Linear and nonlinear optical properties of carbon nanotube-coated single-mode optical fiber gratings

This paper was published in OPTICS LETTERS and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://dx.doi.org/10.1364/OL.36.002104. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law[EN] Single-wall carbon nanotube deposition on the cladding of optical fibers has been carried out to fabricate an all-fiber nonlinear device. Two different nanotube deposition techniques were studied. The first consisted of repeatedly immersing the optical fiber into a nanotube supension, increasing the thickness of the coating in each step. The second deposition involved wrapping a thin film of nanotubes around the optical fiber. For both cases, interaction of transmitted light through the fiber core with the external coating was assisted by the cladding mode resonances of a tilted fiber Bragg grating. Ultrafast nonlinear effects of the nanotube-coated fiber were measured by means of a pump-probe pulses experiment. © 2011 Optical Society of America.This work was financially supported by the European Commission under the FP7 EURO-FOS Network of Excellence (ICT-2007-2-224402), the Ministerio de Educación y Ciencia SINADEC project (TEC2008-06333), and the Natural Sciences and Engineering Research Council of Canada (NSERC). The work of G. E. Villanueva was supported by the Ministerio de Educación y Ciencia Formación de Profesorado Universitario programs. The work of P. Pérez-Millán was supported by the Juan de la Cierva program, JCI-2009-05805.Villanueva Ibáñez, GE.; Jakubinek, M.; Simard, B.; Oton Nieto, CJ.; Matres Abril, J.; Shao, L.; Pérez Millán, P.... (2011). Linear and nonlinear optical properties of carbon nanotube-coated single-mode optical fiber gratings. Optics Letters. 36(11):2104-2106. https://doi.org/10.1364/OL.36.002104S210421063611Sakakibara, Y., Rozhin, A. G., Kataura, H., Achiba, Y., & Tokumoto, M. (2005). Carbon Nanotube-Poly(vinylalcohol) Nanocomposite Film Devices: Applications for Femtosecond Fiber Laser Mode Lockers and Optical Amplifier Noise Suppressors. Japanese Journal of Applied Physics, 44(4A), 1621-1625. doi:10.1143/jjap.44.1621Chow, K. K., Yamashita, S., & Song, Y. W. (2009). A widely tunable wavelength converter based on nonlinear polarization rotation in a carbon-nanotube-deposited D-shaped fiber. Optics Express, 17(9), 7664. doi:10.1364/oe.17.007664Set, S. Y., Yaguchi, H., Tanaka, Y., & Jablonski, M. (2004). Ultrafast Fiber Pulsed Lasers Incorporating Carbon Nanotubes. IEEE Journal of Selected Topics in Quantum Electronics, 10(1), 137-146. doi:10.1109/jstqe.2003.822912Chow, K. K., Tsuji, M., & Yamashita, S. (2010). Single-walled carbon-nanotube-deposited tapered fiber for four-wave mixing based wavelength conversion. Applied Physics Letters, 96(6), 061104. doi:10.1063/1.3304789Chow, K. K., & Yamashita, S. (2009). Four-wave mixing in a single-walled carbon-nanotube-deposited D-shaped fiber and its application in tunable wavelength conversion. Optics Express, 17(18), 15608. doi:10.1364/oe.17.015608Choi, S. Y., Rotermund, F., Jung, H., Oh, K., & Yeom, D.-I. (2009). Femtosecond mode-locked fiber laser employing a hollow optical fiber filled with carbon nanotube dispersion as saturable absorber. Optics Express, 17(24), 21788. doi:10.1364/oe.17.021788Chan, C.-F., Chen, C., Jafari, A., Laronche, A., Thomson, D. J., & Albert, J. (2007). Optical fiber refractometer using narrowband cladding-mode resonance shifts. Applied Optics, 46(7), 1142. doi:10.1364/ao.46.001142Kingston, C. T., Jakubek, Z. J., Dénommée, S., & Simard, B. (2004). Efficient laser synthesis of single-walled carbon nanotubes through laser heating of the condensing vaporization plume. Carbon, 42(8-9), 1657-1664. doi:10.1016/j.carbon.2004.02.020Jakubinek, M. B., Johnson, M. B., White, M. A., Guan, J., & Simard, B. (2010). Novel Method to Produce Single-Walled Carbon Nanotube Films and Their Thermal and Electrical Properties. Journal of Nanoscience and Nanotechnology, 10(12), 8151-8157. doi:10.1166/jnn.2010.3014Vallaitis, T., Koos, C., Bonk, R., Freude, W., Laemmlin, M., Meuer, C., … Leuthold, J. (2008). Slow and fast dynamics of gain and phase in a quantum dot semiconductor optical amplifier. Optics Express, 16(1), 170. doi:10.1364/oe.16.00017

Incorporating truncating variants in PALB2, CHEK2, and ATM into the BOADICEA breast cancer risk model.

PURPOSE: The proliferation of gene panel testing precipitates the need for a breast cancer (BC) risk model that incorporates the effects of mutations in several genes and family history (FH). We extended the BOADICEA model to incorporate the effects of truncating variants in PALB2, CHEK2, and ATM. METHODS: The BC incidence was modeled via the explicit effects of truncating variants in BRCA1/2, PALB2, CHEK2, and ATM and other unobserved genetic effects using segregation analysis methods. RESULTS: The predicted average BC risk by age 80 for an ATM mutation carrier is 28%, 30% for CHEK2, 50% for PALB2, and 74% for BRCA1 and BRCA2. However, the BC risks are predicted to increase with FH burden. In families with mutations, predicted risks for mutation-negative members depend on both FH and the specific mutation. The reduction in BC risk after negative predictive testing is greatest when a BRCA1 mutation is identified in the family, but for women whose relatives carry a CHEK2 or ATM mutation, the risks decrease slightly. CONCLUSIONS: The model may be a valuable tool for counseling women who have undergone gene panel testing for providing consistent risks and harmonizing their clinical management. A Web application can be used to obtain BC risks in clinical practice (http://ccge.medschl.cam.ac.uk/boadicea/).Genet Med 18 12, 1190-1198.This work was funded by Cancer Research UK Grants C12292/A11174 and C1287/A10118. ACA is a Cancer Research UK Senior Cancer Research Fellow. This work was supported by the Governement of Canada through Genome Canada and the Canadian Institutes of Health Research, and the Ministère de l'enseignement supérieur, de la recherche, de la science et de la technologie du Québec through Génome Québec.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/gim.2016.3

Exploring the origin and degree of genetic isolation of Anopheles gambiae from the islands of São Tomé and Príncipe, potential sites for testing transgenic-based vector control

The evolutionary processes at play between island and mainland populations of the malaria mosquito vector Anopheles gambiae sensu stricto are of great interest as islands may be suitable sites for preliminary application of transgenic-based vector control strategies. São Tomé and Príncipe, located off the West African coast, have received such attention in recent years. This study investigates the degree of isolation of An. gambiae s.s. populations between these islands and the mainland based on mitochondrial and ribosomal DNA molecular data. We identify possible continental localities from which these island populations derived. For these purposes, we used FST values, haplotype networks, and nested clade analysis to estimate migration rates and patterns. Haplotypes from both markers are geographically widespread across the African continent. Results indicate that the populations from São Tomé and Príncipe are relatively isolated from continental African populations, suggesting they are promising sites for test releases of transgenic individuals. These island populations are possibly derived from two separate continental migrations. This result is discussed in the context of the history of the African slave trade with respect to São Tomé and Príncipe

Canadian Healthcare Professionals’ Views and Attitudes toward Risk-Stratified Breast Cancer Screening

Given the controversy over the effectiveness of age-based breast cancer (BC) screening, offering risk-stratified screening to women may be a way to improve patient outcomes with detection of earlier-stage disease. While this approach seems promising, its integration requires the buy-in of many stakeholders. In this cross-sectional study, we surveyed Canadian healthcare professionals about their views and attitudes toward a risk-stratified BC screening approach. An anonymous online questionnaire was disseminated through Canadian healthcare professional associations between November 2020 and May 2021. Information collected included attitudes toward BC screening recommendations based on individual risk, comfort and perceived readiness related to the possible implementation of this approach. Close to 90% of the 593 respondents agreed with increased frequency and earlier initiation of BC screening for women at high risk. However, only 9% agreed with the idea of not offering BC screening to women at very low risk. Respondents indicated that primary care physicians and nurse practitioners should play a leading role in the risk-stratified BC screening approach. This survey identifies health services and policy enhancements that would be needed to support future implementation of a risk-stratified BC screening approach in healthcare systems in Canada and other countries

Evaluation of Polygenic Risk Scores for Breast and Ovarian Cancer Risk Prediction in BRCA1 and BRCA2 Mutation Carriers

$\textbf{Background:}$ Genome-wide association studies (GWAS) have identified 94 common single-nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk and 18 associated with ovarian cancer (OC) risk. Several of these are also associated with risk of BC or OC for women who carry a pathogenic mutation in the high-risk BC and OC genes $\textit{BRCA1}$ or $\textit{BRCA2}$. The combined effects of these variants on BC or OC risk for BRCA1 and BRCA2 mutation carriers have not yet been assessed while their clinical management could benefit from improved personalized risk estimates. $\textbf{Methods:}$ We constructed polygenic risk scores (PRS) using BC and OC susceptibility SNPs identified through populationbased GWAS: for BC (overall, estrogen receptor [ER]–positive, and ER-negative) and for OC. Using data from 15 252 female $\textit{BRCA1}$ and 8211 $\textit{BRCA2}$ carriers, the association of each PRS with BC or OC risk was evaluated using a weighted cohort approach, with time to diagnosis as the outcome and estimation of the hazard ratios (HRs) per standard deviation increase in the PRS. $\textbf{Results:}$ The PRS for ER-negative BC displayed the strongest association with BC risk in $\textit{BRCA1}$ carriers (HR = 1.27, 95% confidence interval [CI] = 1.23 to 1.31, $P$ = 8.2 $\times$ 10$^{-53}$). In $\textit{BRCA2}$ carriers, the strongest association with BC risk was seen for the overall BC PRS (HR = 1.22, 95% CI = 1.17 to 1.28, $P$ = 7.2 $\times$ 10$^{-20}$). The OC PRS was strongly associated with OC risk for both $\textit{BRCA1}$ and $\textit{BRCA2}$ carriers. These translate to differences in absolute risks (more than 10% in each case) between the top and bottom AR deciles of the PRS distribution; for example, the OC risk was 6% by age 80 years for $\textit{BRCA2}$ carriers at the 10th percentile of the OC PRS compared with 19% risk for those at the 90th percentile of PRS. $\textbf{Conclusions:}$ BC and OC PRS are predictive of cancer risk in $\textit{BRCA1}$ and $\textit{BRCA2}$ carriers. Incorporation of the PRS into risk prediction models has promise to better inform decisions on cancer risk management.Cancer Research U

Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2

Background: The distribution of ovarian tumour characteristics differs between germline BRCA1 and BRCA2 pathogenic variant carriers and non-carriers. In this study, we assessed the utility of ovarian tumour characteristics as predictors of BRCA1 and BRCA2 variant pathogenicity, for application using the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) variant classification system. Methods: Data for 10,373 ovarian cancer cases, including carriers and non-carriers of BRCA1 or BRCA2 pathogenic variants, were collected from unpublished international cohorts and consortia and published studies. Likelihood ratios (LR) were calculated for the association of ovarian cancer histology and other characteristics, with BRCA1 and BRCA2 variant pathogenicity. Estimates were aligned to ACMG/AMP code strengths (supporting, moderate, strong). Results: No histological subtype provided informative ACMG/AMP evidence in favour of BRCA1 and BRCA2 variant pathogenicity. Evidence against variant pathogenicity was estimated for the mucinous and clear cell histologies (supporting) and borderline cases (moderate). Refined associations are provided according to tumour grade, invasion and age at diagnosis. Conclusions: We provide detailed estimates for predicting BRCA1 and BRCA2 variant pathogenicity based on ovarian tumour characteristics. This evidence can be combined with other variant information under the ACMG/AMP classification system, to improve classification and carrier clinical management.</p

Evaluation of polygenic risk scores for breast and ovarian cancer risk prediction in BRCA1 and BRCA2 mutation carriers

Background: Genome-wide association studies (GWAS) have identified 94 common single-nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk and 18 associated with ovarian cancer (OC) risk. Several of these are also associated with risk of BC or OC for women who carry a pathogenic mutation in the high-risk BC and OC genes BRCA1 or BRCA2. The combined effects of these variants on BC or OC risk for BRCA1 and BRCA2 mutation carriers have not yet been assessed while their clinical management could benefit from improved personalized risk estimates. Methods: We constructed polygenic risk scores (PRS) using BC and OC susceptibility SNPs identified through population-based GWAS: for BC (overall, estrogen receptor [ER]-positive, and ER-negative) and for OC. Using data from 15 252 female BRCA1 and 8211 BRCA2 carriers, the association of each PRS with BC or OC risk was evaluated using a weighted cohort approach, with time to diagnosis as the outcome and estimation of the hazard ratios (HRs) per standard deviation increase in the PRS. Results: The PRS for ER-negative BC displayed the strongest association with BC risk in BRCA1 carriers (HR = 1.27, 95% confidence interval [CI] = 1.23 to 1.31, P = 8.2 x 10(53)). In BRCA2 carriers, the strongest association with BC risk was seen for the overall BC PRS (HR = 1.22, 95% CI = 1.17 to 1.28, P = 7.2 x 10(-20)). The OC PRS was strongly associated with OC risk for both BRCA1 and BRCA2 carriers. These translate to differences in absolute risks (more than 10% in each case) between the top and bottom deciles of the PRS distribution; for example, the OC risk was 6% by age 80 years for BRCA2 carriers at the 10th percentile of the OC PRS compared with 19% risk for those at the 90th percentile of PRS. Conclusions: BC and OC PRS are predictive of cancer risk in BRCA1 and BRCA2 carriers. Incorporation of the PRS into risk prediction models has promise to better inform decisions on cancer risk management

Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation (PERSPECTIVE I&I).

Early detection of breast cancer through screening reduces breast cancer mortality. The benefits of screening must also be considered within the context of potential harms (e.g., false positives, overdiagnosis). Furthermore, while breast cancer risk is highly variable within the population, most screening programs use age to determine eligibility. A risk-based approach is expected to improve the benefit-harm ratio of breast cancer screening programs. The PERSPECTIVE I&I (Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation) project seeks to improve personalized risk assessment to allow for a cost-effective, population-based approach to risk-based screening and determine best practices for implementation in Canada. This commentary describes the four inter-related activities that comprise the PERSPECTIVE I&I project. 1: Identification and validation of novel moderate to high-risk susceptibility genes. 2: Improvement, validation, and adaptation of a risk prediction web-tool for the Canadian context. 3: Development and piloting of a socio-ethical framework to support implementation of risk-based breast cancer screening. 4: Economic analysis to optimize the implementation of risk-based screening. Risk-based screening and prevention is expected to benefit all women, empowering them to work with their healthcare provider to make informed decisions about screening and prevention

BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers

Background: The K3326X variant in BRCA2 (BRCA2*c.9976A&gt;T; p.Lys3326*; rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormone-related cancers. Methods: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76 637 cancer case patients and 83 796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. Results: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9x10- 6) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8x10-3). These associations were stronger for serous ovarian cancer and for estrogen receptor–negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4x10-5 and ORw = 1.50, 95% CI = 1.28 to 1.76, P = 4.1x10-5, respectively). For BRCA1 mutation carriers, there was a statistically significant inverse association of the K3326X variant with risk of ovarian cancer (HR = 0.43, 95% CI = 0.22 to 0.84, P = .013) but no association with breast cancer. No association with prostate cancer was observed. Conclusions: Our study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Further studies are needed to determine the biological mechanism of action responsible for these associations

Evaluation of associations between genetically predicted circulating protein biomarkers and breast cancer risk.

A small number of circulating proteins have been reported to be associated with breast cancer risk, with inconsistent results. Herein, we attempted to identify novel protein biomarkers for breast cancer via the integration of genomics and proteomics data. In the Breast Cancer Association Consortium (BCAC), with 122,977 cases and 105,974 controls of European descendants, we evaluated the associations of the genetically predicted concentrations of >1,400 circulating proteins with breast cancer risk. We used data from a large-scale protein quantitative trait loci (pQTL) analysis as our study instrument. Summary statistics for these pQTL variants related to breast cancer risk were obtained from the BCAC and used to estimate odds ratios (OR) for each protein using the inverse-variance weighted method. We identified 56 proteins significantly associated with breast cancer risk by instrumental analysis (false discovery rate <0.05). Of these, the concentrations of 32 were influenced by variants close to a breast cancer susceptibility locus (ABO, 9q34.2). Many of these proteins, such as insulin receptor, insulin-like growth factor receptor 1 and other membrane receptors (OR: 0.82-1.18, p values: 6.96 × 10-4 -3.28 × 10-8 ), are linked to insulin resistance and estrogen receptor signaling pathways. Proteins identified at other loci include those involved in biological processes such as alcohol and lipid metabolism, proteolysis, apoptosis, immune regulation and cell motility and proliferation. Consistent associations were observed for 22 proteins in the UK Biobank data (p < 0.05). The study identifies potential novel biomarkers for breast cancer, but further investigation is needed to replicate our findings.Includes CRUK and FP7