Stochastic Segmentation Models for Array-Based Comparative Genomic Hybridization Data Analysis

Array-based comparative genomic hybridization (array-CGH) is a high throughput, high resolution technique for studying the genetics of cancer. Analysis of array-CGH data typically involves estimation of the underlying chromosome copy numbers from the log fluorescence ratios and segmenting the chromosome into regions with the same copy number at each location. We propose for the analysis of array-CGH data, a new stochastic segmentation model and an associated estimation procedure that has attractive statistical and computational properties. An important benefit of this Bayesian segmentation model is that it yields explicit formulas for posterior means, which can be used to estimate the signal directly without performing segmentation. Other quantities relating to the posterior distribution that are useful for providing confidence assessments of any given segmentation can also be estimated by using our method. We propose an approximation method whose computation time is linear in sequence length which makes our method practically applicable to the new higher density arrays. Simulation studies and applications to real array-CGH data illustrate the advantages of the proposed approach

Immediate versus Delayed Sequential Bilateral Cataract Surgery: A Systematic Review and Meta-Analysis

BACKGROUND: Immediately sequential bilateral cataract surgery (ISBCS), the cataract surgery that is performed in both eyes simultaneously, is gaining popularity worldwide compared to the traditional treatment paradigm: delayed sequential bilateral cataract surgery (DSBCS), the surgery that is performed in each eye on a different day as a completely separate operation. ISBCS provides advantages to patients and patients\u27 families in the form of fewer hospital visits. Additionally, patients enjoy rapid rehabilitation, lack of anisometropia - potentially reducing accidents and falls, and avoid suboptimal visual function in daily life. The hospital may benefit due to lower cost. OBJECTIVE: To perform a systematic review and meta-analysis to evaluate ISBCS and DSBCS. DATA SOURCES: Databases including MEDLINE, EMBASE, BIOSIS, CINAHL, Health Economic Evaluations Database (HEED), ISI Web of Science (Thomson-Reuters) and the Cochrane Library were searched. PARTICIPANTS: Not applicable. METHODS: Literature was systematically reviewed using EPPI-Reviewer 4 gateway. Meta-analysis was conducted using STATA v. 13.0. Standardized mean difference (SMD) and 95% confidence intervals (CI) were calculated and heterogeneity was assessed using I2 statistics. Fixed-effect and random-effect models were computed based on heterogeneity. Meta-analysis was done by instrument used to calculate utility score. RESULTS: In total, 9,133 records were retrieved from multiple databases and an additional 128 records were identified through grey literature search. Eleven articles with 3,657 subjects were included for analysis. Our meta-analysis results indicated significant improvement in post-operative utility score using TTO, EQ5D, HUI3, VF-7, and VF-14 and a non-significant improvement using Catquest questionnaire for both surgeries. For ISBCS versus DSBCS, utility-specific fixed-effect model provided an overall SMD of the utility score using the TTO method as 0.12 (95% CI: -0.15, 0.40), EQ5D as 0.14 (95% CI: -0.14, 0.41), HUI3 as 0.12 (95% CI: -0.15, 0.40), VF-7 as -0.02 (95% CI: -0.15, 0.10), and Catquest Questionnaire as 1.45 (95% CI: -0.88, 2.01). The results for utility score, which were measured using various instruments, indicated non-significant improvement in the utility due to DSBCS compared to ISBCS. However, a significant improvement in post-operative utility score was seen using Catquest questionnaire for ISBCS compared to DSBCS. The included studies using VF-14 instrument were highly heterogeneous (I2 = 97.1%). Results provided SMD of -0.25 (95% CI:-1.06, 0.57) using VF-14 indicating non-significant improvement in the utility due to DSBCS compared to ISBCS surgery. Best corrected visual acuity (BCVA) significantly improved after both surgeries (overall SMD of BCVA due to ISBCS was -1.79 (95% CI: -2.45, -1.14) and due to DSBCS was -1.53 (95% CI: -2.25, -0.81)). A non-significant improvement was seen in BCVA due to ISBCS when compared to DSBCS (SMD = -0.18; 95% CI: -0.37, 0.01). CONCLUSION: Both surgeries, ISBCS and DSBCS significantly improve patients\u27 quality of life and visual acuity. Further, ISBCS may deliver certain additional benefits at the individual and societal levels as well

Comparison of the Population Excess Fraction of <i>Chlamydia trachomatis</i> Infection on Pelvic Inflammatory Disease at 12-months in the Presence and Absence of Chlamydia Testing and Treatment:Systematic Review and Retrospective Cohort Analysis

Background: The impact of Chlamydia trachomatis (chlamydia) control on the incidence of pelvic inflammatory disease (PID) is theoretically limited by the proportion of PID caused by chlamydia. We estimate the population excess fraction (PEF) of treated chlamydia infection on PID at 12-months in settings with widespread chlamydia control (testing and treatment) and compare this to the estimated PEF of untreated chlamydia. Methods: We used two large retrospective population-based cohorts of women of reproductive age from settings with widespread chlamydia control to calculate the PEF of treated chlamydia on PID at 12-months. We undertook a systematic review to identify further studies that reported the risk of PID in women who were tested for chlamydia (infected and uninfected). We used the same method to calculate the PEF in eligible studies then compared all estimates of PEF. Results: The systematic review identified a single study, a randomised control led trial of chlamydia screening (POPI-RCT). In the presence of testing and treatment <10% of PID at 12-months was attributable to treated (baseline) chlamydia infections (Manitoba: 8.86%(95%CI 7.15-10.75); Denmark: 3.84%(3.26-4.45); screened-arm POPI-RCT: 0.99%(0.00-29.06)). In the absence of active chlamydia treatment 26.44% (11.57-46.32) of PID at 12-months was attributable to untreated (baseline) chlamydia infections (deferred-arm POPI-RCT). The PEFs suggest that eradicating baseline chlamydia infections could prevent 484 cases of PID at 12-months per 100,000 women in the untreated setting and 13- 184 cases of PID per 100,000 tested women in the presence of testing and treatment. Conclusion: Testing and treating chlamydia reduced the PEF of chlamydia on PID by 65% compared to the untreated setting. But in the presence of testing and treatment over 90% of PID could not be attributed to a baseline chlamydia infection. More information is needed about the aetiology of PID to develop effective strategies for improving the reproductive health of women