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Purpose: The purpose of this study is to develop a computer-aided detection system that combines the detection results in 3D digital breast tomosynthesis (DBT) volume and 2D simulated projection (synthesized image which is not provided by the vendor but generated from DBT volume in this study) to improve the accuracy of mass detection in DBT. Methods: The 3D DBT volume has a problem of blurring in the out-of-focus plane because it is reconstructed from a limited number of projection view images acquired over a limited angular range. To solve the problem, the simulated projection is generated by measuring the blurriness of voxels in the DBT volume and adopting conspicuity voxels. A contour-based detection algorithm is applied to detecting masses in the simulated projection. The DBT volume is analyzed by using an unsupervised mass detection algorithm, which results in mass candidates in the DBT volume. The mass likelihood scores estimated for mass candidates on the DBT volume and the simulated projection are merged in a probabilistic manner through a Bayesian network model to differentiate masses and false positives (FPs). Experiments were conducted on a clinical data set of 320 DBT volumes. In 90 volumes, at least one biopsy-proven malignant mass was presented. The longest diameter of masses ranged from 7.0 to 56.4 mm (mean = 25.4 mm). The sizes of masses in the data set were relatively large compared to the sizes of the masses reported in other detection studies. Three image quality measurements (overall sharpness, sharpness of mass boundary, and contrast) were used to evaluate the image quality of the simulated projection compared to the DBT central slice where the mass was most conspicuous and other projection methods (maximum intensity projection and average projection). A free-response receiver operating characteristic (FROC) analysis was adopted for evaluating the accuracy of mass detection in the DBT volume, the simulated projection, and the combined approach. A jackknife FROC analysis (JAFROC) was used to estimate the statistical significance of the difference between two FROC curves. Results: The overall sharpness and the sharpness of mass boundary in the simulated projection are higher than those in the DBT central slice and other projection methods. The contrast of the simulated projection is lower than the DBT central slice. The mass detection in the DBT volume achieved region-based sensitivities of 80% and 85% with 1.75 and 2.11 FPs per DBT volume. The proposed combined mass detection approach achieved same sensitivities with reduced FPs of 1.33 and 1.93 per DBT volume. The difference of the FROC curves between the combined approach and the mass detection in the DBT volume was statistically significant (p < 0.01) by JAFROC analysis. Conclusions: This study indicates that the combined approach that merges the detection results in the DBT volume and the simulated projection is a promising approach to improve the accuracy of mass detection in DBT.

BACKGROUND This study sought to identify novel effectors and markers of localized but potentially life-threatening prostate cancer (PCa), by evaluating chromosomal copy number alterations (CNAs) in tumors from patients who underwent prostatectomy and correlating these with clinicopathologic features and outcome. METHODS CNAs in tumor DNA samples from 125 patients in the discovery cohort who underwent prostatectomy were assayed with high-resolution Affymetrix 6.0 single-nucleotide polymorphism microarrays and then analyzed using the Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm. RESULTS The assays revealed 20 significant regions of CNAs, 4 of them novel, and identified the target genes of 4 of the alterations. By univariate analysis, 7 CNAs were significantly associated with early PCa-specific mortality. These included gains of chromosomal regions that contain the genes MYC, ADAR, or TPD52 and losses of sequences that incorporate SERPINB5, USP10, PTEN, or TP53. On multivariate analysis, only the CNAs of PTEN (phosphatase and tensin homolog) and MYC (v-myc myelocytomatosis viral oncogene homolog) contributed additional prognostic information independent of that provided by pathologic stage, Gleason score, and initial prostate-specific antigen level. Patients whose tumors had alterations of both genes had a markedly elevated risk of PCa-specific mortality (odds ratio = 53; 95% CI = 6.92-405, P = 1 × 10−4). Analyses of 333 tumors from 3 additional distinct patient cohorts confirmed the relationship between CNAs of PTEN and MYC and lethal PCa. CONCLUSIONS This study identified new CNAs and genes that likely contribute to the pathogenesis of localized PCa and suggests that patients whose tumors have acquired CNAs of PTEN, MYC, or both have an increased risk of early PCa-specific mortality. Cancer 2013;119:2405-2412. © 2013 American Cancer Society.

Recently, genome-wide association studies (GWAS) have identified over 12 single-nucleotide polymorphisms (SNPs) associated with bladder cancer risk in populations of European descent. However, effects of these SNPs in bladder cancer have not been systemically evaluated in the Chinese population. We conducted association studies of 12 SNPs in a Chinese population of 184 cases and 962 controls. These SNPs were previously identified in European GWAS and a fine mapping study. The reported risk alleles of rs798766 on TACC3 at 4p16 and rs9624880 on MYC at 8q24 were significantly associated with increased bladder cancer risk with P-values of 0.003 and 0.03, respectively. Next, we performed a meta-analysis, by combining our study with previous association studies performed in Chinese. In the meta-analysis, the reported risk allele for four SNPs were significantly associated with increased bladder cancer risk, including rs798766 on TACC3 at 4p16, rs9624880 on MYC at 8q24, rs2294008 on PSCA at 8q24, and rs2736100 on TERT at 5p15. The meta-analysis P-values for the four SNPs ranged from 0.017 to 5.52E� 05. The results from our study suggest that a sub-set of bladder cancer risk-associated SNPs identified from the European population are also associated with bladder cancer risk in the Chinese population. Additional studies with larger sample sizes are needed to further confirm our results. 2012 Wiley Periodicals, Inc.

We present the most comprehensive comparison to date of the predictive benefit of genetics in addition to currently used clinical variables, using genotype data for 33 single-nucleotide polymorphisms (SNPs) in 1,547 Caucasian men from the placebo arm of the REduction by DUtasteride of prostate Cancer Events (REDUCE®) trial. Moreover, we conducted a detailed comparison of three techniques for incorporating genetics into clinical risk prediction. The first method was a standard logistic regression model, which included separate terms for the clinical covariates and for each of the genetic markers. This approach ignores a substantial amount of external information concerning effect sizes for these Genome Wide Association Study (GWAS)-replicated SNPs. The second and third methods investigated two possible approaches to incorporating meta-analysed external SNP effect estimates - one via a weighted PCa 'risk' score based solely on the meta analysis estimates, and the other incorporating both the current and prior data via informative priors in a Bayesian logistic regression model. All methods demonstrated a slight improvement in predictive performance upon incorporation of genetics. The two methods that incorporated external information showed the greatest receiver-operating-characteristic AUCs increase from 0.61 to 0.64. The value of our methods comparison is likely to lie in observations of performance similarities, rather than difference, between three approaches of very different resource requirements. The two methods that included external information performed best, but only marginally despite substantial differences in complexity.

BACKGROUND: Glioblastoma multiforme (GBM) is the most prevalent and deadly brain tumor. A variety of germline and somatic, genetic and epigenetic alterations at 9p21.3, which encode CDKN2A/CDKN2B tumor suppressor genes, have been isolatedly reported to be associated with GBM risk and prognosis. METHODS: To obtain a comprehensive view of these events, we leveraged the wide-spectrum GBM data available from The Cancer Genome Atlas project and performed an integrated analysis by systematically evaluating 9p21.3-related germline single-nucleotide polymorphisms, somatic copy number alterations (CNAs), DNA methylation, and microRNAs (miRNAs) with regard to CDKN2A/CDKN2B expression and patient prognosis in GBM. RESULTS: Our multivariate analysis indicated that expression of CDKN2A and CDKN2B was both strongly affected by CNAs (P = 1.00 × 10−4 and 2.37 × 10−14). The miRNAs hsa-mir-126, hsa-mir-517a, and hsa-mir-125b exhibited significant negative correlations with CDKN2A expression (P = 0.003, 0.041, and 0.050). Survival analysis showed that complete 9p21.3 loss and low CDKN2B expression were associated with worse prognosis for both tumor progression/recurrence-free survival (P = .041 and .019) and patient overall survival (P = .043 and .021) after adjustment for age and treatment, and that higher methylation at cg17449661 predicted poorer overall survival (P = .048). CONCLUSION: Representing one of the first attempts to systematically integrate various levels of alterations associated with the often complex cancer genomes and phenotypes, our study provided a holistic view and a mechanistic explanation over the functional connections of multiple 9p21.3-related events in GBM, as well as clinically useful biomarker information for predicting disease outcomes. Cancer 2012;. © 2011 American Cancer Society.

BACKGROUND Prostate cancer (PCa) risk-associated single-nucleotide polymorphisms (SNPs) are continuously being discovered. Their ability to identify men at high risk and the impact of increasing numbers of SNPs on predictive performance are not well understood. METHODS Absolute risk for PCa was estimated in a population-based case–control study in Sweden (2,899 cases and 1,722 controls) using family history and three sets of sequentially discovered PCa risk-associated SNPs. Their performance in predicting PCa was assessed by positive predictive values (PPV) and sensitivity. RESULTS SNPs and family history were able to differentiate individual risk for PCa and identify men at higher risk; ∼18% and ∼8% of men in the study had 20-year (55–74 years) absolute risks that were twofold (0.24) or threefold (0.36) greater than the population median risk (0.12), respectively. When predictive performances were compared at absolute risk cutoffs of 0.12, 0.24, or 0.36, PPV increased considerably (∼20%, ∼30%, and ∼37%, respectively) while sensitivity decreased considerably (∼55%, ∼20%, and ∼10%, respectively). In contrast, when increasing numbers of SNPs (5, 11, and 28 SNPs) were used in risk prediction, PPV approached a constant value while sensitivity increased steadily. CONCLUSIONS SNPs discovered to date are suitable for risk prediction while additional SNPs discovered in the future may identify more subjects at higher risk. Men identified as high risk by SNP-based testing may be targeted for PCa screening or chemoprevention. The clinical impact on improving the effectiveness of these interventions can be and should be assessed. Prostate 77:421–430, 2011. © 2010 Wiley-Liss, Inc.

BACKGROUND Genome-wide association studies (GWAS) have led to the discovery of multiple SNPs that are associated with prostate cancer (PCa) risk. These SNPs may potentially be used for risk prediction. To date, there is not a stable estimate of their effect on PCa risk and their contribution to the genetic variation both of which are important for future risk prediction.

Background—Several genome-wide association studies (GWAS) in populations of European descent have identified more than a dozen common genetic variants that are associated with prostate cancer risk. Methods—To determine whether these variants are also associated with prostate cancer risk in the Chinese population, we evaluated 17 prostate cancer susceptibility loci in a population-based case-control study from Shanghai, including 288 prostate cancer cases and 155 population controls. Results—After adjusting for age, two of the 17 loci were significantly associated with prostate cancer risk, while the other 15 loci were suggestively associated with prostate cancer risk in this population. The strongest associations were found for chromosome 8q24 Region 2 (rs1016343: OR=2.07, 95% CI: 1.35-3.20, P=9.4×10 -4 ) and 8q24 Region 1 (rs10090154: OR=2.07, 95% CI: 1.31-3.28, P=0.002); additional single nucleotide polymorphisms (SNPs) assessed in these two 8q24 regions were also significant (ORRegion2=1.92-2.05, P=9.4×10 -4 -0.003, and ORRegion1=1.77-1.81, P=0.01 for all SNPs). Conclusions—Our study shows that multiple prostate cancer risk loci identified in European populations using GWAS are also associated with prostate cancer risk in Chinese men, a low-risk population with mostly clinically relevant cancers. Larger studies in Chinese and Asian populations are needed to confirm these findings and the role of these risk loci in prostate cancer etiology in Asian men.

Background—More than a dozen single nucleotide polymorphisms (SNPs) have been associated with prostate cancer (PCa) risk from genome-wide association studies (GWAS). Their association with PCa aggressiveness and clinicopathologic variables is inconclusive. Methods—Twenty PCa risk SNPs implicated in GWAS and fine mapping studies were evaluated in 5,895 PCa cases treated by radical prostatectomy at Johns Hopkins Hospital, where each tumor was uniformly graded and staged using the same protocol. Results—For 18 of the 20 SNPs examined, no statistically significant differences (P > 0.05) were observed in risk allele frequencies between patients with more aggressive (Gleason Scores ≥ 4+3, or stage ≥ T3b, or N+) or less aggressive disease (Gleason Scores ≤ 3+4, and stage ≤ T2, and N0). For the two SNPs that had significant differences between more and less aggressive disease (rs2735839 in KLK3 (P = 8.4 × 10 −7 ) and rs10993994 in MSMB (P = 0.046), the alleles that are associated with increased risk for PCa were more frequent in patients with less aggressive disease. Since these SNPs are known to be associated with PSA levels in men without PCa diagnoses, these latter associations may reflect the enrichment of low grade, low stage cases diagnosed by contemporary disease screening with PSA.

BACKGROUND TNFRSF10C, is located on 8p21.3, one of the most frequently deleted loci in the genome of prostate cancer (PCa). Hypermethylation of TNFRSF10C promoter CpG island (CGI) had been reported in many tumors including PCa. However, the interplay between somatic deletion and promoter hypermethylation of TNFRSF10C on PCa development has not been investigated. METHODS Methylation status of promoter CGI and deletion status of the TNFRSF10C locus was investigated by bisulfite sequencing and Affymetrix SNP array, respectively, in 59 pairs of PCa tumor and matched normal samples with three PCa cell lines. TNFRSF10C gene expression changes in relation to cancer-associated genetic/epigenetic changes in clinical specimens, and change of TNFRSF10C expression before and after 5-aza-2′-deoxycytidine treatment in the PC3 PCa cell line was assessed by real-time RT-PCR. RESULTS We found that TNFRSF10C promoter CGI was differentially methylated in 46 of 59 primary cancers (78.0%). Hemizygous deletion at TNFRSF10C was found in 44 of the 59 prostate tumors (74.5%). Interestingly, in 94.9% of the tumors (56 out of 59), TNFRSF10C was either hemizygously deleted or its promoter CGI hypermethylated. Deletion and/or methylation of the TNFRSF10C gene were correlated with decreased mRNA expression of the gene in clinical specimens. Demethylation of the TNFRSF10C promoter CGI was accompanied by transcriptional re-activation of TNFRSF10C in the PCa cell line PC3. CONCLUSION We found a notably high frequency of promoter CGI methylation and deletion of TNFRSF10C in PCa tissues. Our results indicated that inactivation of TNFRSF10C by chromosomal deletion and promoter methylation may play an important role in PCa development. Prostate 69:327–335, 2009. © 2008 Wiley-Liss, Inc.

Exposure to DNA-damaging agents can activate cell cycle checkpoint and DNA repair processes to ensure genetic integrity. Such exposures also can affect the transcription of many genes required for these processes. In the budding yeast Saccharomyces cerevisiae, changes of global gene expression as a result of a DNA-damaging agent were previously identified by using DNA chip technology. DNA microarray analysis is a powerful tool for identifying genes whose expressions are changed in response to environmental changes. Transcriptional levels, however, do not necessarily reflect cellular protein levels. Green fluorescent protein (GFP) has been widely used as a reporter of gene expression and subcellular protein localization. We have used 4156 yeast strains expressing full-length, chromosome-tagged GFP fusion proteins to monitor changes of protein levels in response to the DNA-damaging agent, methyl methanesulphonate (MMS). Through flow cytometry, we identified 157 proteins whose levels were increased at least three-fold following treatment with MMS. Of 157 responsible genes, transcriptions of 57 were previously not known to be induced by MMS. Immunoblot experiments with tandem affinity-tagged yeast strains under the same experimental conditions confirmed these newly found proteins as inducible. These results suggest, therefore, that the 57 protein expressions are regulated by different mechanisms, such as post-translational modifications, and not by transcriptional regulation.

Purpose: Neuroprotective therapeutics stop or slowdown the degeneration process in animal models of Parkinson's disease (PD). In the present study, we investigated the anti‐inflammatory effect of bee venom (BV) on lipopolysaccharide (LPS)‐stimulated microglia. Method and Materials: To investigate whether MR techniques have added value in neuroprotection research in the MPTP mouse model, both MRI and MRS were applied to investigate the neuroprotective effects of BV. BV is suggested to stimulate anti‐inflammatory processing indirectly via DA‐dependent mechanisms or γ‐aminobutyric acid (GABA) and glutamate release. Magnetization transfer ratio (MTR) and 1H‐MRS studies were performed on control mice, MPTP‐intoxicated mice and BV treatment mice. The successfully induced lesions were verified by tyrosine hydroxylase immunolabelling on the substantia nigra (SN) and striatum (ST) performed on perchloric extracts of mice brains, after the control mice and the MPTP‐intoxicated mice were killed. All the MTR and 1H‐MRS experiments were performed on a 9.4 T MRI/MRS system using a standard head coil. Outer volume suppression combined with the ultra‐short echo‐time stimulated echo acquisition mode was used for the localized 1H‐MRS. The quantitative analysis of metabolites was determined using jMRUI from the 1H spectra obtained in vivo on the striatum. Results: The peak height of the MTR histograms in the PD model group was significantly lower than that in the BV treatment group (P

We recently developed room-temperature deposited pyrochlore-structure Bi1.5Zn1.0Nb1.5O7 (BZN) insulator having the high dielectric constant (∍=50) and low leakage current. Using the high-K BZN film as a gate insulator, we fabricated pentacene OTFTs operating at low voltage. We fabricated 12 × 12 OTFT-driven OLED. We are integrating the OLED array with the low-voltage high-K pentacene OTFT.