PNPLA3 gene predicts clinical recovery after sustained virological response in decompensated hepatitis C cirrhosis.

BACKGROUND: Patients 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. METHODS: We 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. RESULTS: Forty-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 the PNPLA3 CC 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, the PNPLA3 CG/GG genotypes were associated with a 1.29 (SE=0.30, p<0.0001) point higher CPT score. Most of the difference came from differences in hepatic encephalopathy and bilirubin. The results for rs58542926 and rs641738 were not significant. CONCLUSION: The PNPLA3 CG/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.

Natively oxidized amino acid residues in the spinach cytochrome b 6 f complex.

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.

Intramedullary Nailing of Tibial Shaft Fractures: Size Matters.

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.

Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal.

BACKGROUND: The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. RESULTS: We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. CONCLUSIONS: The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts.

Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection.

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.

Programmed cell death protein 5 interacts with the cytosolic chaperonin containing tailless complex polypeptide 1 (CCT) to regulate ß-tubulin folding.

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 ß-tubulin, a key CCT-folding substrate, and specifically inhibited ß-tubulin folding. Cryo-electron microscopy studies of the PDCD5·CCT complex suggested a possible mechanism of inhibition of ß-tubulin folding. PDCD5 bound the apical domain of the CCTß subunit, projecting above the folding cavity without entering it. Like PDCD5, ß-tubulin also interacts with the CCTß apical domain, but a second site is found at the sensor loop deep within the folding cavity. These orientations of PDCD5 and ß-tubulin suggest that PDCD5 sterically interferes with ß-tubulin binding to the CCTß apical domain and inhibits ß-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 ß-tubulin folding.

Mspire-Simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data.

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.

Metriculator: quality assessment for mass spectrometry-based proteomics.

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.

Resolving double disulfide bond patterns in SNAP25B using liquid chromatography-ion trap mass spectrometry.

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.

The Jones-Powell Classification of open pelvic fractures: a multicenter study evaluating mortality rates.

BACKGROUND: Historically, open pelvic fractures have a high mortality rate. The Jones-Powell Classification system was developed to assist with morbidity and mortality prediction.The purposes of our study were twofold: 1. Apply the Jones-Powell Classification to mortality rates of open pelvic fractures; 2. Because the original article published on the Jones-Powell Classification was from 1997, there have been advances in the early treatment of pelvic fractures to include the use of the pelvic binder, early diverting colostomies, and emergent angiography. We wanted to examine if any of those acute interventions affected mortality rate. METHODS: This is a retrospective review of all patients presenting with open pelvic fractures at six Level I trauma centers between 2000 and 2006. RESULTS: There were 64 patients with an average age of 34 years (range, 17-57 years). Fourteen had stable pelvic fracture patterns, and 50 had unstable fracture patterns. The overall mortality rate in our study was 15 patients (23%). All patients who died had an unstable pelvic fracture and/or rectal laceration. Sixteen patients had diverting colostomies within 48 hours of injury. There were four patients with rectal lacerations and no patients with diverting colostomies who died. DISCUSSION: In our population group, there was an overall mortality rate of 23%. A Jones-Powell Class 3 injury had a 38% mortality rate. The presence of a rectal laceration may serve as a marker for the severity of the patient's injuries and increased risk of mortality. LEVEL OF EVIDENCE: Epidemiologic study, level IV.

Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.

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.

Acute compartment syndrome: obtaining diagnosis, providing treatment, and minimizing medicolegal risk.

Acute compartment syndrome (ACS) is a surgical emergency. Diagnosis depends on a high clinical suspicion and an understanding of risk factors, pathophysiology and subtle physical exam findings. The typical high risk scenario for ACS is a male patient younger than 35 years of age, involved in a high energy sport or roadway collision, resulting in a tibial shaft fracture. He will go on to develop acute compartment syndrome of the leg in less than 10 hours and require emergent fasciotomy. Diagnosis of ACS in this patient is primarily a clinical one but can be confirmed with invasive intracompartmental pressure monitoring or non-invasive near infrared spectroscopy (NIRS). Delaying the diagnosis will likely result in some degree of permanent disability and places the surgeon at high risk for litigation. This article reviews the salient features of acute compartment syndrome that should be understood by all orthopaedic residents and surgeons.

Short and long-term outcomes in patients with acute liver failure due to ischemic hepatitis.

AIMS: 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.

Fulminant hepatitis A virus infection in the United States: Incidence, prognosis, and outcomes.

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 <2,600 IU/L, creatinine >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.

Immune thrombocytopenic purpura following liver transplantation: a case series and review of the literature.

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.