Canonical genetic signatures of the adult human brain.

The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure and function. We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations. Using genes with high differential stability, we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely patterned genes displayed marked shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry.

Preference of endoscopic ablation over medical prevention of esophageal adenocarcinoma by patients with Barrett's esophagus.

BACKGROUND & AIMS: Endoscopic intervention or pharmacologic inhibition of cyclooxygenase might be used to prevent progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC). We investigated whether patients with BE prefer endoscopic therapy or chemoprevention of EAC. METHODS: Eighty-one subjects with nondysplastic BE were given a survey that described 2 scenarios. The survey explained that treatment A (ablation), endoscopy, reduced lifetime risk of EAC by 50%, with 5% risk for esophageal stricture, whereas treatment B (aspirin) reduced lifetime risk of EAC by 50% and the risk of heart attack by 30%, yet increased the risk for ulcer by 75%. Subjects indicated their willingness to undergo either treatment A and/or treatment B if endoscopic surveillance were required every 3-5 years, every 10 years, or were not required. Visual aids were included to represent risk and benefit percentages. RESULTS: When surveillance was required every 3-5 years, more subjects were willing to undergo treatment A than treatment B (78%, 63 of 81 vs 53%, 43 of 81; P < .01). There were no differences in age, sex, education level, or history of cancer, heart disease, or ulcer between patients willing to undergo treatment A and those willing to undergo treatment B. Altering the frequency of surveillance did not affect patients' willingness to undergo either treatment. CONCLUSIONS: In a simulated scenario, patients with BE preferred endoscopic intervention over chemoprevention for EAC. Further investigation of the shared decision-making process regarding preventive strategies for patients with BE may be warranted.

De novo malignancy post-liver transplantation: a single center, population controlled study.

BACKGROUND: With the growing numbers of liver transplant recipients, it is increasingly important to understand the risks of de novo malignancy after liver transplantation. AIM: To characterize the incidence of de novo malignancy after liver transplantation compared with a control non-transplant population. METHODS: We studied 534 Indiana state residents undergoing liver transplantation at our center between 1997 and 2004, followed through August 2010. The incidence and predictors of malignancy were determined. The standardized incidence ratio (SIR) of cancer in our cohort was compared with age-, gender-, and period-matched state population using the Indiana State Cancer Registry. RESULTS: After a mean follow-up of 5.7 ± 3.2 yr, 73 patients (13.7%) developed 80 cancers, with five- and 10-yr incidence rates of 11.7% and 24.8%, respectively. These included 24 (30%) skin, 16 (20%) hematologic, and 40 (50%) solid tumors. The most common solid cancers were aerodigestive. Compared with matched state population, liver transplant recipients had significantly higher incidence of all cancers (SIR: 3.1, 95% CI [Confidence interval]: 2.9-3.2), skin (melanoma) (SIR: 5.8, 95% CI: 4.7-7.0), hematologic (SIR: 7.1, 95% CI: 6.3-8.0), and solid (SIR: 2.7, 95% CI: 2.5-2.8) tumors. CONCLUSION: There is a significantly increased risk of de novo malignancies after liver transplantation, highlighting the need for surveillance strategies in this population.

Gastroenterology trainees can easily learn histologic characterization of diminutive colorectal polyps with narrow band imaging.

BACKGROUND & AIMS: Little is known about how teaching gastroenterology trainees polyp patterns by using narrow band imaging (NBI) affects their ability to characterize the histology of diminutive colorectal polyps. We developed and tested a tool to teach trainees to characterize the histology of diminutive polyps by using NBI. METHODS: Twelve gastroenterology trainees with varying levels of colonoscopy experience watched a teaching tool that described the NBI criteria to distinguish polyp histology. The trainees then watched 80 videos of NBI examination of diminutive polyps, recording their predictions of polyp histology and their degree of confidence. After each video, an expert provided feedback about actual polyp histology and the NBI criteria that supported each diagnosis. Twelve weeks later, without training or feedback during the interval, the trainees watched the same videos and predicted histologies of the polyps. Performance was evaluated by comparing predicted classification with actual histologic findings. Cumulative sum analysis was used to determine the learning curve for each trainee. RESULTS: Trainees made significant improvements in accuracy and the proportion of high-confidence predictions as they progressed through video blocks during the first session (P < .001). With active feedback, all trainees predicted polyp histologies with >90% accuracy, with a negative predictive value >90% for adenomatous histology. A median of 49 videos was required to achieve competency. For diagnoses made with high confidence, trainee performance exceeded 90% during the first and second sessions. Interobserver agreement was substantial (session 1, κ = 0.71; session 2, κ = 0.70). CONCLUSIONS: We developed a computer-based tool, combined with short videos and active feedback, to train gastroenterologists to identify polyp histology by using NBI. After training, gastroenterology trainees characterized the histology of diminutive polyps with ≥ 90% accuracy.

A vertex similarity-based framework to discover and rank orphan disease-related genes.

BACKGROUND: A rare or orphan disease (OD) is any disease that affects a small percentage of the population. While opportunities now exist to accelerate progress toward understanding the basis for many more ODs, the prioritization of candidate genes is still a critical step for disease-gene identification. Several network-based frameworks have been developed to address this problem with varied results. RESULT: We have developed a novel vertex similarity (VS) based parameter-free prioritizing framework to identify and rank orphan disease candidate genes. We validate our approach by using 1598 known orphan disease-causing genes (ODGs) representing 172 orphan diseases (ODs). We compare our approach with a state-of-art parameter-based approach (PageRank with Priors or PRP) and with another parameter-free method (Interconnectedness or ICN). Our results show that VS-based approach outperforms ICN and is comparable to PRP. We further apply VS-based ranking to identify and rank potential novel candidate genes for several ODs. CONCLUSION: We demonstrate that VS-based parameter-free ranking approach can be successfully used for disease candidate gene prioritization and can complement other network-based methods for candidate disease gene ranking. Importantly, our VS-ranked top candidate genes for the ODs match the known literature, suggesting several novel causal relationships for further investigation.

Hepatic and extrahepatic cancer in cirrhosis: a longitudinal cohort study.

OBJECTIVES: We conducted a retrospective cohort study in cirrhotic patients to understand (i) the risk of developing hepatocellular carcinoma (HCC) after an initial negative screening computed tomography (CT) scan and its relationship with underlying etiology and (ii) the risk of extrahepatic cancers (EHCs). METHODS: Our cohort consisted of 952 cirrhotics who had at least one contrast-enhanced CT scan over a 5-year period from 1997 to 2002. We assessed their risk of HCC and EHC until the study closure (31 December 2007). Using data from the Indiana State Cancer Registry (ISCR), standardized incidence ratios (SIRs) were calculated for HCC and EHC. RESULTS: The cohort's follow-up was 4.7±3.0 years. The frequency of HCC at baseline and during follow-up was 6.9 and 7.2%, respectively. The 1-, 3-, and 5-year HCC incidence after an initial negative CT scan was 1.2, 4.4, and 7.8%, respectively. The 1-, 3-, and 5-year EHC incidence was 2.2, 4.5, and 6.8%, respectively. The most common EHCs were breast, lung, and lymphoma. Incidence of both HCC (P=0.016) and EHC (P=0.004) varied significantly by the etiology of underlying cirrhosis. The SIRs for HCC and EHC were 186 (95% confidence interval (CI) 140-238) and 1.83 (95% CI 1.36-2.36), respectively. Compared with adjusted ISCR data, cirrhosis due to alcohol (SIR 2.73, 95% CI 1.14-4.33) but not other etiologies had significantly higher incidence of EHC. CONCLUSIONS: This study furthers our understanding of HCC and EHC risk in cirrhosis. If confirmed by other studies, these data will assist in developing optimal strategies for monitoring of cancer in individuals with cirrhosis.

Incidence and predictors of 30-day readmission among patients hospitalized for advanced liver disease.

BACKGROUND & AIMS: The rate of readmission to the hospital 30 days after discharge (30-day readmission rate) is used as a quality measure for hospitalized patients, but it has not been studied adequately for patients with advanced liver disease. We investigated the incidence and factors that predict this rate and its relationship with mortality at 90 days. METHODS: We analyzed data from patients with advanced liver disease who were hospitalized to an inpatient hepatology service at 2 large academic medical centers in 2008. Patients with elective admission and recipients of liver transplants were not included. During the study period, there were 447 patients and a total of 554 eligible admissions. Multivariate analyses were performed to identify variables associated with 30-day readmission and to examine its relationship with mortality at 90 days. RESULTS: The 30-day readmission rate was 20%. After adjusting for multiple covariates, readmission within 30 days was associated independently with model for end-stage liver disease scores at discharge (odds ratio [OR], 1.06; 95% confidence interval [CI], 1.02-1.09; P = .002), the presence of diabetes (OR, 1.78; 95% CI, 1.07-2.95; P = .027), and male sex (OR, 1.73; 95% CI, 1.03-2.89; P = .038). After adjusting for age, sex, and model for end-stage liver disease score at discharge, the 90-day mortality rate was significantly higher among patients who were readmitted to the hospital within 30 days than those who were not (26.8% vs 9.8%; OR, 2.6; 95% CI, 1.36-5.02; P = .004). CONCLUSIONS: Patients with advanced liver disease frequently are readmitted to the hospital within 30 days after discharge; these patients have a higher 90-day mortality rate than those who are not readmitted in 30 days. These data might be used to develop strategies to reduce early readmission of hospitalized patients with cirrhosis.

Multicentric outcome analysis of sirolimus-based immunosuppression in 252 liver transplant recipients.

SUMMARY: The use of sirolimus (SRL) in orthotopic liver transplantation (OLT) has been controversial after experimental data suggested an increased risk of hepatic artery thrombosis (HAT). To assess the safety and efficacy of SRL as de novo immunosuppression in OLT recipients. Outcomes of 252 OLT patients who received SRL were compared with outcomes of 291 OLT recipients who received calcineurin inhibitor in a retrospective study. Primary outcomes of this study were: patient- and graft survivals, vascular, biliary, wound complications and rejection rates. Secondary outcomes were: postoperative infection rate, bone marrow and renal function and changes of lipid levels. Patient- and graft survivals, rejection and infection rates were similar. In the SRL group, HAT occurred in 1.2%, biliary complications in 19.4%, and incisional hernias in 9.1%. In the control group the incidence of HAT was 5.8% (P = 0.004), biliary complications 18.5% (P = NS) and incisional hernias 7.2% (P = NS). Patients on SRL experienced significantly higher levels of serum triglycerides but fewer acute cellular rejections. Bone marrow and renal functions were similar in both the groups. Our findings would suggest that SRL is safe and effective for very selected OLT recipients. Randomized controlled trials are necessary to confirm our results.

Boceprevir, an NS3 protease inhibitor of HCV.

Hepatitis C virus (HCV) is a major cause of chronic liver disease leading to death from liver failure or hepatocellular carcinoma. Hepatitis C is the most common indication for liver transplantation worldwide and is a major cause of the increased incidence of hepatocellular cancer in the United States. The current paradigm for HCV treatment relies on pegylated interferon and ribavirin as agents that enhance endogenous mechanisms for viral clearance and are dependent on host factors. In patients with genotype 1 HCV infection, sustained viral response (SVR) rates remain suboptimal, with less than half of genotype 1-infected individuals going on to achieve SVR. This has led to a shift in the investigational focus for treatment of HCV toward specifically targeted antiviral therapy for HCV agents. This review focuses on boceprevir, a protease inhibitor, and discusses its mechanism of action, effects on HCV, and viral resistance.

Predictors of nonadherence to screening colonoscopy.

BACKGROUND: Colonoscopy has become a preferred colorectal cancer (CRC) screening modality. Little is known about why patients who are referred for colonoscopy do not complete the recommended procedures. Prior adherence studies have evaluated colonoscopy only in combination with flexible sigmoidoscopy, failed to differentiate between screening and diagnostic procedures, and have examined cancellations/no-shows, but not nonscheduling, as mechanisms of nonadherence. METHODS: Sociodemographic predictors of screening completion were assessed in a retrospective cohort of 647 patients referred for colonoscopy at a major university hospital. Then, using a qualitative study design, a convenience sample of patients who never completed screening after referral (n=52) was interviewed by telephone, and comparisons in reported reasons for nonadherence were made by gender. RESULTS: Half of all patients referred for colonoscopy failed to complete the procedure, overwhelmingly because of nonscheduling. In multivariable analysis, female sex, younger age, and insurance type predicted poorer adherence. Patient-reported barriers to screening completion included cognitive-emotional factors (e.g., lack of perceived risk for CRC, fear of pain, and concerns about modesty and the bowel preparation), logistic obstacles (e.g., cost, other health problems, and competing demands), and health system barriers (e.g., scheduling challenges, long waiting times). Women reported more concerns about modesty and other aspects of the procedure than men. Only 40% of patients were aware of alternative screening options. CONCLUSIONS: Adherence to screening colonoscopy referrals is sub-optimal and may be improved by better communication with patients, counseling to help resolve logistic barriers, and improvements in colonoscopy referral and scheduling mechanisms.