Citations

Abstract In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

Abstract Background: There are several well-established environmental risk factors for ovarian cancer, and recent genome-wide association studies have also identified six variants that influence disease risk. However, the interplay between such risk factors and susceptibility loci has not been studied. Methods: Data from 14 ovarian cancer case–control studies were pooled, and stratified analyses by each environmental risk factor with tests for heterogeneity were conducted to determine the presence of interactions for all histologic subtypes. A genetic “risk score” was created to consider the effects of all six variants simultaneously. A multivariate model was fit to examine the association between all environmental risk factors and genetic risk score on ovarian cancer risk. Results: Among 7,374 controls and 5,566 cases, there was no statistical evidence of interaction between the six SNPs or genetic risk score and the environmental risk factors on ovarian cancer risk. In a main effects model, women in the highest genetic risk score quartile had a 65% increased risk of ovarian cancer compared with women in the lowest [95% confidence interval (CI), 1.48–1.84]. Analyses by histologic subtype yielded risk differences across subtype for endometriosis (Phet < 0.001), parity (Phet < 0.01), and tubal ligation (Phet = 0.041). Conclusions: The lack of interactions suggests that a multiplicative model is the best fit for these data. Under such a model, we provide a robust estimate of the effect of each risk factor that sets the stage for absolute risk prediction modeling that considers both environmental and genetic risk factors. Further research into the observed differences in risk across histologic subtype is warranted. Cancer Epidemiol Biomarkers Prev; 22(5); 880–90. ©2013 AACR.

BackgroundEndocardial ablation approaches targeting the retroatrial cardiac ganglia to treat atrial fibrillation (AF) have been proposed. However, the potential value using this approach is unknown. Disruption of the autonomic inputs with orthotropic heart transplant (OHT) provides a unique opportunity to study the effects of autonomic innervation on AF genesis and maintenance. We hypothesized that due to denervation, the risk of postoperative AF would be lower following OHT compared to surgical maze even though both groups get isolation of the pulmonary veins.Methods and ResultsWe reviewed 155 OHTs (mean age 52 ± 11 years, 72% males) and used 1:1 age‐, sex‐, and date‐of‐surgery‐matched two control groups from patients undergoing surgical maze or only coronary artery bypass grafting (CABG). Using conditional logistic regression we compared the odds of AF within 2 weeks following OHT versus controls. Postoperative AF occurred in 10/155 (6.5%) OHT patients. The conditional odds of postoperative AF were lower for OHT as compared to controls (vs maze: odds ratio [OR] 0.27 [95% confidence interval (CI) 0.13–0.57], vs CABG: OR 0.38 [0.17–0.81], P = 0.003; and on additional adjustment for left atrial enlargement, vs maze: OR 0.28 [0.13–0.60], vs CABG: OR 0.14 [0.04–0.47], P = 0.0009).ConclusionsRisk of postoperative AF is significantly lower with OHT as in comparison to surgical maze. As both surgeries entail isolation of the pulmonary veins but only OHT causes disruption of autonomic innervation, this observation supports a mechanistic role of autonomic nervous system in AF. The benefit of targeting the cardiac autonomic system to treat AF needs further investigation.

ObjectiveObesity, insulin resistance, and diabetes disproportionately affect African‐American (AA) women. Abnormal adipose tissue free fatty acid (FFA) release is associated with these conditions. Resting energy expenditure (REE) and sex predict FFA release in Caucasians, but whether this is true in AA is unknown. The sex‐specific relationships between FFA release, REE, and race was compared.Design and Methods100 adults (47% AA, 50% male, age 32 ± 8 years [mean ± SD]) from three different centers underwent duplicate measures of FFA release ([U‐13C] palmitate) and REE (indirect calorimetry). Body composition was determined by DXA and abdominal imaging.ResultsAA participants had lower REE, but similar FFA concentrations and flux compared with Caucasian participants. The significant predictors of palmitate release were REE, sex, and race. REE and FFA flux were correlated in both sexes and both races. In a multiple linear regression analysis with palmitate flux as the dependent variable and REE, sex, race, total fat mass, fat‐free mass, and insulin as independent variables, REE was the only independent predictor of FFA release in men. Both REE and race predicted palmitate flux in women.ConclusionsFFA flux is related to REE, but the relationship differs in AA and Caucasian women.

Object Resection of cancer and the involved artery in the neck has been applied with some success, but the indications for such an aggressive approach at the skull base are less well defined. The authors therefore evaluated the outcomes of advanced skull base malignancies in patients who were treated with bypass and resection of the internal carotid artery (ICA). Methods The authors retrospectively reviewed the charts of all patients with advanced head and neck cancers who underwent ICA sacrifice with revascularization in which an extracranial-intracranial bypass was used between 1995 and 2010 at the Barrow Neurological Institute. Results Eighteen patients (11 male and 7 female patients; mean age 46 years, range 7–69 years) were identified. There were 4 sarcomas and 14 carcinomas that involved the ICA at the skull base. All patients underwent ICA sacrifice with revascularization. One patient died of a stroke after revascularization. A second patient died of the effects of a fistula between the oral and cranial cavities (surgery-related mortality rate 11.1%). Eight months after the operation, 1 patient developed occlusion of the bypass and died. Complications associated with the bypass surgery included 1 case of subdural hematoma (SDH) with blindness, 1 case of status epilepticus, and 1 case of asymptomatic bypass occlusion (bypass-related morbidity 16.7%). Complications associated with tumor resection included 3 cases of CSF leakage requiring repair and shunting, 1 case of hydrocephalus requiring shunting, 1 case of SDH, and 1 case of contralateral ICA injury requiring a bypass (tumor resection morbidity rate 33.3%). In 1 patient treated with adjuvant therapy before surgery, the authors identified only a radiation effect and no tumor on resection. In a second patient the bypass was occluded, and her tumor was not resected. The other 16 patients underwent gross-total resection of their tumor. Excluding the surgery-related deaths, the mean and median lengths of survival in this series were 13.2 and 8.3 months, respectively (range 1.5–48 months). Including the surgery-related deaths, the mean and median lengths of survival were 11.8 and 8 months, respectively (range 17 days–48 months). At last follow-up all patients had died of cancer or cancer-related causes. Conclusions Despite maximal surgical intervention, including ICA sacrifice at the skull base with revascularization, patient survival was dismal, and the complication rate was significant. The authors no longer advocate such an aggressive approach in this patient population. On rare occasions, however, such an approach may be considered for low-grade malignancies.

Implanted cardiac devices, including pacemakers, defibrillators, and resynchronization devices, are known to develop thrombus on their intravascular leads. Patent foramen ovale (PFO) occurs in approximately one‐quarter of the adult population. It is unclear whether paradoxical cardioembolism and clinically relevant stroke occur in patients with implanted cardiac leads and PFO. We present a case series of four patients with cardioembolic stroke, presumed to arise from intravascular cardiac leads and associated PFO that required device closure of the PFO.(PACE 2013; 36:50–54)