Simultaneous Multiple Surface Segmentation Using Deep Learning

The task of automatically segmenting 3-D surfaces representing boundaries of objects is important for quantitative analysis of volumetric images, and plays a vital role in biomedical image analysis. Recently, graph-based methods with a global optimization property have been developed and optimized for various medical imaging applications. Despite their widespread use, these require human experts to design transformations, image features, surface smoothness priors, and re-design for a different tissue, organ or imaging modality. Here, we propose a Deep Learning based approach for segmentation of the surfaces in volumetric medical images, by learning the essential features and transformations from training data, without any human expert intervention. We employ a regional approach to learn the local surface profiles. The proposed approach was evaluated on simultaneous intraretinal layer segmentation of optical coherence tomography (OCT) images of normal retinas and retinas affected by age related macular degeneration (AMD). The proposed approach was validated on 40 retina OCT volumes including 20 normal and 20 AMD subjects. The experiments showed statistically significant improvement in accuracy for our approach compared to state-of-the-art graph based optimal surface segmentation with convex priors (G-OSC). A single Convolution Neural Network (CNN) was used to learn the surfaces for both normal and diseased images. The mean unsigned surface positioning errors obtained by G-OSC method 2.31 voxels (95% CI 2.02-2.60 voxels) was improved to $1.27$ voxels (95% CI 1.14-1.40 voxels) using our new approach. On average, our approach takes 94.34 s, requiring 95.35 MB memory, which is much faster than the 2837.46 s and 6.87 GB memory required by the G-OSC method on the same computer system.Comment: 8 page

Pion mass dependence of the Kl3K_{l3} semileptonic scalar form factor within finite volume

We calculate the scalar semileptonic kaon decay in finite volume at the momentum transfer $t_{m} = (m_{K} - m_{\pi})^2$, using chiral perturbation theory. At first we obtain the hadronic matrix element to be calculated in finite volume. We then evaluate the finite size effects for two volumes with $L = 1.83 fm$ and $L= 2.73 fm$ and find that the difference between the finite volume corrections of the two volumes are larger than the difference as quoted in \cite{Boyle2007a}. It appears then that the pion masses used for the scalar form factor in ChPT are large which result in large finite volume corrections. If appropriate values for pion mass are used, we believe that the finite size effects estimated in this paper can be useful for Lattice data to extrapolate at large lattice size.Comment: 19 pages, 5 figures, accepted for publication in EPJ

A new approach to calculate the gluon polarization

We derive the Leading-Order master equation to extract the polarized gluon distribution G(x;Q^2) = x \deltag(x;Q^2) from polarized proton structure function, g1p(x;Q^2). By using a Laplace-transform technique, we solve the master equation and derive the polarized gluon distribution inside the proton. The test of accuracy which are based on our calculations with two different methods confirms that we achieve to the correct solution for the polarized gluon distribution. We show that accurate experimental knowledge of g1p(x;Q^2) in a region of Bjorken x and Q^2, is all that is needed to determine the polarized gluon distribution in that region. Therefore, to determine the gluon polarization \deltag /g,we only need to have accurate experimental data on un-polarized and polarized structure functions (F2p (x;Q^2) and g1p(x;Q^2)).Comment: 12 pages, 5 figure

Risk Factors for Hepatitis C Virus Transmission to Health Care Workers after Occupational Exposure: A European Case-Control Study

Background. Additional studies are required to identify risk factors for hepatitis C virus (HCV) transmission to health care workers after occupational exposure to HCV. Methods. We conducted a matched case-control study in 5 European countries from 1 January 1991 through 31 December 2002. Case patients were health care workers who experienced seroconversion after percutaneous or mucocutaneous exposure to HCV. Control subjects were HCV-exposed health care workers who did not experience seroconversion and were matched with case patients for center and period of exposure. Results. Sixty case patients and 204 control subjects were included in the study. All case patients were exposed to HCV-infected fluids through percutaneous injuries. The 37 case patients for whom information was available were exposed to viremic source patients. As risk factors for HCV infection, multivariate analysis identified needle placement in a source patient's vein or artery (odds ratio [OR], 100.1; 95% confidence interval [CI], 7.3-1365.7), deep injury (OR, 155.2; 95% CI, 7.1-3417.2), and sex of the health care worker (OR for male vs. female, 3.1; 95% CI, 1.0-10.0). Source patient HCV load was not introduced in the multivariate model. In unmatched univariate analysis, the risk of HCV transmission increased 11-fold for health care workers exposed to source patients with a viral load >6 log10 copies/mL (95% CI, 1.1-114.1), compared with exposures to source patients with a viral load ⩽4 log10 copies/mL. Conclusion. In this study, HCV occupational transmission was found to occur after percutaneous exposures. The risk of HCV transmission after percutaneous exposure increased with deep injuries and procedures involving hollow-bore needle placement in the source patient's vein or artery. These results highlight the need for widespread adoption of needlestick-prevention devices in health care settings, together with other preventive measure

Week 96 efficacy and safety results of the phase 3, randomized EMERALD trial to evaluate switching from boosted-protease inhibitors plus emtricitabine/tenofovir disoproxil fumarate regimens to the once daily, single-tablet regimen of darunavir/cobicistat/emtricitabine/tenofovir alafenamide (D/C/F/TAF) in treatment-experienced, virologically-suppressed adults living with HIV-1

Darunavir/cobicistat/emtricitabine/tenofovir alafenamide (D/C/F/TAF) 800/150/200/10 mg was investigated through 96 weeks in EMERALD (NCT02269917). Virologically-suppressed, HIV-1-positive treatment-experienced adults (previous non-darunavir virologic failure [VF] allowed) were randomized (2:1) to D/C/F/TAF or boosted protease inhibitor (PI) plus emtricitabine/tenofovir-disoproxil-fumarate (F/TDF) over 48 weeks. At week 52 participants in the boosted PI arm were offered switch to D/C/F/TAF (late-switch, 44 weeks D/C/F/TAF exposure). All participants were followed on D/C/F/TAF until week 96. Efficacy endpoints were percentage cumulative protocol-defined virologic rebound (PDVR; confirmed viral load [VL] >= 50 copies/mL) and VL = 50 copies/mL (VF) (FDA-snapshot analysis). Of 1141 randomized patients, 1080 continued in the extension phase. Few patients had PDVR (D/C/F/TAF: 3.1%, 24/763 cumulative through week 96; late-switch: 2.3%, 8/352 week 52-96). Week 96 virologic suppression was 90.7% (692/763) (D/C/F/TAF) and 93.8% (330/352) (late-switch). VF was 1.2% and 1.7%, respectively. No darunavir, primary PI, tenofovir or emtricitabine resistance-associated mutations were observed post-baseline. No patients discontinued for efficacy-related reasons. Few discontinued due to adverse events (2% D/C/F/TAF arm). Improved renal and bone parameters were maintained in the D/C/F/TAF arm and observed in the late-switch arm, with small increases in total cholesterol/high-density-lipoprotein-cholesterol ratio. A study limitation was the lack of a control arm in the week 96 analysis. Through 96 weeks, D/C/F/TAF resulted in low PDVR rates, high virologic suppression rates, very few VFs, and no resistance development. Late-switch results were consistent with D/C/F/TAF week 48 results. EMERALD week 96 results confirm the efficacy, high genetic barrier to resistance and safety benefits of D/C/F/TAF

Clinical use of HIV integrase inhibitors : a systematic review and meta-analysis

Background: Optimal regimen choice of antiretroviral therapy is essential to achieve long-term clinical success. Integrase inhibitors have swiftly been adopted as part of current antiretroviral regimens. The purpose of this study was to review the evidence for integrase inhibitor use in clinical settings. Methods: MEDLINE and Web-of-Science were screened from April 2006 until November 2012, as were hand-searched scientific meeting proceedings. Multiple reviewers independently screened 1323 citations in duplicate to identify randomized controlled trials, nonrandomized controlled trials and cohort studies on integrase inhibitor use in clinical practice. Independent, duplicate data extraction and quality assessment were conducted. Results: 48 unique studies were included on the use of integrase inhibitors in antiretroviral therapy-naive patients and treatment-experienced patients with either virological failure or switching to integrase inhibitors while virologically suppressed. On the selected studies with comparable outcome measures and indication (n = 16), a meta-analysis was performed based on modified intention-to-treat (mITT), on-treatment (OT) and as-treated (AT) virological outcome data. In therapy-naive patients, favorable odds ratios (OR) for integrase inhibitor-based regimens were observed, (mITT OR 0.71, 95% CI 0.59-0.86). However, integrase inhibitors combined with protease inhibitors only did not result in a significant better virological outcome. Evidence further supported integrase inhibitor use following virological failure (mITT OR 0.27; 95% CI 0.11-0.66), but switching to integrase inhibitors from a high genetic barrier drug during successful treatment was not supported (mITT OR 1.43; 95% CI 0.89-2.31). Integrase inhibitor-based regimens result in similar immunological responses compared to other regimens. A low genetic barrier to drug-resistance development was observed for raltegravir and elvitegravir, but not for dolutegravir. Conclusion: In first-line therapy, integrase inhibitors are superior to other regimens. Integrase inhibitor use after virological failure is supported as well by the meta-analysis. Careful use is however warranted when replacing a high genetic barrier drug in treatment-experienced patients switching successful treatment

Engaging new migrants in infectious disease screening: a qualitative semi-structured interview study of UK migrant community health-care leads.

Migration to Europe - and in particular the UK - has risen dramatically in the past decades, with implications for public health services. Migrants have increased vulnerability to infectious diseases (70% of TB cases and 60% HIV cases are in migrants) and face multiple barriers to healthcare. There is currently considerable debate as to the optimum approach to infectious disease screening in this often hard-to-reach group, and an urgent need for innovative approaches. Little research has focused on the specific experience of new migrants, nor sought their views on ways forward. We undertook a qualitative semi-structured interview study of migrant community health-care leads representing dominant new migrant groups in London, UK, to explore their views around barriers to screening, acceptability of screening, and innovative approaches to screening for four key diseases (HIV, TB, hepatitis B, and hepatitis C). Participants unanimously agreed that current screening models are not perceived to be widely accessible to new migrant communities. Dominant barriers that discourage uptake of screening include disease-related stigma present in their own communities and services being perceived as non-migrant friendly. New migrants are likely to be disproportionately affected by these barriers, with implications for health status. Screening is certainly acceptable to new migrants, however, services need to be developed to become more community-based, proactive, and to work more closely with community organisations; findings that mirror the views of migrants and health-care providers in Europe and internationally. Awareness raising about the benefits of screening within new migrant communities is critical. One innovative approach proposed by participants is a community-based package of health screening combining all key diseases into one general health check-up, to lessen the associated stigma. Further research is needed to develop evidence-based community-focused screening models - drawing on models of best practice from other countries receiving high numbers of migrants

Mobile HIV Screening in Cape Town, South Africa: Clinical Impact, Cost and Cost-Effectiveness

Background: Mobile HIV screening may facilitate early HIV diagnosis. Our objective was to examine the cost-effectiveness of adding a mobile screening unit to current medical facility-based HIV testing in Cape Town, South Africa. Methods and Findings: We used the Cost Effectiveness of Preventing AIDS Complications International (CEPAC-I) computer simulation model to evaluate two HIV screening strategies in Cape Town: 1) medical facility-based testing (the current standard of care) and 2) addition of a mobile HIV-testing unit intervention in the same community. Baseline input parameters were derived from a Cape Town-based mobile unit that tested 18,870 individuals over 2 years: prevalence of previously undiagnosed HIV (6.6%), mean CD4 count at diagnosis (males 423/µL, females 516/µL), CD4 count-dependent linkage to care rates (males 31%–58%, females 49%–58%), mobile unit intervention cost (includes acquisition, operation and HIV test costs, $29.30 per negative result and$31.30 per positive result). We conducted extensive sensitivity analyses to evaluate input uncertainty. Model outcomes included site of HIV diagnosis, life expectancy, medical costs, and the incremental cost-effectiveness ratio (ICER) of the intervention compared to medical facility-based testing. We considered the intervention to be “very cost-effective” when the ICER was less than South Africa's annual per capita Gross Domestic Product (GDP) ($8,200 in 2012). We projected that, with medical facility-based testing, the discounted (undiscounted) HIV-infected population life expectancy was 132.2 (197.7) months; this increased to 140.7 (211.7) months with the addition of the mobile unit. The ICER for the mobile unit was$2,400/year of life saved (YLS). Results were most sensitive to the previously undiagnosed HIV prevalence, linkage to care rates, and frequency of HIV testing at medical facilities. Conclusion: The addition of mobile HIV screening to current testing programs can improve survival and be very cost-effective in South Africa and other resource-limited settings, and should be a priority