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The cytochrome b 6 f complex of oxygenic photosynthesis produces substantial levels of reactive oxygen species (ROS). It has been observed that the ROS production rate by b 6 f is 10–20 fold higher than that observed for the analogous respiratory cytochrome bc1 complex. The types of ROS produced (O2•−, 1O2, and, possibly, H2O2) and the site(s) of ROS production within the b 6 f complex have been the subject of some debate. Proposed sources of ROS have included the heme b p , PQ p •− (possible sources for O2•−), the Rieske iron–sulfur cluster (possible source of O2•− and/or 1O2), Chl a (possible source of 1O2), and heme c n (possible source of O2•− and/or H2O2). Our working hypothesis is that amino acid residues proximal to the ROS production sites will be more susceptible to oxidative modification than distant residues. In the current study, we have identified natively oxidized amino acid residues in the subunits of the spinach cytochrome b 6 f complex. The oxidized residues were identified by tandem mass spectrometry using the MassMatrix Program. Our results indicate that numerous residues, principally localized near p-side cofactors and Chl a, were oxidatively modified. We hypothesize that these sites are sources for ROS generation in the spinach cytochrome b 6 f complex.

Arginine methylation is a common posttranslational modification that has been shown to regulate both gene expression and extranuclear signaling events. We recently reported defects in protein arginine methyltransferase 1 (PRMT1) activity and arginine methylation in the livers of cirrhosis patients with a history of recurrent infections. To examine the role of PRMT1 in innate immune responses in vivo, we created a cell type-specific knock-out mouse model. We showed that myeloid-specific PRMT1 knock-out mice demonstrate higher proinflammatory cytokine production and a lower survival rate after cecal ligation and puncture. We found that this defect is because of defective peroxisome proliferator-activated receptor γ (PPARγ)-dependent M2 macrophage differentiation. PPARγ is one of the key transcription factors regulating macrophage polarization toward a more anti-inflammatory and pro-resolving phenotype. We found that PRMT1 knock-out macrophages failed to up-regulate PPARγ expression in response to IL4 treatment resulting in 4-fold lower PPARγ expression in knock-out cells than in wild-type cells. Detailed study of the mechanism revealed that PRMT1 regulates PPARγ gene expression through histone H4R3me2a methylation at the PPARγ promoter. Supplementing with PPARγ agonists rosiglitazone and GW1929 was sufficient to restore M2 differentiation in vivo and in vitro and abrogated the difference in survival between wild-type and PRMT1 knock-out mice. Taken together these data suggest that PRMT1-dependent regulation of macrophage PPARγ expression contributes to the infection susceptibility in PRMT1 knock-out mice.

The high cost associated with antiviral treatment for chronic hepatitis C virus (HCV) infection mandates further investigation in the context of preventing complications such as type 2 diabetes mellitus (DM2). We determined the cumulative incidence of DM2 in subjects with chronic HCV infection who received concomitant pegylated interferon (Peg-IFN) and ribavirin. We conducted a retrospective analysis of data obtained from Veterans Administrations Informatics and Computing Infrastructure (VINCI) to identify an adult cohort of patients without diabetes with chronic HCV infection who received Peg-IFN-based therapy between October 2001 and December 2011. Patients with history of HIV, hepatitis B infection, hepatocellular cancer (HCC), non-HCC cancers, and history of transplantation were excluded. Sustained virological response (SVR) was defined as negative HCV RNA 3 months after completion of therapy. Using Cox proportional hazards regression for multivariable analysis, we determined that patients who achieved SVR were at a significantly less risk of developing DM2. Adjusted survival rates showed that the responders' group was significantly less likely to develop DM2 over time (HR 0.60, CI 0.48 to 0.74, p

Hepatorenal syndrome (HRS) is one of the leading causes of hospitalizations in patients with chronic liver disease (CLD). We conducted a retrospective national database study to determine the epidemiology of HRS in hospitalized patients with CLD. Data from a Nationwide Inpatient Sample were extracted from 2002 to 2012 using ICD-9-CM codes related to CLD and HRS. The following outcomes were examined: in-hospital mortality, total charges, length of stay (LOS), patient demographics, procedures, complications, and comorbidities. Statistical analysis including regression was performed to examine factors associated with HRS. During 2002–2012, hospital discharges related to CLD increased from 407,246 to 836,475 with an increase of 37.9% for HRS as a complication in this population. Patients with CLD and HRS had worse outcomes compared with patients with CLD without HRS. This was manifested as a higher mortality rate (32.0% vs 10.3%), increased LOS (median 7 vs 5 days), and increased hospital costs (median $16,000 vs $11,000). Logistic regression demonstrated that HIV/AIDS (adjusted OR 2.9, 95% CI 2.2 to 3.9), pneumonia (aOR 2.8, 95% CI 2.3 to 3.2), and esophageal variceal bleeding (aOR 1.9, 95% CI 1.7 to 2.0) were associated with higher mortality in patients with HRS. Conversely, liver transplantation (aOR 0.1, 95% CI 0.1 to 0.1), transjugular intrahepatic portosystemic shunt (aOR 0.5, 95% CI 0.4 to 0.6), and hospitalization in the Midwest region of the USA (aOR 0.7, 95% CI 0.6 to 0.7) were associated with reduced mortality. The incidence of HRS in hospitalized patients with CLD increased during 2002–2012. HRS is associated with significant mortality and morbidity in these patients.

The cytochromeb6fcomplex of oxygenic photosynthesis produces substantial levels of reactive oxygen species (ROS). It has been observed that the ROS production rate byb6fis 10-20 fold higher than that observed for the analogous respiratory cytochromebc1complex. The types of ROS produced (O2•−,1O2, and, possibly, H2O2) and the site(s) of ROS production within theb6fcomplex has been the subject of some debate. Proposed sources of ROS have include the hemebp, PQp•−(possible sources for O2•−), the Rieske iron-sulfur cluster (possible source of O2•−and/or H2O2), Chla(possible source of1O2) and hemeCn(possible source of O2•−and/or H2O2). Our working hypothesis is that amino acid residues proximal to the ROS production sites will be more susceptible to oxidative modification than distant residues. In the current study, we have identified natively oxidized amino acid residues in the subunits of the spinach cytochromeb6fcomplex. The oxidized residues were identified by tandem mass spectrometry using the MassMatrix Program. Our results indicate that numerous residues, principally localized nearp-side cofactors and Chla, were oxidatively modified. We hypothesize that these sites are sources for ROS generation in the spinach cytochromeb6fcomplex.

Esophageal variceal bleeding (EVB) is a frequent complication in cirrhotic patients resulting in considerable mortality and morbidity. The aim of this study was to investigate the occurrence, impact, and trends of EVB in hospitalized cirrhotic patients on a nationwide level in the United States. We interrogated data from the Nationwide Inpatient Sample from 2002 to 2012. Utilizing International Classification of Diseases, Ninth Revision, Clinical Modification codes, we analyzed hospital discharges for cirrhosis and related EVB in adult patients. EVB in cirrhotic patients was independently associated with overall worse outcomes with respect to in-hospital mortality (10% vs 5%; P

The cytochrome b

A shortage of donor organs is a major limitation to liver transplantation. Expansion of donor pool criteria to include patients with schistosomiasis diagnosed on liver biopsy might allow the allocation of more transplant livers. Schistosomiasis is a chronic parasitic disease affecting millions in endemic areas including sub-Sahara Africa that might lead to the development of granulomas as a response to the parasite’s ova and might cause chronic liver disease and portal hypertension. Due to increased mobility globally, schistosomiasis may be encountered in non-endemic areas. Currently, the usage of donor livers with known Schistosomiasis is not universally defined.

Open distal humeral fractures remain an especially difficult injury pattern to treat. The complex anatomy of the distal part of the humerus in combination with the challenge of treating the traumatized and relatively thin soft-tissue envelope, addressing bone and articular cartilage loss, and

Motivation: Isotope trace (IT) detection is a fundamental step for liquid or gas chromatography mass spectrometry (XC-MS) data analysis that faces a multitude of technical challenges on complex samples. The Kalman filter (KF) application to IT detection addresses some of these challenges; it discriminates closely eluting ITs in the m/z dimension, flexibly handles heteroscedastic m/z variances and does not bin the m/z axis. Yet, the behavior of this KF application has not been fully characterized, as no cost-free open-source implementation exists and incomplete evaluation standards for IT detection persist. Results: Massifquant is an open-source solution for KF IT detection that has been subjected to novel and rigorous methods of performance evaluation. The presented evaluation with accompanying annotations and optimization guide sets a new standard for comparative IT detection. Compared with centWave, matchedFilter and MZMine2—alternative IT detection engines—Massifquant detected more true ITs in a real LC-MS complex sample, especially low-intensity ITs. It also offers competitive specificity and equally effective quantitation accuracy. Availability and implementation: Massifquant is integrated into XCMS with GPL license ≥ 2.0 and hosted by Bioconductor: http://bioconductor.org . Annotation data are archived at http://hdl.lib.byu.edu/1877/3232 . Parameter optimization code and documentation is hosted at https://github.com/topherconley/optimize-it . Contact: cjconley@ucdavis.edu or jtprince@chem.byu.edu Supplementary information: Supplementary data are available at Bioinformatics online.

BackgroundPatients with decompensated hepatitis C virus (HCV) cirrhosis experience various outcomes after sustained virological response (SVR), ranging from clinical recovery to further deterioration. We hypothesised that the genetic risk for steatosis, namely the polymorphisms rs738409 of Patatin-like Phospholipase Domain-Containing 3 (PNPLA3), rs58542926 of Transmembrane-6-Superfamily-2 (TM6SF2), and rs641738 of Membrane-bound O-acyltransferase Domain-Containing 7 (MBOAT7), is predictive of recovery.MethodsWe prospectively enrolled 56 patients with Child-Pugh (CPT) B/C cirrhosis who underwent antiviral therapy. The primary outcome was change in CPT score at 12, 24, and 48 weeks after SVR. We used a linear mixed-effects model for analysis.ResultsForty-five patients (PNPLA3: 21 CC, 19 CG, 5 GG) survived to the first endpoint without liver transplantation. The mean change in CPT score at 12, 24, and 48 weeks was −1.57 (SE=0.30), –1.76 (SE=0.32), and −2.0 (SE=0.36), respectively, among the patients with thePNPLA3CC genotype and −0.50 (SE=0.20), –0.41 (SE=0.25), and −0.24 (SE=0.27), respectively, among the other 24 patients. After adjustment for baseline characteristics, thePNPLA3CG/GG genotypes were associated with a 1.29 (SE=0.30, pConclusionThePNPLA3CG/GG genotypes could identify a subgroup of patients with decompensated HCV cirrhosis that had suboptimal clinical recovery despite SVR. An understanding of the genetic factors that influence clinical outcomes will help target patients for liver transplant based on individual genetic risk factors and provide insight leading to new therapeutic approaches.

The most important step in any quantitative proteomic pipeline is feature detection (aka peak picking). However, generating quality hand-annotated data sets to validate the algorithms, especially for lower abundance peaks, is nearly impossible. An alternative for creating gold standard data is to simulate it with features closely mimicking real data. We present Mspire-Simulator, a free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components. It also includes machine-learned models for retention time and peak intensity prediction and a genetic algorithm to custom fit model parameters for experimental data sets. We show that these methods are applicable to data from three different mass spectrometers, including two fundamentally different types, and show visually and analytically that simulated peaks are nearly indistinguishable from actual data. Researchers can use simulated data to rigorously test quantitation software, and proteomic researchers may benefit from overlaying simulated data on actual data sets.

Complex disulfide bond patterns in synaptosomal-associated protein of 25 kD B (SNAP25B) are thought to regulate neurotransmitter release in response to oxidative stress. However, the steric feasibility of each possible disulfide pattern in SNAP25B has not been assessed. To assess the steric feasibility of hypothesized closely spaced complex disulfide patterning in SNAP25B and also the feasibility of identifying complex disulfide bond patterns with MS, we have developed a novel probabilistic analysis to unambiguously resolve complex double disulfide bond patterns by using an ion trap mass spectrometer. We analyzed fragmentation patterns of singly linked peptides to determine likely fragmentation events in an ion trap mass spectrometer and observed double and single backbone cleavage along with heterolytic cleavage of the disulfide bond. We modeled these same events in the doubly disulfide linked SNAP25B peptide and used a cumulative hypergeometric distribution with top–down scoring to both identify and differentiate these bonding patterns. Because of the presence of unique MS/MS peaks, two of the bonding patterns were directly identified. The third was assigned on the basis of full chromatographic separation and confirmed by modeling triple breakage fragments. In total, this work demonstrates the feasibility – and also limitations – of identification of complex intradisulfide patterns by using ion trap-based collision-induced dissociation-based fragmentation methods. Copyright © 2013 John Wiley & Sons, Ltd.

Objectives To determine optimal ratio of intramedullary nail diameter to tibial canal diameter that leads to reliable and timely healing in tibial shaft fractures. Design Retrospective case series. Setting Level I trauma center. Patients One hundred thirty-three fractures in 132 patients with tibial shaft fractures that underwent intramedullary nailing as definitive fixation were identified between June 2004 and July 2012 at our level I trauma center. Of these, 78 had serial radiographs out to 12 months that could be analyzed for radiographic healing with an average age of 37 years old (range 16-86 years). There were 52 males and 26 females. Intervention All patients underwent intramedullary nailing of the tibia with documentation of both the diameter of the nail and radiographic canal width at the isthmus to determine the nail to canal ratio. Main outcome measures Patients were followed with serial radiographs for at least 12 months to determine time to healing as a function of nail to canal ratio. The senior author assessed healing at 3, 6, 9, and 12 months using RUST criteria. Results Patients with an intramedullary nail to canal diameter ratio of less than 0.8 or greater than 0.99 were 4.4 times more likely not to heal than patients with a ratio of between 0.8 and 0.99. Conclusion The ideal intramedullary nail to tibial canal diameter ratio to optimize tibial shaft fracture healing is between 0.8 and 0.99. Level of evidence Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

Halophage CW02 infects a Salinivibrio costicola -like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, mass spectrometry, and electron microscopy. A conserved module of structural genes places CW02 in the T7 supergroup, members of which are found in diverse aquatic environments, including marine and freshwater ecosystems. CW02 has morphological similarities to viruses of the Podoviridae family. The structure of CW02, solved by cryogenic electron microscopy and three-dimensional reconstruction, enabled the fitting of a portion of the bacteriophage HK97 capsid protein into CW02 capsid density, thereby providing additional evidence that capsid proteins of tailed double-stranded DNA phages have a conserved fold. The CW02 capsid consists of bacteriophage lambda gpD-like densities that likely contribute to particle stability. Turret-like densities were found on icosahedral vertices and may represent a unique adaptation similar to what has been seen in other extremophilic viruses that infect archaea, such as Sulfolobus turreted icosahedral virus and halophage SH1.

Fractures of the calcaneal tuberosity, although rare, present a challenge for the treating surgeon. The goal of treatment is restoration of function of the gastrocnemius-soleus complex and the Achilles tendon. These fractures often occur in diabetics and elderly osteoporotic patients and therefore fixation of the displaced fragment is difficult. Displaced fractures, if not recognized and promptly reduced, often result in secondary soft tissue compromise. Often, the fragment is a small shell of osteoporotic bone, which is less than optimal for bony fixation. We present our technique for surgical fixation of calcaneal tuberosity fractures using a suture placed through bone tunnels in the calcaneal body. This technique is used by itself for smaller fragments or supplemented with screw fixation for larger fragments.

The purpose of this study is to describe the incidence and presenting features of patients with acute liver failure (ALF) due to ischemic hepatitis and the prognostic factors associated with short (three-week) and long-term outcomes.Retrospective cohort analysis of adult patients enrolled in the Acute Liver Failure Study Group between 1998 and 2008 with ALF due to ischemic hepatitis. Predictors of adverse outcomes three weeks after presentation were identified by univariate and multivariate analysis.Ischemic hepatitis accounted for 51 (4.4%) of the 1147 ALF patients enrolled. Mean age was 50 years, 63% were female, and only 31% had known heart disease before presentation. However, a cardiopulmonary precipitant of hepatic ischemia was identified in 69%. Three-week spontaneous survival was 71%, two patients (4%) underwent liver transplantation, and the remaining 13 patients (25%) died of multi-organ failure. Adverse outcomes were more frequent in subjects with higher admission phosphate levels (HR 1.3, 95% CI 1.1-1.6, P = 0.008) and in subjects with grade 3/4 encephalopathy at presentation (HR: 8.4, 95% CI 1.1-66.5, P = 0.04). Nineteen of the 28 short-term survivors (68%) were still alive at a median follow-up of 3.7 years whereas nine (32%) others had died at a median follow-up of 2 months.A higher admission serum phosphate level and more advanced encephalopathy are associated with a lower likelihood of short-term survival of hospitalized patients with ALF due to ischemic hepatitis. Long-term outcomes are largely determined by underlying cardiovascular morbidity and mortality.

Liver response to injury includes a relatively narrow spectrum of morphologic changes, and accordingly there are only several pathologic patterns that can be recognized microscopically. First of all one must determine if the liver biopsy is from a native liver or from a liver transplant. If it is native liver one must decide if the liver was biopsied for a mass lesion requiring a tumor diagnosis or a diffuse liver disease. Relevant patient data provided by the clinician is always welcome and encouraged to provide appropriate contextual review. First, diffue liver disease should be divided into acute and chronic liver disease. Next, the liver is classified according the predominent pattern of injury. Then, after incorporation of clinical information and laboratory data, a differential diagnosis can be rendered.

Common medical disease affecting the liver include acute and chronic viral hepatitis, drug-induced liver injury, autoimmune hepatitis, primary biliary cirrhosis, primary sclerosing cholangitis, biliary obstruction, alcohol induced liver disease, non-alcohol fatty liver disease, hereditary hemochromatosis, Wilson disease, and α1-antitrypsin deficiency.

An important part of learning liver pathology and understanding liver pathology reports is knowing the unique vocabulary used to describe the histologic features. This can be challenging due to the inconsistent use of terms among pathologists, the overlap of histologic features among different diseases, and the presence of multiple names for the same histologic feature. This chapter functions as a glossary of terms with illustrative photos for each definition.

Liver tumors are classified as benign or malignant and malignant tumors can be primary or metastatic. Primary liver tumors may originate from hepatocytes, bile duct epithelium or endothelial cells. The most common tumors of liver are hemangiomas and the most common malignant tumors of the liver are hepatocellular carcinomas. Metastases are much more common than primary malignant tumors.

Liver transplantion is the treatment for end stage chronic liver diasese, acute liver failure with massive liver necrosis, malignant liver tumors, and chronic metabolic or genetic diseases. The interpretation of liver biopsies to evaluate the donor liver as well as the changes that occur after transplant requires specialized knowledge related to liver transplantation such as the following: graft preservation/reperfusion injury, vascular and biliary tract injuries, cell mediated and antibody mediated rejection, complications of immunosuppression, and recurrence of original liver disease.

Handling and processing of the liver biopsy includes gross examination and identification, fixation, embedding in paraffin and sectioning, and routine and special staining of sections.

Generally speaking liver pathology may be studied in many pathologic samples, such as those obtained at autopsy, hepatectomy, partial liver resection, surgical and medical biopsy. The latter two modalities are of greatest significance for the clinicians and accordingly in this book we will mostly discuss the pathology of the liver as seen in liver biopsies.

Patients who sustain orthopaedic trauma are at risk for developing deep venous thrombosis and symptomatic pulmonary emboli. The prevention of venous thromboembolism has moved to the forefront of patient safety initiatives, resulting in the formation of various guidelines to assist the practitioner. Recommendations for venous thromboembolism prophylaxis in the orthopaedic trauma patient exist, but there is insufficient evidence in the literature to make strong recommendations regarding type and duration of prophylaxis. The associated morbidity of chemical anticoagulants used in the orthopaedic trauma patient must also be taken into consideration, specifically the increased risk of bleeding. Mechanical prophylaxis is used in place of, or in addition to, these medications in certain situations. New, potentially superior anticoagulants have been developed but are still understudied. Larger studies are needed to further define the type and duration of deep venous thrombosis prophylaxis in the orthopaedic trauma patient.

Motivation: Modern lipidomics is largely dependent upon structural ontologies because of the great diversity exhibited in the lipidome, but no automated lipid classification exists to facilitate this partitioning. The size of the putative lipidome far exceeds the number currently classified, despite a decade of work. Automated classification would benefit ongoing classification efforts by decreasing the time needed and increasing the accuracy of classification while providing classifications for mass spectral identification algorithms. Results: We introduce a tool that automates classification into the LIPID MAPS ontology of known lipids with >95% accuracy and novel lipids with 63% accuracy. The classification is based upon simple chemical characteristics and modern machine learning algorithms. The decision trees produced are intelligible and can be used to clarify implicit assumptions about the current LIPID MAPS classification scheme. These characteristics and decision trees are made available to facilitate alternative implementations. We also discovered many hundreds of lipids that are currently misclassified in the LIPID MAPS database, strongly underscoring the need for automated classification. Availability and implementation: Source code and chemical characteristic lists as SMARTS search strings are available under an open-source license at https://www.github.com/princelab/lipid_classifier. Contact: ryanmt@byu.net Supplementary information: Supplementary data are available at Bioinformatics online.

Programmed cell death protein 5 (PDCD5) has been proposed to act as a pro-apoptotic factor and tumor suppressor. However, the mechanisms underlying its apoptotic function are largely unknown. A proteomics search for binding partners of phosducin-like protein, a co-chaperone for the cytosolic chaperonin containing tailless complex polypeptide 1 (CCT), revealed a robust interaction between PDCD5 and CCT. PDCD5 formed a complex with CCT and β-tubulin, a key CCT-folding substrate, and specifically inhibited β-tubulin folding. Cryo-electron microscopy studies of the PDCD5·CCT complex suggested a possible mechanism of inhibition of β-tubulin folding. PDCD5 bound the apical domain of the CCTβ subunit, projecting above the folding cavity without entering it. Like PDCD5, β-tubulin also interacts with the CCTβ apical domain, but a second site is found at the sensor loop deep within the folding cavity. These orientations of PDCD5 and β-tubulin suggest that PDCD5 sterically interferes with β-tubulin binding to the CCTβ apical domain and inhibits β-tubulin folding. Given the importance of tubulins in cell division and proliferation, PDCD5 might exert its apoptotic function at least in part through inhibition of β-tubulin folding.

Injuries to the anterior or posterior pelvic ring rarely occur in isolation. Disruption to the anterior pelvic ring, indicated by a fracture of the superior or inferior pubic ramus, or injury to the pubic symphysis, may be indicative of additional pelvic ring disruption. The purpose of this retrospective study was to determine whether displaced inferior pubic ramus fractures warrant a more detailed investigation of the posterior ring in an effort to predict unstable posterior pelvic ring injuries.All patients with a displaced inferior ramus fracture on AP pelvic radiograph were identified at a single level I trauma center over a 5-year period. Complete pelvic radiographs and computed tomography scans were then evaluated for additional pelvic ring injuries. The data were analyzed using the chi-square test to determine the association between inferior ramus fractures and posterior pelvic ring injury.Sixty-three of the 93 patients with a fracture of the inferior ramus (68 %) were found to have a posterior ring injury; 60 % of these injuries were unstable. Patients with concurrent superior ramus fractures were more likely to have a posterior ring injury (p0.001) and an unstable pelvis (p = 0.018). Of those with a displaced unilateral inferior ramus fracture, parasymphyseal involvement was associated with higher incidence of posterior ring injury (p = 0.047) and pelvic instability (p = 0.028).The anterior pelvic ring can be used to help identify unstable injuries to the posterior pelvis. Patients with displaced inferior pubic ramus fractures warrant a detailed examination of their posterior ring to identify additional injuries and instability.

The rs738409 G>C single nucleotide polymorphism occurring in the patatin-like phospholipase 3 gene has been identified as a novel genetic marker for hepatic steatosis. Recent studies also associated rs738409 with fibrosis in hepatitis C (HCV). Therefore, we sought to determine the impact of donor and recipient rs738409 genotype on the progression of fibrosis after liver transplantation for HCV. This cohort study included 101 patients infected with HCV who underwent liver transplantation between January 2008, and June 2011. Donor and recipient rs738409 genotypes were determined from donor wedge biopsies and recipient explants. The time to Ishak stage 3 fibrosis, or HCV-related mortality/graft loss was analyzed by the Cox model adjusting for HCV-Donor Risk Index, warm ischemic time, pretransplant Model for Endstage Liver Disease (MELD) and viral load. The rs738409 CC variant was present in 56% of donors and 57% of recipients. The median follow-up period was 620 days. A total of 39 patients developed the primary outcome of ≥stage 3 fibrosis or HCV-related mortality/graft loss, the time to which differed by donor (P = 0.019) but not recipient (P = 0.89) genotype. In the multivariate model, donor GC or GG variants had 2.53 times the risk (95% confidence interval [CI] 1.25-5.02, P = 0.008) compared to CC variants. In the alternative endpoint: stage 3 fibrosis or all-cause mortality/graft loss, the effect of donor genotype was attenuated but remained significant at 1.98 (95% CI 1.11-3.53). Conclusions: The rs738409 genotype is an important predictor of posttransplant outcome in HCV. Liver, and not adipocytes, is the site at which this effect occurs. Our finding may be useful in donor selection for liver transplantation with HCV, and may guide decisions regarding early antiviral treatment. (Hepatology 2014;59:453–460)

Summary: Quality control in mass spectrometry-based proteomics remains subjective, labor-intensive and inconsistent between laboratories. We introduce Metriculator, a software designed to facilitate long-term storage of extensive performance metrics as introduced by NIST in 2010. Metriculator features a web interface that generates interactive comparison plots for contextual understanding of metric values and an automated metric generation toolkit. The comparison plots are designed for at-a-glance determination of outliers and trends in the datasets, together with relevant statistical comparisons. Easy-to-use quantitative comparisons and a framework for integration plugins will encourage a culture of quality assurance within the proteomics community. Availability and Implementation: Available under the MIT license at http://github.com/princelab/metriculator. Contact: jtprince@chem.byu.edu

Fractures of the calcaneal tuberosity are relatively uncommon and are seen most frequently in elderly and diabetic patients. These injuries are typically avulsion fractures caused by concentric contraction of the gastrocnemius-soleus muscle complex. Displacement of these fractures can compromise the skin over the posterior aspect of the heel; therefore, early recognition and management are imperative. Surgical management of calcaneal tuberosity fractures requires reduction and stable fixation of the displaced fragment. When the patient has preexisting tightness of the gastrocnemius-soleus complex, successful management must also address this pathology to improve outcome.

The current study tests a hypothesis that nuclear receptor signaling is altered in chronic hepatitis C patients and that the altered pattern is specific to alcohol drinking history. The expression of a panel of more than 100 genes encoding nuclear receptors, coregulators, and their direct/indirect targets was studied in human livers. Gene expression pattern was compared between 15 normal donor livers and 23 hepatitis C virus (HCV) genotype 1-positive livers from patients without a drinking history (matched for age, sex, and body mass index). HCV infection increased the expression of nuclear receptors small heterodimer partner and constitutive androstane receptor (CAR) as well as genes involved in fatty acid trafficking, bile acid synthesis and uptake, and inflammatory response. However, the expression of retinoid X receptor (RXR) α, peroxisomal proliferator-activated receptor (PPAR) α and β as well as steroid regulatory element-binding protein (SREBP)-1c was decreased in HCV-infected livers. Gene expression pattern was compared in chronic hepatitis C patients with and without a drinking history. Alcohol drinking increased the expression of genes involved in fatty acid uptake, trafficking, and oxidation, but decreased the expression of genes responsible for gluconeogenesis. These changes were consistent with reduced fasting plasma glucose levels and altered expression of upstream regulators that include RXRα, PPARα, and CAR. The messenger RNA levels of fibroblast growth factor 21, interleukin-10, and fatty acid synthase, which are all regulated by nuclear receptors, showed independent correlation with hepatic HCV RNA levels.Our findings suggest that those genes and pathways that showed altered expression could potentially be therapeutic targets for HCV infection and/or alcohol drinking-induced liver injury.

The reason(s) that hepatitis A virus (HAV) infection may progress infrequently to acute liver failure are poorly understood. We examined host and viral factors in 29 consecutive adult patients with HAV-associated acute liver failure enrolled at 10 sites participating in the US ALF Study Group. Eighteen of twenty-four acute liver failure sera were PCR positive while six had no detectable virus. HAV genotype was determined using phylogenetic analysis and the full-length genome sequences of the HAV from a cute liver failure sera were compared to those from self-limited acute HAV cases selected from the CDC database. We found that rates of nucleotide substitution did not vary significantly between the liver failure and non-liver failure cases and there was no significant variation in amino acid sequences between the two groups. Four of 18 HAV isolates were sub-genotype IB, acquired from the same study site over a 3.5-year period. Sub-genotype IB was found more frequently among acute liver failure cases compared to the non-liver failure cases (chi-square test, P

BACKGROUND: Esophageal variceal bleeding (EVB) is a frequent complication in cirrhotic patients resulting in considerablemortality andmorbidity. However, recent large-scale studies are lacking. We AIMS: To conduct a retrospective analysis using a national U.S. database to study the differences in demographic characteristics, rate of complications, and outcomes, and temporal trends in hospitalized cirrhotic patients with and without EVB. METHODS: We interrogated data from the Nationwide Inpatient Sample 2002 2012. Utilizing International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes, we studied hospital discharges for cirrhosis and related EVB in adult patients. Cases were queried for complications well-recognized in cirrhotic patients. These included infections including Clostridium difficile infection and spontaneous bacterial peritonitis, hepatic encephalopathy and hepatorenal syndrome. Comorbid conditions were assessed using the Elixhauser comorbidity. We used high-dimensional propensity scores in a 1:5 matching ratio with a greedy matching algorithm generated by regression analysis. For trend analysis, we used the Cochrane-Armitage test. RESULTS: Patients with EVB suffered a significantly higher rate of alcohol abuse (63.90% versus 48.80%; p

Acute liver failure (ALF) due to hepatitis A virus (HAV) infection is an uncommon but potentially lethal illness. The aim of this study was to identify readily available laboratory and clinical features associated with a poor prognosis among ALF patients with HAV infection. The presenting features of 29 adults with anti-HAV IgM positive ALF enrolled in the ALFSG between 1998 and 2005 were reviewed. The HAV patients listed for transplantation by UNOS were also reviewed. Acute HAV accounted for 3.1% of patients enrolled in the ALFSG. At 3 weeks follow-up, 16 had spontaneously recovered (55%), 9 underwent transplantation (31%), and 4 had died (14%). A prognostic model incorporating 4 presenting features (serum ALT 2.0 mg/dL, intubation, pressors) had an AUROC for transplant/death of 0.899 which was significantly better than the King’s College criteria (0.623, P=.018) and MELD scores (0.707, P=.0503). Between 1988 and 2005, the frequency of patients requiring liver transplantation for HAV in the UNOS database significantly decreased from 0.7 % to 0.1% (P < .001). In addition, the proportion of HAV cases enrolled in the ALFSG significantly decreased from 5% to 0.8% (P = .007). In conclusion, the frequency of HAV patients enrolling in the ALFSG and being listed for liver transplantation in the United States has declined in parallel. A prognostic index consisting of 4 clinical and laboratory features predicted the likelihood of transplant/death significantly better than other published models suggesting that disease specific prognostic models may be of value in non-acetaminophen ALF.

Thrombocytopenia is common among liver transplant candidates and recipients. The aim of our study was to determine the incidence and outcome of new-onset immune-mediated thrombocytopenic purpura (ITP) following liver transplantation at a single center. Among the 256 liver transplant recipients with an International Classification of Diseases, Ninth Edition code for thrombocytopenia, 8 cases of new-onset ITP were identified, leading to an overall incidence of 0.7% in 1,105 consecutive liver transplant recipients over a 15-year period. All 8 patients were Caucasian, 5 (63%) were male, and the median age at ITP onset was 54 years (range, 15-63). The median platelet count at presentation was 3,500 cells/mL (range, 1,000-12,000) and liver disease was due to hepatitis C (38%), primary sclerosing cholangitis (38%), and cryptogenic cirrhosis (25%). The median time from transplant to ITP onset was 53.5 months (range, 1.9-173). Three of the 6 patients tested (50%) had cell-bound antiplatelet antibodies, 1 patient had an underlying hematological malignancy, and none of the organ donors had a history of ITP. Corticosteroids and/or immunoglobulin infusions were effective in 4 patients. However, serial rituximab infusions were required in 4 patients with persistent thrombocytopenia, and 3 of them eventually required splenectomy to induce disease remission. At a median follow-up of 19.7 months, 7 long-term survivors remain in remission with a median platelet count of 267,000 cells/mL. In conclusion, new-onset ITP is an infrequent but important cause of severe thrombocytopenia in liver transplant recipients. Corticosteroids and immunoglobulin infusions were effective in 50% while the remainder of patients required rituximab infusions or eventual splenectomy for long-term disease remission.

SNAP-25 contains two of the four helixes that form the SNARE complex, critical for neuronal exocytosis. The helixes are linked together with a cysteine-rich domain, which is the site of various post-translational modifications such as palmitoylation and possibly oxidation. SNAP-25's linker contains 4 cysteines and thus could be both palmitoylated and oxidized. Palmitoylation anchors SNAP-25 to the membrane, while the level of oxidation may regulate transmitter release.Using standard MS/MS collision-induced dissociation (CID) in an Ion Trap mass spectrometer we analyzed peptide fragmentation patterns to determine fragmentation events, and observed single and double backbone cleavage along with heterolytic cleavage of disulfide bonds. We modeled these same events in the doubly disulfide linked SNAP25B peptide and used a cumulative hypergeometric distribution with top-down scoring to first identify, and then to differentiate all three bonding patterns. This is the first study to assign all double disulfide bonding patterns in a protein, and uses methodology fully compatible with standard large scale shotgun proteomics.In addition, the structural stability of oxidized and reduced SNAP-25 was determined with Circular Dichroism (CD). We observe that oxidized protein is less stable (lower melting temperature) than reduced protein. Additional experiments focus on the stability of the SNARE complex with oxidized samples and on the extent of SNAP-25 oxidation in brain tissue, with the ultimate goal to elucidate the effects of palmitoylation and oxidative stress on SNARE complex formation and vesicle fusion.