an important emerging threat to public health. It is thought that sialic acid (sia) receptors are barriers in cross-species transmission where the binding preferences of AIV and human influenza viruses are sias α2,3 versus α2,6, respectively. In this study, we show that a normal fully differentiated, primary human bronchial epithelial cell model is readily infected by low pathogenic H5N1, H5N2 and H5N3 AIV, which primarily bind to sia α2,3 moieties, and replicate in these cells independent of specific sias on the cell surface. NHBE cells treated with neuraminidase prior to infection are infected by AIV despite removal of sia α2,3 moieties. Following AIV infection, higher levels of IP-10 and RANTES are secreted compared to human influenza virus infection, indicating differential chemokine expression patterns, a feature that may contribute to differences in disease pathogenesis between avian and human influenza virus infections in humans

Observational study on efficacy of negative expiratory pressure test proposed as screening for obstructive sleep apnea syndrome among commercial interstate bus drivers - protocol study

<p>Abstract</p> <p>Background</p> <p>Obstructive sleep apnea (OSA) is a respiratory disease characterized by the collapse of the extrathoracic airway and has important social implications related to accidents and cardiovascular risk. The main objective of the present study was to investigate whether the drop in expiratory flow and the volume expired in 0.2 s during the application of negative expiratory pressure (NEP) are associated with the presence and severity of OSA in a population of professional interstate bus drivers who travel medium and long distances.</p> <p>Methods/Design</p> <p>An observational, analytic study will be carried out involving adult male subjects of an interstate bus company. Those who agree to participate will undergo a detailed patient history, physical examination involving determination of blood pressure, anthropometric data, circumference measurements (hips, waist and neck), tonsils and Mallampati index. Moreover, specific questionnaires addressing sleep apnea and excessive daytime sleepiness will be administered. Data acquisition will be completely anonymous. Following the medical examination, the participants will perform a spirometry, NEP test and standard overnight polysomnography. The NEP test is performed through the administration of negative pressure at the mouth during expiration. This is a practical test performed while awake and requires little cooperation from the subject. In the absence of expiratory flow limitation, the increase in the pressure gradient between the alveoli and open upper airway caused by NEP results in an increase in expiratory flow.</p> <p>Discussion</p> <p>Despite the abundance of scientific evidence, OSA is still underdiagnosed in the general population. In addition, diagnostic procedures are expensive, and predictive criteria are still unsatisfactory. Because increased upper airway collapsibility is one of the main determinants of OSA, the response to the application of NEP could be a predictor of this disorder. With the enrollment of this study protocol, the expectation is to encounter predictive NEP values for different degrees of OSA in order to contribute toward an early diagnosis of this condition and reduce its impact and complications among commercial interstate bus drivers.</p> <p>Trial registration</p> <p><it>Registro Brasileiro de Ensaios Clinicos </it>(local acronym RBEC) [Internet]: Rio de Janeiro (RJ): <it>Instituto de Informaçao Cientifica e Tecnologica em Saude </it>(Brazil); 2010 - Identifier RBR-7dq5xx. Cross-sectional study on efficacy of negative expiratory pressure test proposed as screening for obstructive sleep apnea syndrome among commercial interstate bus drivers; 2011 May 31 [7 pages]. Available from <url>http://www.ensaiosclinicos.gov.br/rg/RBR-7dq5xx/</url>.</p