747 research outputs found

    The PhoBR two-component system regulates antibiotic biosynthesis in Serratia in response to phosphate

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    <p>Abstract</p> <p>Background</p> <p>Secondary metabolism in <it>Serratia </it>sp. ATCC 39006 (<it>Serratia </it>39006) is controlled via a complex network of regulators, including a LuxIR-type (SmaIR) quorum sensing (QS) system. Here we investigate the molecular mechanism by which phosphate limitation controls biosynthesis of two antibiotic secondary metabolites, prodigiosin and carbapenem, in <it>Serratia </it>39006.</p> <p>Results</p> <p>We demonstrate that a mutation in the high affinity phosphate transporter <it>pstSCAB-phoU</it>, believed to mimic low phosphate conditions, causes upregulation of secondary metabolism and QS in <it>Serratia </it>39006, via the PhoBR two-component system. Phosphate limitation also activated secondary metabolism and QS in <it>Serratia </it>39006. In addition, a <it>pstS </it>mutation resulted in upregulation of <it>rap</it>. Rap, a putative SlyA/MarR-family transcriptional regulator, shares similarity with the global regulator RovA (regulator of virulence) from <it>Yersina </it>spp. and is an activator of secondary metabolism in <it>Serratia </it>39006. We demonstrate that expression of <it>rap</it>, <it>pigA-O </it>(encoding the prodigiosin biosynthetic operon) and <it>smaI </it>are controlled via PhoBR in <it>Serratia </it>39006.</p> <p>Conclusion</p> <p>Phosphate limitation regulates secondary metabolism in <it>Serratia </it>39006 via multiple inter-linked pathways, incorporating transcriptional control mediated by three important global regulators, PhoB, SmaR and Rap.</p

    Impact of disease severity on outcome of antiviral therapy for chronic hepatitis C: Lessons from the HALT-C trial

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    In patients with chronic hepatitis C, advanced fibrosis and cirrhosis are associated with lower rates of sustained virologic response (SVR) to interferon (IFN)-based therapy. In this study, we assessed virologic response to retreatment with peginterferon alfa-2a and ribavirin (RBV), as a function of the baseline fibrosis score (Ishak staging) and platelet count, in 1,046 patients enrolled in the Hepatitis C Antiviral Long-term Treatment against Cirrhosis (HALT-C) Trial. All patients had failed prior treatment with IFN or peginterferon ± RBV and had Ishak fibrosis scores ≥ 3. Four groups of patients with increasingly severe liver disease were compared: (A) bridging fibrosis (Ishak 3 and 4) with platelet counts >125,000/mm 3 (n = 559); (B) bridging fibrosis with platelet counts ≤125,000/mm 3 (n = 96); (C) cirrhosis (Ishak 5 and 6) with platelet counts >125,000/mm 3 (n = 198); and (D) cirrhosis with platelet counts ≤125,000/mm 3 (n = 193). SVR rates were 23%, 17%, 10%, and 9% in groups A, B, C, and D, respectively ( P < .0001 for trend). Reduction in SVR as a function of increasingly severe disease was independent of age, percent African American, HCV genotype, HCV level, and type of prior therapy. Dose reduction lowered SVR frequencies, but to a lesser extent than disease severity. By logistic regression, cirrhosis ( P < .0001) was the major determinant that impaired virologic response, independent of dose reduction or platelet count. In conclusion , disease severity is a major independent determinant of rate of SVR in patients with advanced chronic hepatitis C. New strategies are needed to optimize antiviral therapy in these “difficult-to-cure” patients. (H EPATOLOGY 2006;44:1675–1684.)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55880/1/21440_ftp.pd

    Dietary N-3 polyunsaturated fatty acids decrease biliary cholesterol saturation in gallstone disease

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    Because fatty acid composition of biliary phospholipids influences cholesterol secretion into bile, we investigated whether replacement of n-1 monounsaturated or n-6 polyunsaturated fatty acids with n-3 polyunsaturated fatty acids in biliary phosphatidylcholines reduces supersaturation with cholesterol and prevents precipitation of cholesterol crystals in bile of gallstone patients. Seven patients with radiolucent gallstones in functioning gallbladders were studied before (control) and after 5 wk of dietary supplementation with marine fish oil (11.3 gm/day = 3.75 gm n-3 polyunsaturated fatty acids/day). Duodenal bile was collected for analysis during intravenous infusion of cholecystokinin. Gallbladder emptying in response to cholecystokinin was comparable before and during intake of n-3 polyunsaturated fatty acids. Intake of n-3 polyunsaturated fatty acids increased (p < 0.001) the fractions of eicosapentaenoic and docosahexaenoic acids and decreased the fractions of linoleic (p < 0.001) and arachidonic acids (p < 0.02) in biliary phospholipids. Concomitantly, the molar ratio of cholesterol to phospholipids decreased (-19%; p < 0.05). As a consequence, the cholesterol saturation index was reduced by -25% (p = 0.01), from 1.60 ± 0.44 to 1.24 ± 0.38. However, in vitro nucleation time of duodenal bile was not prolonged. The decrease in cholesterol saturation was not sufficient to prevent nucleation of cholesterol crystals in bile of gallstone patients. In conclusion, our data suggest that cholesterol saturation can be influenced by the fatty acid composition of the phosphatidylcholines secreted in bile

    Experiments in lifelog organisation and retrieval at NTCIR

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    Lifelogging can be described as the process by which individuals use various software and hardware devices to gather large archives of multimodal personal data from multiple sources and store them in a personal data archive, called a lifelog. The Lifelog task at NTCIR was a comparative benchmarking exercise with the aim of encouraging research into the organisation and retrieval of data from multimodal lifelogs. The Lifelog task ran for over 4 years from NTCIR-12 until NTCIR-14 (2015.02–2019.06); it supported participants to submit to five subtasks, each tackling a different challenge related to lifelog retrieval. In this chapter, a motivation is given for the Lifelog task and a review of progress since NTCIR-12 is presented. Finally, the lessons learned and challenges within the domain of lifelog retrieval are presented

    Obstructive Jaundice in Polycystic Liver Disease Related to Coexisting Cholangiocarcinoma

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    Although jaundice rarely complicates polycystic liver disease (PLD), secondary benign or malignant causes cannot be excluded. In a 72-year-old female who presented with increased abdominal girth, dyspnea, weight loss and jaundice, ultrasound and computed tomography confirmed the diagnosis of PLD by demonstrating large liver cysts causing extrahepatic bile duct compression. Percutaneous cyst aspiration failed to relief jaundice due to distal bile duct cholangiocarcinoma, suspected by magnetic resonance cholangiopancreatography (MRCP) and confirmed by endoscopic retrograde cholangiopancreatography (ERCP). Coexistence of PLD with distal common bile duct cholangiocarcinoma has not been reported so far

    Liver transplantation for alcoholic cirrhosis: Long term follow-up and impact of disease recurrence

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    Background. Alcoholic liver disease has emerged as a leading indication for hepatic transplantation, although it is a controversial use of resources. We aimed to examine all aspects of liver transplantation associated with alcohol abuse. Methods. Retrospective cohort analysis of 123 alcoholic patients with a median of 7 years follow-up at one center. Results. In addition to alcohol, 43 (35%) patients had another possible factor contributing to cirrhosis. Actuarial patient and graft survival rates were, respectively, 84% and 81% (1 year); 72% and 66% (5 years); and 63% and 59% (7 years). After transplantation, 18 patients (15%) manifested 21 noncutaneous de novo malignancies, which is significantly more than controls (P=0.0001); upper aerodigestive squamous carcinomas were over-represented (P=0.03). Thirteen patients had definitely relapsed and three others were suspected to have relapsed. Relapse was predicted by daily ethanol consumption (P=0.0314), but not by duration of pretransplant sobriety or explant histology. No patient had alcoholic hepatitis after transplantation and neither late onset acute nor chronic rejection was significantly increased. Multiple regression analyses for predictors of graft failure identified major biliary/vascular complications (P=0.01), chronic bile duct injury on biopsy (P=0.002), and pericellular fibrosis on biopsy (P=0.05); graft viral hepatitis was marginally significant (P=0.07) on univariate analysis. Conclusions. Alcoholic liver disease is an excellent indication for liver transplantation in those without coexistent conditions. Recurrent alcoholic liver disease alone is not an important cause of graft pathology or failure. Potential recipients should be heavily screened before transplantation for coexistent conditions (e.g., hepatitis C, metabolic diseases) and other target-organ damage, especially aerodigestive malignancy, which are greater causes of morbidity and mortality than is recurrent alcohol liver disease

    A clinically interpretable convolutional neural network for the real time prediction of early squamous cell cancer of the esophagus; comparing diagnostic performance with a panel of expert European and Asian endoscopists

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    BACKGROUND AND AIMS: Intrapapillary capillary loops (IPCLs) are microvascular structures that correlate with invasion depth of early squamous cell neoplasia (ESCN) and allow accurate prediction of histology. Artificial intelligence may improve human recognition of IPCL patterns and prediction of histology to allow prompt access to endoscopic therapy of ESCN where appropriate METHODS: One hundred fifteen patients were recruited at 2 academic Taiwanese hospitals. ME-NBI videos of squamous mucosa were labeled as dysplastic or normal according to their histology and IPCL patterns classified by consensus of 3 experienced clinicians. A convolutional neural network (CNN) was trained to classify IPCLs, using 67742 high quality ME-NBI by 5-fold cross validation. Performance measures were calculated to give an average F1 score, accuracy, sensitivity, and specificity. A panel of 5 Asian and 4 European experts predicted the histology of a random selection of 158 images using the JES IPCL classification; accuracy, sensitivity, specificity, positive and negative predictive values were calculated. RESULTS: Expert European Union (EU) and Asian endoscopists attained F1 scores (a measure of binary classification accuracy) of 97.0% and 98%, respectively. Sensitivity and accuracy of the EU and Asian clinicians were 97%, 98% and 96.9%, 97.1% respectively. The CNN average F1 score was 94%, sensitivity 93.7% and accuracy 91.7%. Our CNN operates at video rate and generates class activation maps that can be used to visually validate CNN predictions. CONCLUSIONS: We report a clinically interpretable CNN developed to predict histology based on IPCL patterns, in real-time, using the largest reported dataset of images for this purpose. Our CNN achieved diagnostic performance comparable to an expert panel of endoscopists
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