901 results on '"Rubin, MA"'
Search Results
2. WHO 2022 classification of penile and scrotal cancers: updates and evolution
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Menon, S, primary, Moch, H, additional, Berney, DM, additional, Cree, IA, additional, Srigley, JR, additional, Tsuzuki, T, additional, Compérat, E, additional, Hartmann, A, additional, Netto, G, additional, Rubin, MA, additional, Gill, AJ, additional, Turajlic, S, additional, Tan, PH, additional, Raspollini, MR, additional, Tickoo, SK, additional, and Amin, M B, additional
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- 2022
- Full Text
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3. A Rapid Performance Assessment Method for Microfluidic Chips.
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Rubin Ma, Karan V. I. S. Kaler, and Christopher J. Backhouse
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- 2004
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4. WHO 2022 classification of penile and scrotal cancers: updates and evolution.
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Menon, S, Moch, H, Berney, DM, Cree, IA, Srigley, JR, Tsuzuki, T, Compérat, E, Hartmann, A, Netto, G, Rubin, MA, Gill, AJ, Turajlic, S, Tan, PH, Raspollini, MR, Tickoo, SK, and Amin, M B
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PENILE cancer ,BASAL cell carcinoma ,HUMAN papillomavirus ,SQUAMOUS cell carcinoma ,TUMOR classification ,BIOLOGICAL nomenclature - Abstract
Squamous cell carcinoma (SCC) is the most common malignant tumour of the penis. The 2022 WHO classification reinforces the 2016 classification and subclassifies precursor lesions and tumours into human papillomavirus (HPV)‐associated and HPV‐independent types. HPV‐associated penile intraepithelial neoplasia (PeIN) is a precursor lesion of invasive HPV‐ associated SCC, whereas differentiated PeIN is a precursor lesion of HPV‐independent SCC. Block‐type positivity of p16 immunohistochemistry is the most practical daily utilised method to separate HPVassociated from HPVindependent penile SCC. If this is not feasible, the term SCC, not otherwise specified (NOS) is appropriate. Certain histologies that were previously classified as "subtypes" are now grouped, and coalesced as "patterns", under the rubric of usual type SCC and verrucous carcinoma (e.g. usual‐type SCC includes pseudohyperplastic and acantholytic/pseudoglandular carcinoma, and carcinoma cuniculatum is included as a pattern of verrucous carcinoma). If there is an additional component of the usual type of invasive SCC (formerly termed hybrid histology), the tumour would be a mixed carcinoma (e.g. carcinoma cuniculatum or verrucous carcinoma with usual invasive SCC); in such cases, reporting of the relative percentages in mixed tumours may be useful. The consistent use of uniform nomenclature and reporting of percentages will inform the refinement of future reporting classification schemes and guidelines/recommendations. The classification of scrotal tumours is provided for the first time in the fifth edition of the WHO Blue book, and it follows the schema of penile cancer classification for both precursor lesions and the common SCC of the scrotum. Basal cell carcinoma of the scrotum may have a variable clinical course and finds a separate mention. [ABSTRACT FROM AUTHOR]
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- 2023
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5. Integrated planar waveguide devices for evanescent field sensing and spectroscopy.
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Pavel Cheben, Siegfried Janz, N. Sabourin, Dan-Xia Xu, H. Ding, Shurui Wang, Jens H. Schmid, André Delâge, Jean Lapointe, W. Sinclair, Rubin Ma, S. Logan, R. MacKenzie, Q. Y. Liu, M. Gilmour, Robert Halir, Carlos Alonso-Ramos, J. Gonzalo Wangüemert-Pérez, Alejandro Ortega-Moñux, íñigo Molina-Fernández, X. Le Roux, L. Laurent, A. Villafranca Velasco, and Maria Luisa Calvo
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- 2014
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6. The 2019 Genitourinary Pathology Society (GUPS) White Paper on Contemporary Grading of Prostate Cancer
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Epstein, JI, Amin, MB, Fine, SW, Algaba, F, Aron, M, Baydar, DE, Beltran, AL, Brimo, F, Cheville, JC, Colecchia, M, Comperat, E, da Cunha, IW, Delprado, W, DeMarzo, AM, Giannico, GA, Gordetsky, JB, Guo, CC, Hansel, DE, Hirsch, MS, Huang, JT, Humphrey, PA, Jimenez, RE, Khani, F, Kong, QN, Kryvenko, ON, Kunju, LP, Lal, P, Latour, M, Lotan, T, Maclean, F, Magi-Galluzzi, C, Mehra, R, Menon, S, Miyamoto, H, Montironi, R, Netto, GJ, Nguyen, JK, Osunkoya, AO, Parwani, A, Robinson, BD, Rubin, MA, Shah, RB, So, JS, Takahashi, H, Tavora, F, Tretiakova, MS, True, L, Wobker, SE, Yang, XMJ, Zhou, M, Zynger, DL, and Trpkov, K
- Abstract
Context.-Controversies and uncertainty persist in prostate cancer grading. prostate cancer grading. Objective.-To update grading recommendations Data Sources.-Critical review of the literature along with pathology and clinician surveys. Conclusions.-Percent Gleason pattern 4 (%GP4) is as follows: (1) report %GP4 in needle biopsy with Grade Groups (GrGp) 2 and 3, and in needle biopsy on other parts (jars) of lower grade in cases with at least 1 part showing Gleason score (GS) 4 + 4 = 8; and (2) report %GP4: less than 5% or less than 10% and 10% increments thereafter. Tertiary grade patterns are as follows: (1) replace "tertiary grade pattern'' in radical prostatectomy (RP) with "minor tertiary pattern 5 (TP5),'' and only use in RP with GrGp 2 or 3 with less than 5% Gleason pattern 5; and (2) minor TP5 is noted along with the GS, with the GrGp based on the GS. Global score and magnetic resonance imaging (MRI)targeted biopsies are as follows: (1) when multiple undesignated cores are taken from a single MRI-targeted lesion, an overall grade for that lesion is given as if all the involved cores were one long core; and (2) if providing a global score, when different scores are found in the standard and the MRI-targeted biopsy, give a single global score (factoring both the systematic standard and the MRI-targeted positive cores). Grade Groups are as follows: (1) Grade Groups (GrGp) is the terminology adopted by major world organizations; and (2) retain GS 3 + 5 = 8 in GrGp 4. Cribriform carcinoma is as follows: (1) report the presence or absence of cribriform glands in biopsy and RP with Gleason pattern 4 carcinoma. Intraductal carcinoma (IDCP) is as follows: (1) report IDC-P in biopsy and RP; (2) use criteria based on dense cribriform glands (>50% of the gland is composed of epithelium relative to luminal spaces) and/or solid nests and/or marked pleomorphism/necrosis; (3) it is not necessary to perform basal cell immunostains on biopsy and RP to identify IDC-P if the results would not change the overall (highest) GS/GrGp part per case; (4) do not include IDC-P in determining the final GS/GrGp on biopsy and/or RP; and (5) "atypical intraductal proliferation (AIP)'' is preferred for an intraductal proliferation of prostatic secretory cells which shows a greater degree of architectural complexity and/or cytological atypia than typical high-grade prostatic intraepithelial neoplasia, yet falling short of the strict diagnostic threshold for IDC-P. Molecular testing is as follows: (1) Ki67 is not ready for routine clinical use; (2) additional studies of active surveillance cohorts are needed to establish the utility of PTEN in this setting; and (3) dedicated studies of RNA-based assays in active surveillance populations are needed to substantiate the utility of these expensive tests in this setting. Artificial intelligence and novel grading schema are as follows: (1) incorporating reactive stromal grade, percent GP4, minor tertiary GP5, and cribriform/intraductal carcinoma are not ready for adoption in current practice.
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- 2021
7. Integrated photonic correlation spectroscopy for faint exoplanet biosignature detection
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Daniele Melati, Ernst J. W. de Mooij, Jens H. Schmid, Ross Cheriton, Siegfried Janz, Mohsen Kamandar Dezfouli, Rubin Ma, Jean Lapointe, Dan-Xia Xu, Shurui Wang, Adam Densmore, Luc Simard, and Suresh Sivanandam
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Physics ,Spectrometer ,business.industry ,Astrophysics::Instrumentation and Methods for Astrophysics ,Spectral line ,Exoplanet ,Starlight ,Resonator ,Optics ,Transmittance ,Astrophysics::Earth and Planetary Astrophysics ,Photonics ,business ,Spectroscopy - Abstract
Exoplanetary biosignatures, molecular compounds which indicate a likelihood of extraterrestrial life, can be detected by highly sensitive spectroscopy of starlight which passes through the atmospheres of exoplanets towards the Earth. Such sensitive measurements can only be accomplished with the next generation of telescopes, leading to a corresponding increase in cost and complexity spectrometers. Integrated astrophotonic instruments are well-suited to address these challenges through their low-cost fabrication and compact geometries. We propose and characterize an integrated photonic gas sensor which detects the correlation between the near-infrared quasi-periodic vibronic absorption line spectrum of a gas and a silicon waveguide ring resonator transmittance comb. This technique enables lock-in amplification detection for real-time detection of faint biosignatures for reduced observation timescales and rapid exoplanetary atmosphere surveys using highly compact instrumentation.
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- 2020
8. Spectrum-free integrated photonic remote molecular identification and sensing
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Dan-Xia Xu, Luc Simard, Pavel Cheben, Ernst J. W. de Mooij, Jens H. Schmid, Jean Lapointe, Mohsen Kamandar Dezfouli, Siegfried Janz, Shurui Wang, Rubin Ma, Daniele Melati, Adam Densmore, Ross Cheriton, and Suresh Sivanandam
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Physics - Instrumentation and Detectors ,Materials science ,Absorption spectroscopy ,Infrared ,FOS: Physical sciences ,Applied Physics (physics.app-ph) ,02 engineering and technology ,01 natural sciences ,Signal ,Fourier transform spectroscopy ,010309 optics ,Resonator ,Optics ,0103 physical sciences ,Instrumentation and Methods for Astrophysics (astro-ph.IM) ,Spectral signature ,business.industry ,Hyperspectral imaging ,Instrumentation and Detectors (physics.ins-det) ,Physics - Applied Physics ,021001 nanoscience & nanotechnology ,Atomic and Molecular Physics, and Optics ,Photonics ,Astrophysics - Instrumentation and Methods for Astrophysics ,0210 nano-technology ,business - Abstract
Absorption spectroscopy is widely used in sensing and astronomy to understand molecular compositions on microscopic to cosmological scales. However, typical dispersive spectroscopic techniques require multichannel detection, fundamentally limiting the ability to detect extremely weak signals when compared to direct photometric methods. We report the realization of direct spectral molecular detection using a silicon nanophotonic waveguide resonator, obviating dispersive spectral acquisition. We use a thermally tunable silicon ring resonator with a transmission spectrum matched and cross-correlated to the quasi-periodic vibronic absorption lines of hydrogen cyanide. We show that the correlation peak amplitude is proportional to the number of overlapping ring resonances and gas lines, and that molecular specificity is obtained from the phase of the correlation signal in a single detection channel. Our results demonstrate on-chip correlation spectroscopy that is less restricted by the signal-to-noise penalty of other spectroscopic approaches, enabling the detection of faint spectral signatures.
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- 2020
9. Towards integrated astrophotonic instruments for exoplanet biosignature detection
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Rubin Ma, Mohsen Kamandar Dezfouli, Ross Cheriton, Jean Lapointe, Siegfried Janz, Dan-Xia Xu, Suresh Sivanandam, Luc Simard, Adam Densmore, Shurui Wang, Pavel Cheben, Daniele Melati, Ernst J. W. de Mooij, and Jens H. Schmid
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Physics ,business.industry ,Astrophysics::Instrumentation and Methods for Astrophysics ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Space (mathematics) ,01 natural sciences ,Exoplanet ,010309 optics ,Optics ,0103 physical sciences ,Biosignature ,Focal length ,0210 nano-technology ,Adaptive optics ,business ,Electron-beam lithography - Abstract
We present the design of integrated astrophotonic instruments for high background atmospheric gas detection. Such instruments can be fibre-coupled to long focal length space telescopes as compact, flexure-free, instruments., Conference on Lasers and Electro-Optics/Pacific Rim 2020, August 3-5, 2020, Sydney Australia
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- 2020
10. High Sensitivity Remote Gas Sensing using Integrated Photonic Correlation Filters
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Adam Densmore, Shurui Wang, Ernst J. W. de Mooij, Siegfried Janz, Luc Simard, Daniele Melati, Jean Lapointe, Pavel Cheben, Ross Cheriton, Rubin Ma, Suresh Sivanandam, Mohsen Kamandar Dezfouli, Dan-Xia Xu, and Jens H. Schmid
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spectroscopy ,Materials science ,Channel (digital image) ,Absorption spectroscopy ,02 engineering and technology ,integrated ,01 natural sciences ,Signal ,010309 optics ,ring resonator ,gas ,0103 physical sciences ,Gas composition ,Sensitivity (control systems) ,Spectroscopy ,sensing ,Silicon photonics ,silicon photonics ,business.industry ,feature extraction ,resonator filters ,sensitivity ,021001 nanoscience & nanotechnology ,remote ,real-time systems ,correlation ,Optoelectronics ,Photonics ,0210 nano-technology ,business - Abstract
Absorption spectroscopy is a powerful technique for characterizing remote gas composition where direct interaction with a target it not possible. While dispersive spectroscopy is typically used to acquire a spectrum with which the gas presence is determined, correlation spectroscopy can directly detect such spectral features in a single detection channel. Here we present a novel integrated photonics correlation technique on an integrated photonic platform which uses real-time spectral processing to generate a multiline gas specific detection signal., 2020 Photonics North (PN), May 26-28, 2020, Niagara Falls, ON, Canada
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- 2020
11. Impacts on access resistance of InP high electron mobility transistors from wafer processing
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Jean-Paul Noel, Alexandre W. Walker, Philip J. Poole, Adam Densmore, Jean Lapointe, Alireza Seyfollahi, C. Storey, Rubin Ma, A. Kam, and Frank Jiang
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Materials science ,business.industry ,Process Chemistry and Technology ,Transistor ,Contact resistance ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,law.invention ,Wafer fabrication ,Stack (abstract data type) ,law ,Materials Chemistry ,Degradation (geology) ,Optoelectronics ,Wafer ,Electrical and Electronic Engineering ,business ,High electron ,Instrumentation ,Ohmic contact - Abstract
In this work, the authors evaluated the access resistance of InP high electron mobility transistors (HEMTs) and their degradation during wafer processing. The transfer resistance, which was rarely separated from other components of the total access resistance of InP HEMTs in the literature, was found to be the dominant component of the access resistance. It was also found that the transfer resistance degraded during wafer processing. The selection of the ohmic metal stack and its impact on both the metal-cap contact resistance and the transfer resistance was also investigated. The observations in their experiments and relevant discussions in the report are expected to be useful in the identification of improvement opportunities in both material growth and wafer fabrication of InP HEMTs.
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- 2020
12. Sex differences in oncogenic mutational processes
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Li, CH, Prokopec, SD, Sun, RX, Yousif, F, Schmitz, N, Al-Shahrour, F, Atwal, G, Bailey, PJ, Biankin, AV, Boutros, PC, Campbell, PJ, Chang, DK, Cooke, SL, Deshpande, V, Faltas, BM, Faquin, WC, Garraway, L, Getz, G, Grimmond, SM, Haider, S, Hoadley, KA, Jiao, W, Kaiser, VB, Karlić, R, Kato, M, Kübler, K, Lazar, AJ, Louis, DN, Margolin, A, Martin, S, Nahal-Bose, HK, Nielsen, GP, Nik-Zainal, S, Omberg, L, P’ng, C, Perry, MD, Polak, P, Rheinbay, E, Rubin, MA, Semple, CA, Sgroi, DC, Shibata, T, Siebert, R, Smith, J, Stein, LD, Stobbe, MD, Thai, K, Wright, DW, Wu, CL, Yuan, K, Zhang, J, Aaltonen, LA, Abascal, F, Abeshouse, A, Aburatani, H, Adams, DJ, Agrawal, N, Ahn, KS, Ahn, SM, Aikata, H, Akbani, R, Akdemir, KC, Al-Ahmadie, H, Al-Sedairy, ST, Alawi, M, Albert, M, Aldape, K, Alexandrov, LB, Ally, A, Alsop, K, Alvarez, EG, Amary, F, Amin, SB, Aminou, B, Ammerpohl, O, Anderson, MJ, Ang, Y, Antonello, D, Anur, P, Aparicio, S, Appelbaum, EL, Arai, Y, Aretz, A, Arihiro, K, Ariizumi, SI, Armenia, J, Arnould, L, Asa, S, Assenov, Y, Aukema, S, Auman, JT, Aure, MR, Awadalla, P, Aymerich, M, Bader, GD, Baez-Ortega, A, Li, CH, Prokopec, SD, Sun, RX, Yousif, F, Schmitz, N, Al-Shahrour, F, Atwal, G, Bailey, PJ, Biankin, AV, Boutros, PC, Campbell, PJ, Chang, DK, Cooke, SL, Deshpande, V, Faltas, BM, Faquin, WC, Garraway, L, Getz, G, Grimmond, SM, Haider, S, Hoadley, KA, Jiao, W, Kaiser, VB, Karlić, R, Kato, M, Kübler, K, Lazar, AJ, Louis, DN, Margolin, A, Martin, S, Nahal-Bose, HK, Nielsen, GP, Nik-Zainal, S, Omberg, L, P’ng, C, Perry, MD, Polak, P, Rheinbay, E, Rubin, MA, Semple, CA, Sgroi, DC, Shibata, T, Siebert, R, Smith, J, Stein, LD, Stobbe, MD, Thai, K, Wright, DW, Wu, CL, Yuan, K, Zhang, J, Aaltonen, LA, Abascal, F, Abeshouse, A, Aburatani, H, Adams, DJ, Agrawal, N, Ahn, KS, Ahn, SM, Aikata, H, Akbani, R, Akdemir, KC, Al-Ahmadie, H, Al-Sedairy, ST, Alawi, M, Albert, M, Aldape, K, Alexandrov, LB, Ally, A, Alsop, K, Alvarez, EG, Amary, F, Amin, SB, Aminou, B, Ammerpohl, O, Anderson, MJ, Ang, Y, Antonello, D, Anur, P, Aparicio, S, Appelbaum, EL, Arai, Y, Aretz, A, Arihiro, K, Ariizumi, SI, Armenia, J, Arnould, L, Asa, S, Assenov, Y, Aukema, S, Auman, JT, Aure, MR, Awadalla, P, Aymerich, M, Bader, GD, and Baez-Ortega, A
- Abstract
Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
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- 2020
13. Pathway and network analysis of more than 2500 whole cancer genomes
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Reyna, MA, Haan, D, Paczkowska, M, Verbeke, LPC, Vazquez, M, Kahraman, A, Pulido-Tamayo, S, Barenboim, J, Wadi, L, Dhingra, P, Shrestha, R, Getz, G, Lawrence, MS, Pedersen, JS, Rubin, MA, Wheeler, DA, Brunak, S, Izarzugaza, JMG, Khurana, E, Marchal, K, von Mering, C, Sahinalp, SC, Valencia, A, Reimand, J, Stuart, JM, Raphael, BJ, Reyna, MA, Haan, D, Paczkowska, M, Verbeke, LPC, Vazquez, M, Kahraman, A, Pulido-Tamayo, S, Barenboim, J, Wadi, L, Dhingra, P, Shrestha, R, Getz, G, Lawrence, MS, Pedersen, JS, Rubin, MA, Wheeler, DA, Brunak, S, Izarzugaza, JMG, Khurana, E, Marchal, K, von Mering, C, Sahinalp, SC, Valencia, A, Reimand, J, Stuart, JM, and Raphael, BJ
- Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
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- 2020
14. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
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Rheinbay, E, Nielsen, MM, Abascal, F, Wala, JA, Shapira, O, Tiao, G, Hornshoj, H, Hess, JM, Juul, RI, Lin, Z, Feuerbach, L, Sabarinathan, R, Madsen, T, Kim, J, Mularoni, L, Shuai, S, Lanzos, A, Herrmann, C, Maruvka, YE, Shen, C, Amin, SB, Bandopadhayay, P, Bertl, J, Boroevich, KA, Busanovich, J, Carlevaro-Fita, J, Chakravarty, D, Chan, CWY, Craft, D, Dhingra, P, Diamanti, K, Fonseca, NA, Gonzalez-Perez, A, Guo, Q, Hamilton, MP, Haradhvala, NJ, Hong, C, Isaev, K, Johnson, TA, Juul, M, Kahles, A, Kahraman, A, Kim, Y, Komorowski, J, Kumar, K, Kumar, S, Lee, D, Lehmann, K-V, Li, Y, Liu, EM, Lochovsky, L, Park, K, Pich, O, Roberts, ND, Saksena, G, Schumacher, SE, Sidiropoulos, N, Sieverling, L, Sinnott-Armstrong, N, Stewart, C, Tamborero, D, Tubio, JMC, Umer, HM, Uuskula-Reimand, L, Wadelius, C, Wadi, L, Yao, X, Zhang, C-Z, Zhang, J, Haber, JE, Hobolth, A, Imielinski, M, Kellis, M, Lawrence, MS, von Mering, C, Nakagawa, H, Raphael, BJ, Rubin, MA, Sander, C, Stein, LD, Stuart, JM, Tsunoda, T, Wheeler, DA, Johnson, R, Reimand, J, Gerstein, M, Khurana, E, Campbell, PJ, Lopez-Bigas, N, Weischenfeldt, J, Beroukhim, R, Martincorena, I, Pedersen, JS, Getz, G, Bader, GD, Barenboim, J, Brunak, S, Chen, K, Choi, JK, Deu-Pons, J, Fink, JL, Frigola, J, Gambacorti-Passerini, C, Garsed, DW, Gut, IG, Haan, D, Harmanci, AO, Helmy, M, Hodzic, E, Izarzugaza, JMG, Kim, JK, Korbel, JO, Larsson, E, Li, S, Li, X, Lou, S, Marchal, K, Martinez-Fundichely, A, McGillivray, PD, Meyerson, W, Muinos, F, Paczkowska, M, Pons, T, Pulido-Tamayo, S, Reyes-Salazar, I, Reyna, MA, Rubio-Perez, C, Sahinalp, SC, Salichos, L, Shackleton, M, Shrestha, R, Valencia, A, Vazquez, M, Verbeke, LPC, Wang, J, Warrell, J, Waszak, SM, Wu, G, Yu, J, Zhang, X, Zhang, Y, Zhao, Z, Zou, L, Akdemir, KC, Alvarez, EG, Baez-Ortega, A, Boutros, PC, Bowtell, DDL, Brors, B, Burns, KH, Chan, K, CortesCiriano, I, Dueso-Barroso, A, Dunford, AJ, Edwards, PA, Estivill, X, Etemadmoghadam, D, Frenkel-Morgenstern, M, Gordenin, DA, Hutter, B, Jones, DTW, Ju, YS, Kazanov, MD, Klimczak, LJ, Koh, Y, Lee, EA, Lee, JJ-K, Lynch, AG, Macintyre, G, Markowetz, F, Meyerson, M, Miyano, S, Navarro, FCP, Ossowski, S, Park, PJ, Pearson, J, Puiggros, M, Rippe, K, Roberts, SA, RodriguezMartin, B, Scully, R, Torrents, D, Villasante, I, Waddell, N, Yang, L, Yoon, S-S, Zamora, J, Rheinbay, E, Nielsen, MM, Abascal, F, Wala, JA, Shapira, O, Tiao, G, Hornshoj, H, Hess, JM, Juul, RI, Lin, Z, Feuerbach, L, Sabarinathan, R, Madsen, T, Kim, J, Mularoni, L, Shuai, S, Lanzos, A, Herrmann, C, Maruvka, YE, Shen, C, Amin, SB, Bandopadhayay, P, Bertl, J, Boroevich, KA, Busanovich, J, Carlevaro-Fita, J, Chakravarty, D, Chan, CWY, Craft, D, Dhingra, P, Diamanti, K, Fonseca, NA, Gonzalez-Perez, A, Guo, Q, Hamilton, MP, Haradhvala, NJ, Hong, C, Isaev, K, Johnson, TA, Juul, M, Kahles, A, Kahraman, A, Kim, Y, Komorowski, J, Kumar, K, Kumar, S, Lee, D, Lehmann, K-V, Li, Y, Liu, EM, Lochovsky, L, Park, K, Pich, O, Roberts, ND, Saksena, G, Schumacher, SE, Sidiropoulos, N, Sieverling, L, Sinnott-Armstrong, N, Stewart, C, Tamborero, D, Tubio, JMC, Umer, HM, Uuskula-Reimand, L, Wadelius, C, Wadi, L, Yao, X, Zhang, C-Z, Zhang, J, Haber, JE, Hobolth, A, Imielinski, M, Kellis, M, Lawrence, MS, von Mering, C, Nakagawa, H, Raphael, BJ, Rubin, MA, Sander, C, Stein, LD, Stuart, JM, Tsunoda, T, Wheeler, DA, Johnson, R, Reimand, J, Gerstein, M, Khurana, E, Campbell, PJ, Lopez-Bigas, N, Weischenfeldt, J, Beroukhim, R, Martincorena, I, Pedersen, JS, Getz, G, Bader, GD, Barenboim, J, Brunak, S, Chen, K, Choi, JK, Deu-Pons, J, Fink, JL, Frigola, J, Gambacorti-Passerini, C, Garsed, DW, Gut, IG, Haan, D, Harmanci, AO, Helmy, M, Hodzic, E, Izarzugaza, JMG, Kim, JK, Korbel, JO, Larsson, E, Li, S, Li, X, Lou, S, Marchal, K, Martinez-Fundichely, A, McGillivray, PD, Meyerson, W, Muinos, F, Paczkowska, M, Pons, T, Pulido-Tamayo, S, Reyes-Salazar, I, Reyna, MA, Rubio-Perez, C, Sahinalp, SC, Salichos, L, Shackleton, M, Shrestha, R, Valencia, A, Vazquez, M, Verbeke, LPC, Wang, J, Warrell, J, Waszak, SM, Wu, G, Yu, J, Zhang, X, Zhang, Y, Zhao, Z, Zou, L, Akdemir, KC, Alvarez, EG, Baez-Ortega, A, Boutros, PC, Bowtell, DDL, Brors, B, Burns, KH, Chan, K, CortesCiriano, I, Dueso-Barroso, A, Dunford, AJ, Edwards, PA, Estivill, X, Etemadmoghadam, D, Frenkel-Morgenstern, M, Gordenin, DA, Hutter, B, Jones, DTW, Ju, YS, Kazanov, MD, Klimczak, LJ, Koh, Y, Lee, EA, Lee, JJ-K, Lynch, AG, Macintyre, G, Markowetz, F, Meyerson, M, Miyano, S, Navarro, FCP, Ossowski, S, Park, PJ, Pearson, J, Puiggros, M, Rippe, K, Roberts, SA, RodriguezMartin, B, Scully, R, Torrents, D, Villasante, I, Waddell, N, Yang, L, Yoon, S-S, and Zamora, J
- Abstract
The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
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- 2020
15. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
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Carlevaro-Fita, J, Lanzos, A, Feuerbach, L, Hong, C, Mas-Ponte, D, Pedersen, JS, Johnson, R, Abascal, F, Amin, SB, Bader, GD, Barenboim, J, Beroukhim, R, Bertl, J, Boroevich, KA, Brunak, S, Campbell, PJ, Chakravarty, D, Chan, CWY, Chen, K, Choi, JK, Deu-Pons, J, Dhingra, P, Diamanti, K, Fink, JL, Fonseca, NA, Frigola, J, Gambacorti-Passerini, C, Garsed, DW, Gerstein, M, Getz, G, Gonzalez-Perez, A, Guo, Q, Gut, IG, Haan, D, Hamilton, MP, Haradhvala, NJ, Harmanci, AO, Helmy, M, Herrmann, C, Hess, JM, Hobolth, A, Hodzic, E, Hornshoj, H, Isaev, K, Izarzugaza, JMG, Johnson, TA, Juul, M, Juul, RI, Kahles, A, Kahraman, A, Kellis, M, Khurana, E, Kim, J, Kim, JK, Kim, Y, Komorowski, J, Korbel, JO, Kumar, S, Larsson, E, Lawrence, MS, Lee, D, Lehmann, K-V, Li, S, Li, X, Lin, Z, Liu, EM, Lochovsky, L, Lou, S, Madsen, T, Marchal, K, Martincorena, I, Martinez-Fundichely, A, Maruvka, YE, McGillivray, PD, Meyerson, W, Muinos, F, Mularoni, L, Nakagawa, H, Nielsen, MM, Paczkowska, M, Park, K, Pich, O, Pons, T, Pulido-Tamayo, S, Raphael, BJ, Reimand, J, Reyes-Salazar, I, Reyna, MA, Rheinbay, E, Rubin, MA, Rubio-Perez, C, Sabarinathan, R, Sahinalp, SC, Saksena, G, Salichos, L, Sander, C, Schumacher, SE, Shackleton, M, Shapira, O, Shen, C, Shrestha, R, Shuai, S, Sidiropoulos, N, Sieverling, L, Sinnott-Armstrong, N, Stein, LD, Stuart, JM, Tamborero, D, Tiao, G, Tsunoda, T, Umer, HM, Uuskula-Reimand, L, Valencia, A, Vazquez, M, Verbeke, LPC, Wadelius, C, Wadi, L, Wang, J, Warrell, J, Waszak, SM, Weischenfeldt, J, Wheeler, DA, Wu, G, Yu, J, Zhang, J, Zhang, X, Zhang, Y, Zhao, Z, Zou, L, von Mering, C, Carlevaro-Fita, J, Lanzos, A, Feuerbach, L, Hong, C, Mas-Ponte, D, Pedersen, JS, Johnson, R, Abascal, F, Amin, SB, Bader, GD, Barenboim, J, Beroukhim, R, Bertl, J, Boroevich, KA, Brunak, S, Campbell, PJ, Chakravarty, D, Chan, CWY, Chen, K, Choi, JK, Deu-Pons, J, Dhingra, P, Diamanti, K, Fink, JL, Fonseca, NA, Frigola, J, Gambacorti-Passerini, C, Garsed, DW, Gerstein, M, Getz, G, Gonzalez-Perez, A, Guo, Q, Gut, IG, Haan, D, Hamilton, MP, Haradhvala, NJ, Harmanci, AO, Helmy, M, Herrmann, C, Hess, JM, Hobolth, A, Hodzic, E, Hornshoj, H, Isaev, K, Izarzugaza, JMG, Johnson, TA, Juul, M, Juul, RI, Kahles, A, Kahraman, A, Kellis, M, Khurana, E, Kim, J, Kim, JK, Kim, Y, Komorowski, J, Korbel, JO, Kumar, S, Larsson, E, Lawrence, MS, Lee, D, Lehmann, K-V, Li, S, Li, X, Lin, Z, Liu, EM, Lochovsky, L, Lou, S, Madsen, T, Marchal, K, Martincorena, I, Martinez-Fundichely, A, Maruvka, YE, McGillivray, PD, Meyerson, W, Muinos, F, Mularoni, L, Nakagawa, H, Nielsen, MM, Paczkowska, M, Park, K, Pich, O, Pons, T, Pulido-Tamayo, S, Raphael, BJ, Reimand, J, Reyes-Salazar, I, Reyna, MA, Rheinbay, E, Rubin, MA, Rubio-Perez, C, Sabarinathan, R, Sahinalp, SC, Saksena, G, Salichos, L, Sander, C, Schumacher, SE, Shackleton, M, Shapira, O, Shen, C, Shrestha, R, Shuai, S, Sidiropoulos, N, Sieverling, L, Sinnott-Armstrong, N, Stein, LD, Stuart, JM, Tamborero, D, Tiao, G, Tsunoda, T, Umer, HM, Uuskula-Reimand, L, Valencia, A, Vazquez, M, Verbeke, LPC, Wadelius, C, Wadi, L, Wang, J, Warrell, J, Waszak, SM, Weischenfeldt, J, Wheeler, DA, Wu, G, Yu, J, Zhang, J, Zhang, X, Zhang, Y, Zhao, Z, Zou, L, and von Mering, C
- Abstract
Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.
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- 2020
16. Common deleterious germline variants shape the urothelial cancer genome
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Vosoughi, A, primary, Zhang, T, additional, Shohdy, KS, additional, Vlachostergios, PJ, additional, Wilkes, DC, additional, Tagawa, ST, additional, Nanus, SM, additional, Molina, AM, additional, Beltran, H, additional, Sternberg, CN, additional, Motanagh, S, additional, Robinson, BD, additional, Xiang, J, additional, Chung, WK, additional, Rubin, MA, additional, Elemento, O, additional, Sboner, A, additional, Mosquera, JM, additional, and Faltas, BM, additional
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- 2020
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17. TTF1 expression in non-small cell lung carcinoma: association with TTF1 gene amplification and improved survival
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Perner, S, Wagner, PL, Soltermann, A, LaFargue, C, Tischler, V, Weir, BA, Weder, W, Meyerson, M, Giordano, TJ, Moch, H, and Rubin, MA
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- 2009
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18. Characterization of the ERG-regulated Kinome in Prostate Cancer Identifies TNIK as a Potential Therapeutic Target
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Lee, RS, Zhang, L, Berger, A, Lawrence, MG, Song, J, Niranjan, B, Davies, RG, Lister, NL, Sandhu, SK, Rubin, MA, Risbridger, GP, Taylor, RA, Rickman, DS, Horvath, LG, Daly, RJ, Lee, RS, Zhang, L, Berger, A, Lawrence, MG, Song, J, Niranjan, B, Davies, RG, Lister, NL, Sandhu, SK, Rubin, MA, Risbridger, GP, Taylor, RA, Rickman, DS, Horvath, LG, and Daly, RJ
- Abstract
Approximately 50% of prostate cancers harbor the TMPRSS2:ERG fusion, resulting in elevated expression of the ERG transcription factor. Despite the identification of this subclass of prostate cancers, no personalized therapeutic strategies have achieved clinical implementation. Kinases are attractive therapeutic targets as signaling networks are commonly perturbed in cancers. The impact of elevated ERG expression on kinase signaling networks in prostate cancer has not been investigated. Resolution of this issue may identify novel therapeutic approaches for ERG-positive prostate cancers. In this study, we used quantitative mass spectrometry-based kinomic profiling to identify ERG-mediated changes to cellular signaling networks. We identified 76 kinases that were differentially expressed and/or phosphorylated in DU145 cells engineered to express ERG. In particular, the Traf2 and Nck-interacting kinase (TNIK) was markedly upregulated and phosphorylated on multiple sites upon ERG overexpression. Importantly, TNIK has not previously been implicated in prostate cancer. To validate the clinical relevance of these findings, we characterized expression of TNIK and TNIK phosphorylated at serine 764 (pS764) in a localized prostate cancer patient cohort and showed that nuclear enrichment of TNIK (pS764) was significantly positively correlated with ERG expression. Moreover, TNIK protein levels were dependent upon ERG expression in VCaP cells and primary cells established from a prostate cancer patient-derived xenograft. Furthermore, reduction of TNIK expression and activity by silencing TNIK expression or using the TNIK inhibitor NCB-0846 reduced cell viability, colony formation and anchorage independent growth. Therefore, TNIK represents a novel and actionable therapeutic target for ERG-positive prostate cancers that could be exploited to develop new treatments for these patients.
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- 2019
19. Management of Patients with Advanced Prostate Cancer: The Report of the Advanced Prostate Cancer Consensus Conference APCCC 2017 [Figure presented]
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Gillessen, S, Attard, G, Beer, TM, Beltran, H, Bossi, A, Bristow, R, Carver, B, Castellano, D, Chung, BH, Clarke, N, Daugaard, G, Davis, ID, de Bono, J, Borges dos Reis, R, Drake, CG, Eeles, R, Efstathiou, E, Evans, CP, Fanti, S, Feng, F, Fizazi, K, Frydenberg, M, Gleave, M, Halabi, S, Heidenreich, A, Higano, CS, James, N, Kantoff, P, Kellokumpu-Lehtinen, PL, Khauli, RB, Kramer, G, Logothetis, C, Maluf, F, Morgans, AK, Morris, MJ, Mottet, N, Murthy, V, Oh, W, Ost, P, Padhani, AR, Parker, C, Pritchard, CC, Roach, M, Rubin, MA, Ryan, C, Saad, F, Sartor, O, Scher, H, Sella, A, Shore, N, Smith, M, Soule, H, Sternberg, CN, Suzuki, H, Sweeney, C, Sydes, MR, Tannock, I, Tombal, B, Valdagni, R, Wiegel, T, and Omlin, A
- Abstract
© 2017 European Association of Urology Background In advanced prostate cancer (APC), successful drug development as well as advances in imaging and molecular characterisation have resulted in multiple areas where there is lack of evidence or low level of evidence. The Advanced Prostate Cancer Consensus Conference (APCCC) 2017 addressed some of these topics. Objective To present the report of APCCC 2017. Design, setting, and participants Ten important areas of controversy in APC management were identified: high-risk localised and locally advanced prostate cancer; “oligometastatic” prostate cancer; castration-naïve and castration-resistant prostate cancer; the role of imaging in APC; osteoclast-targeted therapy; molecular characterisation of blood and tissue; genetic counselling/testing; side effects of systemic treatment(s); global access to prostate cancer drugs. A panel of 60 international prostate cancer experts developed the program and the consensus questions. Outcome measurements and statistical analysis The panel voted publicly but anonymously on 150 predefined questions, which have been developed following a modified Delphi process. Results and limitations Voting is based on panellist opinion, and thus is not based on a standard literature review or meta-analysis. The outcomes of the voting had varying degrees of support, as reflected in the wording of this article, as well as in the detailed voting results recorded in Supplementary data. Conclusions The presented expert voting results can be used for support in areas of management of men with APC where there is no high-level evidence, but individualised treatment decisions should as always be based on all of the data available, including disease extent and location, prior therapies regardless of type, host factors including comorbidities, as well as patient preferences, current and emerging evidence, and logistical and economic constraints. Inclusion of men with APC in clinical trials should be strongly encouraged. Importantly, APCCC 2017 again identified important areas in need of trials specifically designed to address them. Patient summary The second Advanced Prostate Cancer Consensus Conference APCCC 2017 did provide a forum for discussion and debates on current treatment options for men with advanced prostate cancer. The aim of the conference is to bring the expertise of world experts to care givers around the world who see less patients with prostate cancer. The conference concluded with a discussion and voting of the expert panel on predefined consensus questions, targeting areas of primary clinical relevance. The results of these expert opinion votes are embedded in the clinical context of current treatment of men with advanced prostate cancer and provide a practical guide to clinicians to assist in the discussions with men with prostate cancer as part of a shared and multidisciplinary decision-making process. At the Advanced Prostate Cancer Consensus Conference, 10 important areas of controversy in advanced prostate cancer management were identified, discussed, and the experts voted on 150 predefined consensus questions. The full report of the results is summarised here.
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- 2018
20. 39 Family presence during resuscitation – a protocol of a cochrane systematic review
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Rubin, MA, primary, Herling, SF, additional, Klausen, TW, additional, Jabre, P, additional, and Møller, AM, additional
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- 2019
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21. Clinical Outcome of Prostate Cancer Patients with Germline DNA Repair Mutations: Retrospective Analysis from an International Study
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Mateo, J, Cheng, HH, Beltran, H, Dolling, D, Xu, W, Pritchard, CC, Mossop, H, Rescigno, P, Perez-Lopez, R, Sailer, V, Kolinsky, M, Balasopoulou, A, Bertan, C, Nanus, DM, Tagawa, ST, Thorne, H, Montgomery, B, Carreira, S, Sandhu, S, Rubin, MA, Nelson, PS, de Bono, JS, Mateo, J, Cheng, HH, Beltran, H, Dolling, D, Xu, W, Pritchard, CC, Mossop, H, Rescigno, P, Perez-Lopez, R, Sailer, V, Kolinsky, M, Balasopoulou, A, Bertan, C, Nanus, DM, Tagawa, ST, Thorne, H, Montgomery, B, Carreira, S, Sandhu, S, Rubin, MA, Nelson, PS, and de Bono, JS
- Abstract
BACKGROUND: Germline DNA damage repair gene mutation (gDDRm) is found in >10% of metastatic prostate cancer (mPC). Their prognostic and predictive impact relating to standard therapies is unclear. OBJECTIVE: To determine whether gDDRm status impacts benefit from established therapies in mPC. DESIGN, SETTING, AND PARTICIPANTS: This is a retrospective, international, observational study. Medical records were reviewed for 390 mPC patients with known gDDRm status. All 372 patients from Royal Marsden (UK), Weill-Cornell (NY), and University of Washington (WA) were previously included in a prevalence study (Pritchard, NEJM 2016); the remaining 18 were gBRCA1/2m carriers, from the kConFab consortium, Australia. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Response rate (RR), progression-free survival (PFS), and overall survival (OS) data were collected. To account for potential differences between cohorts, a mixed-effect model (Weibull distribution) with random intercept per cohort was used. RESULTS AND LIMITATIONS: The gDDRm status was known for all 390 patients (60 carriers of gDDRm [gDDRm+], including 37 gBRCA2m, and 330 cases not found to carry gDDRm [gDDRm-]); 74% and 69% were treated with docetaxel and abiraterone/enzalutamide, respectively, and 36% received PARP inhibitors (PARPi) and/or platinum. Median OS from castration resistance was similar among groups (3.2 vs 3.0 yr, p=0.73). Median docetaxel PFS for gDDRm+ (6.8 mo) was not significantly different from that for gDDRm- (5.1 mo), and RRs were similar (gDDRm+=61%; gDDRm-=54%). There were no significant differences in median PFS and RR on first-line abiraterone/enzalutamide (gDDRm+=8.3 mo, gDDRm-=8.3 mo; gDDRm+=46%, gDDRm-=56%). Interaction test for PARPi/platinum and gDDRm+ resulted in an OS adjusted hazard ratio of 0.59 (95% confidence interval 0.28-1.25; p=0.17). Results are limited by the retrospective nature of the analysis. CONCLUSIONS: mPC patients with gDDRm appeared to benefit from standard therapies s
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- 2018
22. Refractive Index Engineering With Subwavelength Gratings in Silicon Microphotonic Waveguides
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Rubin Ma, Siegfried Janz, Adam Densmore, Przemek J. Bock, Robert Halir, Íñigo Molina-Fernández, Trevor J. Hall, J-M. Fedeli, Pavel Cheben, Jean Lapointe, Dan-Xia Xu, Jens H. Schmid, Andre Delage, and Boris Lamontagne
- Subjects
lcsh:Applied optics. Photonics ,Materials science ,Silicon photonics ,Nanophotonics ,Physics::Optics ,Grating ,Waveguide (optics) ,law.invention ,Optics ,law ,lcsh:QC350-467 ,Electrical and Electronic Engineering ,Nonlinear Sciences::Pattern Formation and Solitons ,Diffraction grating ,subwavelength gratings (SWGs) ,business.industry ,lcsh:TA1501-1820 ,waveguides ,Cladding (fiber optics) ,Atomic and Molecular Physics, and Optics ,nanophotonics ,Optoelectronics ,Photonics ,Photolithography ,business ,lcsh:Optics. Light - Abstract
In this review, we summarize and discuss our recent studies of subwavelength grating (SWG) structures for engineering the refractive index of silicon microphotonic waveguides. The SWG effect allows control of the effective refractive index of a waveguide core over a range spanning the values of the cladding material and silicon by lithographic patterning. We demonstrate this effect with the example of segmented photonic wire waveguides, which are shown to exhibit low propagation loss, and can be used to make highly efficient waveguide crossings and in-plane fiber-chip coupling structures. Other applications of SWG structures in silicon photonic waveguide devices include surface grating couplers with enhanced performance and simplified fabrication requirements, as well as a novel curved waveguide sidewall grating micro-spectrometer, in which an SWG structure fulfills a dual purpose by acting as an effective slab waveguide for diffracted light and as a lateral cladding for a channel waveguide.
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- 2011
23. Initiation and termination of antibiotic regimens in Veterans Affairs hospitals
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Huttner, B, Jones, M, Madaras-kelly, K, Neuhauser, MM, Rubin, MA, Goetz, MB, and Samore, MH
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Male ,Special ,Pharmacology and Pharmaceutical Sciences ,Infections ,infectious diseases ,Microbiology ,Hospitals ,Anti-Bacterial Agents ,Hospitalization ,antibiotic use ,Medical Microbiology ,Humans ,Female ,Infection ,Veterans ,practice variation - Abstract
Objectives: To assess rates of starting or stopping antibiotics across different hospitals. Methods: We used barcode medication administration data to measure antibiotic use on acute-care wards in 128 Veterans Affairs medical centres (VAMCs) in 2010. A treatment day (TD) was defined as the administration of any antibiotic on a given day. A treatment period (TP) was defined as an interval of inpatient antimicrobial therapy with gaps of ≤1 day in TDs. The rate of starting antibiotics was calculated for inpatients who had not yet started antibiotics, as the number of start events divided by the 'person-time at risk'. The rate of stopping antibiotics was calculated analogously for inpatients that were on antibiotics. Once individuals had stopped antibiotics they were removed from further analysis. Per-day start and stop rates were also calculated for each day of hospitalization. Results: The hospital mean rate of starting the first TP was 18.1 start events/100 days at risk (range 8.4-25.6/100 days at risk). The mean hospital stopping rate was 21.1 stop events/100 days at risk (range 13.3-29.5/100 days at risk). The ratio of a facility's starting and stopping rates was highly correlated with overall antibiotic use in TDs/1000 patient-days (rs=0.92, P
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- 2015
24. Management of patients with advanced prostate cancer: recommendations of the St Gallen Advanced Prostate Cancer Consensus Conference (APCCC) 2015
- Author
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Gillessen, S, Omlin, A, Attard, G, de Bono, JS, Efstathiou, E, Fizazi, K, Halabi, S, Nelson, PS, Sartor, O, Smith, MR, Soule, HR, Akaza, H, Beer, TM, Beltran, H, Chinnaiyan, AM, Daugaard, G, Davis, ID, De Santis, M, Drake, CG, Eeles, RA, Fanti, S, Gleave, ME, Heidenreich, A, Hussain, M, James, ND, Lecouvet, FE, Logothetis, CJ, Mastris, K, Nilsson, S, Oh, WK, Olmos, D, Padhani, AR, Parker, C, Rubin, MA, Schalken, JA, Scher, HI, Sella, A, Shore, ND, Small, EJ, Sternberg, CN, Suzuki, H, Sweeney, CJ, Tannock, IF, Tombal, B, Gillessen, S, Omlin, A, Attard, G, de Bono, JS, Efstathiou, E, Fizazi, K, Halabi, S, Nelson, PS, Sartor, O, Smith, MR, Soule, HR, Akaza, H, Beer, TM, Beltran, H, Chinnaiyan, AM, Daugaard, G, Davis, ID, De Santis, M, Drake, CG, Eeles, RA, Fanti, S, Gleave, ME, Heidenreich, A, Hussain, M, James, ND, Lecouvet, FE, Logothetis, CJ, Mastris, K, Nilsson, S, Oh, WK, Olmos, D, Padhani, AR, Parker, C, Rubin, MA, Schalken, JA, Scher, HI, Sella, A, Shore, ND, Small, EJ, Sternberg, CN, Suzuki, H, Sweeney, CJ, Tannock, IF, and Tombal, B
- Abstract
The first St Gallen Advanced Prostate Cancer Consensus Conference (APCCC) Expert Panel identified and reviewed the available evidence for the ten most important areas of controversy in advanced prostate cancer (APC) management. The successful registration of several drugs for castration-resistant prostate cancer and the recent studies of chemo-hormonal therapy in men with castration-naïve prostate cancer have led to considerable uncertainty as to the best treatment choices, sequence of treatment options and appropriate patient selection. Management recommendations based on expert opinion, and not based on a critical review of the available evidence, are presented. The various recommendations carried differing degrees of support, as reflected in the wording of the article text and in the detailed voting results recorded in supplementary Material, available at Annals of Oncology online. Detailed decisions on treatment as always will involve consideration of disease extent and location, prior treatments, host factors, patient preferences as well as logistical and economic constraints. Inclusion of men with APC in clinical trials should be encouraged.
- Published
- 2015
25. Subwavelength structures in integrated optics
- Author
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Delphine Marris-Morini, Robert Halir, Martin Vachon, A. Ortega-Moux, A. Maese, Jens H. Schmid, Trevor J. Hall, Pavel Cheben, Marc Ibrahim, J-M. Fedeli, Maria L. Calvo, Przemek J. Bock, Rubin Ma, Jean Lapointe, Siegfried Janz, Dan-Xia Xu, Íñigo Molina-Fernández, A. Villafranca Velasco, Winnie N. Ye, Laurent Vivien, Carlos Alonso-Ramos, and Andre Delage
- Subjects
Computer science ,business.industry ,Near-field optics ,Nanotechnology ,law.invention ,law ,Optoelectronics ,Integrated optics ,Photolithography ,business ,Effective refractive index ,Diffraction grating ,Lithography ,Refractive index - Abstract
Subwavelenth structures offer exciting new opportunities for integrated optics. Effective refractive index can be chosen from a broad range by lithographic patterning using just two materials. Many practical subwavelength engineered devices already demonstrated, with superior performance compared to their conventional counterparts and likely many more to come.
- Published
- 2013
26. Integrative annotation of variants from 1092 humans: application to cancer genomics
- Author
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Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F and 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, McVean GA.
- Abstract
Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating the latter. We found regions particularly sensitive to mutations ("ultrasensitive") and variants that are disruptive because of mechanistic effects on transcription-factor binding (that is, "motif-breakers"). We also found variants in regions with higher network centrality tend to be deleterious. Insertions and deletions followed a similar pattern to single-nucleotide variants, with some notable exceptions (e.g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers.
- Published
- 2013
- Full Text
- View/download PDF
27. Temperature-independent silicon waveguides comprising bridged subwavelength gratings
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Boris Lamontagne, Marc Ibrahim, Przemek J. Bock, Alireza Aleali, Rubin Ma, Pavel Cheben, Adam Densmore, D.-X. Xu, Jens H. Schmid, Jean Lapointe, Siegfried Janz, and Winnie N. Ye
- Subjects
sub-wave length grating ,Materials science ,Silicon ,photonics ,chemistry.chemical_element ,Grating ,athermal ,law.invention ,Optics ,law ,electric losses ,Silicon photonics ,silicon photonics ,business.industry ,silicon ,thermo-optic coefficients ,waveguides ,grating duty cycle ,Transverse mode ,chemistry ,Duty cycle ,Optoelectronics ,Photonics ,business ,Waveguide ,Order of magnitude - Abstract
Athermal operation of silicon waveguides for the TM and TE mode is achieved using the bridged subwavelength grating (BSWG) waveguide geometry. For the TM mode the experimental results show that the temperature-induced wavelength shift (dλ/dT) is an order of magnitude smaller for the BSWG waveguides with grating duty cycle, waveguide and bridge widths of 42%, 490 nm and 220 nm, respectively, as compared to standard photonics wires (PW). For the TE mode similar results are achieved by using the bridge width of 200 nm and similar duty cycle and waveguide width. A temperature-induced shift of only -2.5 pm/°C is reported for the TM polarized light. Propagation losses of BSWG waveguides for both polarizations were measured to be about 8 dB/cm, comparable to that of PWs. © 2012 SPIE., Photonics North 2012, June 6-8, 2012, Montreal, QC, Canada, Series: Proceedings of SPIE; no. 8412
- Published
- 2012
28. Label-free Biosensor Array Based on Silicon-on-Insulator Ring Resonators Addressed Using a WDM Approach
- Author
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Y. Li, D. Zhang, Jens H. Schmid, Pavel Cheben, Siegfried Janz, Rubin Ma, Q. Y. Liu, Dan-Xia Xu, Jean Lapointe, André Delâge, Gregory P. Lopinski, Martin Vachon, and Adam Densmore
- Subjects
Silicon ,Materials science ,Orders of magnitude (temperature) ,business.industry ,Optical communication ,Silicon on insulator ,Serum Albumin, Bovine ,Port (circuit theory) ,Biosensing Techniques ,Multiplexing ,Atomic and Molecular Physics, and Optics ,Resonator ,Optics ,Immunoglobulin G ,Wavelength-division multiplexing ,Animals ,Microtechnology ,Cattle ,business ,Biosensor - Abstract
We report a silicon-on-insulator ring resonator biosensor array with one output port, using wavelength division multiplexing as the addressing scheme. With the use of on-chip referencing for environmental drift cancellation, simultaneous monitoring of multiplexed molecular bindings is demonstrated, with a resolution of 0.3 pg/mm(2) (40 ag of total mass) for protein concentrations over 4 orders of magnitude down to 20 pM. Reactions are measured over time periods as long as 3 h with high stability.
- Published
- 2012
29. Single etch grating couplers for mass fabrication with DUV lithography
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Jens H. Schmid, Pavel Cheben, L. Zavargo-Peche, Adam Densmore, M. Fournier, Íñigo Molina-Fernández, Dan-Xia Xu, J-M. Fedeli, Rubin Ma, Siegfried Janz, Robert Halir, and Alejandro Ortega-Moñux
- Subjects
Optical fiber ,Fabrication ,Materials science ,02 engineering and technology ,Grating ,01 natural sciences ,law.invention ,010309 optics ,Planar ,Optics ,law ,fiber-to-chip grating coupler ,0103 physical sciences ,Electrical and Electronic Engineering ,Lithography ,Electronic circuit ,Coupling ,business.industry ,021001 nanoscience & nanotechnology ,Atomic and Molecular Physics, and Optics ,Electronic, Optical and Magnetic Materials ,single etch process ,deep ultraviolet lithography ,Optoelectronics ,0210 nano-technology ,business ,Waveguide - Abstract
Surface grating couplers enable efficient coupling of light between optical fibers and planar waveguide circuits. While traditional grating designs require two etch steps for efficient coupling to silicon-on-insulator waveguides, recently proposed subwavelength structured gratings can achieve the same coupling efficiencies with a single etch step, thereby significantly reducing fabrication complexity. Here we demonstrate that such couplers can be fabricated on a large scale with ultra-violet lithography, achieving a 5 dB coupling efficiency at 1,550 nm. Through both simulations and experiments we give physical insight on how pattern fidelity impacts the performance of these couplers, and propose strategies to deal with inevitable process variations.
- Published
- 2012
30. Diffractive and subwavelength grating couplers for microphotonic waveguides
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Martin Vachon, Jean Lapointe, Jens H. Schmid, Przemek J. Bock, L. Zavargo-Peche, Íñigo Molina-Fernández, Dan-Xia Xu, Andre Delage, Robert Halir, Siegfried Janz, J-M. Fedeli, Carlos Alonso Ramos, Rubin Ma, Alejandro Ortega-Moñux, and Pavel Cheben
- Subjects
Materials science ,Optical fiber ,sub-wave length grating ,surface grating ,excitation field ,fabrication ,Grating ,law.invention ,back reflection ,Optics ,transparent optical networks ,fabrication tolerances ,law ,Blazed grating ,multimodes ,Stepper ,Diffraction grating ,microphotonic waveguides ,wavelength dependence ,wavelength ranges ,sub-wavelength ,I-line steppers ,Multi-mode optical fiber ,refractive index ,business.industry ,fundamental modes ,ridge waveguides ,grating couplers ,coupling efficiency ,waveguides ,effective medium ,silicon rib waveguides ,Optoelectronics ,3 dB bandwidth ,Photonics ,business ,single etch ,Waveguide ,higher-order modes - Abstract
We review our advances in diffractive and subwavelength grating coupler structures for microphotonic waveguides. We present a subwavelength grating fiber-chip edge coupler with a loss as low as 0.9 dB and with minimal wavelength dependence over a broad wavelength range exceeding 200 nm. We also present fiber-to-chip surface grating couplers based on subwavelength effective medium. The effective medium refractive index is engineered to control the strength of the grating and thereby maximize coupling efficiency, while mitigating back reflections at the same time. We analyze the fabrication tolerances of the coupler, which are of particular relevance for large scale photonic fabrication. Furthermore, we present the first grating coupler for micrometric silicon rib waveguides, which is particularly challenging since the coupler waveguide region is multimode. We experimentally demonstrate grating couplers in 1.5 μm thick silicon ridge waveguides with a coupling efficiency of 2.2 dB and a 3 dB bandwidth of 40 nm. An inverse taper is used to match the fundamental mode of the interconnection waveguide with the optimum grating coupler excitation field, with negligible higher order mode excitation. The coupler was fabricated using i-line stepper lithography and single etch step. © 2012 IEEE., 14th International Conference on Transparent Optical Networks, ICTON 2012, 2 July 2012 through 5 July 2012, Coventry
- Published
- 2012
31. Selecting the polarization in silicon photonic wire components
- Author
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Siegfried Janz, Jens H. Schmid, Dan-Xia Xu, André Delâge, Pavel Cheben, Rubin Ma, Jean Lapointe, Martin Vachon, and Shurui Wang
- Subjects
Fabrication ,Materials science ,Silicon ,Physics::Optics ,chemistry.chemical_element ,optical waveguides ,law.invention ,photonic devices ,Resonator ,Optics ,ring resonator ,law ,polarization ,Silicon photonics ,Birefringence ,Polarization rotator ,polarization conversion ,polarization diversity ,polarization independence ,silicon photonics ,birefringence ,business.industry ,waveguides ,Polarization (waves) ,chemistry ,Optoelectronics ,business ,Waveguide ,directional couplers - Abstract
Silicon photonic wire waveguides are usually highly birefringent, so they are generally designed to operate for one particular polarization. For commonly used waveguides with a silicon thickness of 220 nm, TE polarization is preferred since TM is only weakly guided. For waveguides with a silicon thickness larger than 250 nm, both TE and TM polarizations have been employed. Overall, the choice of polarization has largely appeared arbitrary. In this presentation we review the pertinent polarization-dependent waveguide properties, including losses, back-reflection, polarization conversion and fabrication tolerances, with the intent to suggest guidelines for choosing the proper polarization. Through experimental evidence, we show that TM polarization has several important advantages and can support high performance resonators with a radius down to 2 μm. © 2012 SPIE., Silicon Photonics VII, January 22-25, 2012, San Francisco, CA, USA, Series: Proceedings of SPIE; no. 8266
- Published
- 2012
32. Silicon Nanowire based Optical XOR Logic Gate at 40Gb/s for DPSK Data
- Author
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Tony Vo, Benjamin J. Eggleton, Dan-Xia Xu, F. Li, Mark Pelusi, David J. Moss, Rubin Ma, Chad Husko, and Siegfried Janz
- Subjects
Physics ,Silicon ,business.industry ,Nanowire ,chemistry.chemical_element ,Four-wave mixing ,Optics ,chemistry ,Band-pass filter ,Bit error rate ,Optoelectronics ,business ,Silicon nanowires ,XOR gate ,Mixing (physics) - Abstract
We demonstrate all-optical XOR logic function for 40Gb/s DPSK signals in the C-band, based on four-wave mixing (FWM) in a silicon nanowire. Error-free operation with a system penalty of ∼ 4.3dB at 10−9 BER has been achieved.
- Published
- 2012
33. Wavelength Conversion via FWM in a Silicon Ring Resonator at 10 Gb/s for DPSK Signals
- Author
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Benjamin J. Eggleton, Siegfried Janz, Mark Pelusi, F. Li, David J. Moss, D.-X. Xu, and Rubin Ma
- Subjects
Resonator ,Optics ,Materials science ,Silicon ,chemistry ,Optical signal to noise ratio ,business.industry ,chemistry.chemical_element ,Wavelength conversion ,business ,Ring (chemistry) ,Light modulation - Abstract
We demonstrate all-optical wavelength conversion at 10 Gb/s for differential phase-shift keyed (DPSK) data in the C-band, based on four-wave mixing (FWM) in a silicon ring resonator. Error-free operation with a system penalty of ∼ 4.1 dB at 10−9 BER is achieved.
- Published
- 2012
34. Chemical microanalysis with cavity-enhanced optical waveguide devices
- Author
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Dan-Xia Xu, John Saunders, Andrew Brzezinski, Helen Waechter, Gianluca Gagliardi, Rubin Ma, Klaus Bescherer, Siegfried Janz, Jack A. Barnes, Grant Ongo, Dorit Munzke, Adam Gribble, and Hans-Peter Loock
- Subjects
Spheres ,cavity enhanced spectroscopy ,Materials science ,genetic structures ,microphotonics ,Absorption spectroscopy ,microsphere resonators ,Wavelength ,Physics::Optics ,Cavity ring-down spectroscopy ,Ethylene ,cavity ring-down ,symbols.namesake ,Optics ,waveguide cavity ,Dispersion (optics) ,Resonators ,Light absorption ,Rayleigh scattering ,Absorption (electromagnetic radiation) ,Spectroscopy ,refractive index ,business.industry ,Silica ,Microspheres ,Nucleic acids ,symbols ,Adsorption ,sense organs ,silicon-on-insulator (SOI) ,business ,Refractive index ,Silicon-on-insulators - Abstract
Three examples of cavity-enhanced measurements of refractive index and optical absorption are discussed. Using microphotonic silicon-on-insulator ring-resonators we determine the concentration of cyclohexane and m-xylene at detection levels of 300-3000 ppm. The gases are first absorbed into a siloxane polymer and its refractive index change is detected by a characteristic wavelength shift of the cavity resonance. In a second device phase-shift cavity ring-down spectroscopy is applied to simultaneously measure the optical absorption at two wavelengths of either a dye, nucleic acids or a pharmaceutical component. Multiplexing the ring-down measurement permits dual wavelength absorption spectroscopy without the use of a dispersion element. Finally, a combination of resonance wavelength measurements and cavity ring-down spectroscopy is used to simultaneously determine the change in refractive index and the absorption induced by adsorption of ethylene diamine on a 300 μm silica sphere. A whispering gallery mode of the microsphere resonator is excited with intensity modulated light and the intensity and AM modulation phase of the Rayleigh backscattered light is measured. © 2012 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE)., Photonics and Optoelectronics Meetings (POEM) 2011: Optoelectronic Sensing and Imaging, November 2-5, 2011, Wuhan, Series: Proceedings of SPIE; no. 8332
- Published
- 2011
35. Refractive Index Engineering with Subwavelength Gratings in Silicon Microphotonic Waveguides
- Author
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Pavel Cheben, Rubin Ma, Przemek J. Bock, Trevor J. Hall, Andre Delage, Jens H. Schmid, Dan-Xia Xu, Boris Lamontagne, Jean Lapointe, Adam Densmore, and Siegfried Janz
- Subjects
Materials science ,Silicon photonics ,Silicon ,business.industry ,chemistry.chemical_element ,Physics::Optics ,Hardware_PERFORMANCEANDRELIABILITY ,Multiplexer ,Waveguide (optics) ,GeneralLiterature_MISCELLANEOUS ,Core (optical fiber) ,Computer Science::Hardware Architecture ,Optics ,chemistry ,Hardware_INTEGRATEDCIRCUITS ,Optoelectronics ,Photonics ,business ,Diffraction grating ,Refractive index ,Nonlinear Sciences::Pattern Formation and Solitons - Abstract
We present a method of engineering the waveguide core refractive index locally on a silicon photonic chip using subwavelength gratings. Applications such as efficient waveguide crossings, fiber-chip couplers and multiplexer circuits are discussed., The 2011 Photonics Society Winter Topicals, Keystone, Colorado, January 10-12, 2011
- Published
- 2011
36. Subwavelength structures in SOI waveguides
- Author
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Jean-Marc Fedeli, Winnie N. Ye, Robert Halir, Rubin Ma, Pavel Cheben, Dan-Xia Xu, Alejandro Ortega-Moñux, Jens H. Schmid, Adam Densmore, Trevor J. Hall, Siegfried Janz, Przemek J. Bock, Jean Lapointe, Marc Ibrahim, Inigo Molina Fernandez, Andre Delage, and Boris Lamontagne
- Subjects
practical implementation ,sub-wave length grating ,Materials science ,Silicon ,photonics ,Physics::Optics ,chemistry.chemical_element ,Silicon on insulator ,Grating ,Waveguide (optics) ,Optics ,waveguide crossing ,silicon waveguide ,sub-wavelength structures ,waveguide crossings ,Nonlinear Sciences::Pattern Formation and Solitons ,Fiber gratings ,business.industry ,grating couplers ,waveguides ,Physics::Classical Physics ,SOI waveguides ,chemistry ,Optoelectronics ,periodic waveguides ,Integrated optics ,Photonics ,business - Abstract
Our progress in subwavelength structures in silicon waveguides is reviewed. Several practical implementations of subwavelength grating waveguides are discussed, including fibre-chip couplers, waveguide crossings and athermal waveguides. © 2011 IEEE., 8th IEEE International Conference on Group IV Photonics, GFP 2011, 14 September 2011 through 16 September 2011, London
- Published
- 2011
37. Athermal silicon subwavelength grating waveguides
- Author
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Marc Ibrahim, Adam Densmore, Jean Lapointe, Siegfried Janz, Dan-Xia Xu, Winnie N. Ye, Rubin Ma, Pavel Cheben, Boris Lamontagne, Jens H. Schmid, and Przemek J. Bock
- Subjects
sub-wave length grating ,Fabrication ,Materials science ,duty ratios ,Silicon ,photonics ,Physics::Optics ,chemistry.chemical_element ,Grating ,athermal ,Waveguide (optics) ,law.invention ,grating ,Optics ,fabrication tolerances ,law ,Thermal ,computer simulation ,light polarization ,Nonlinear Sciences::Pattern Formation and Solitons ,Diffraction grating ,sub-wavelength ,chemistry.chemical_classification ,Silicon photonics ,silicon photonics ,business.industry ,silicon ,thermo-optic coefficients ,Polymer ,waveguides ,Physics::Classical Physics ,Core (optical fiber) ,Wavelength ,chemistry ,Duty cycle ,Optoelectronics ,thermooptics ,Photonics ,business ,Waveguide ,Refractive index - Abstract
In this paper, athermal subwavelength grating (SWG) waveguides are investigated. Both numerical simulations and experimental results show that a temperature independent behaviour can be achieved by combining two materials with opposite thermo-optic coefficients within the waveguide. SU-8 polymer with a negative thermo-optic coefficient (dn/dT = -1.1×10-4 K -1) is used in our silicon SWG waveguides to compensate for silicon's positive thermo-optic coefficient of 1.9×10-4 K-1. The grating duty ratio required to achieve an athermal behavior is reported to vary as a function of the operating wavelength and the waveguide dimensions. For example, for athermal waveguides of 260 nm in height, duty ratios of 61.3% and 83.3% were calculated for TE and TM polarized light respectively for a 450 nm wide waveguide, compared to ratios of 79% and 90% for a 350 nm wide waveguide. It is also reported that with increasing width, and increasing height, a smaller grating duty ratio is necessary to achieve an athermal behaviour. A smaller fraction of silicon would hence be needed to compensate for the polymer's negative thermo-optic effect in the waveguide core. Subwavelength sidewall grating (SWSG) waveguides are also proposed here as alternatives to high duty ratio SWG waveguides that are required for guiding TM polarized light. Assuming a duty ratio of 50%, the width of the narrow segments for temperature- independent behavior is found by numerical simulations to be 125 nm and 143 nm for TE and TM polarized light, respectively. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE)., Photonics North 2011, May 16-18, 2011, Ottawa, Ontario, Canada, Series: Proceedings of SPIE; no. 8007
- Published
- 2011
38. A fully integrated silicon photonic wire sensor array chip and reader instrument
- Author
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Jens H. Schmid, Siegfried Janz, Andre Delage, G. Lopinski, W. Sinclair, Jean Lapointe, Pavel Cheben, H. McIntosh, Adam Densmore, Rubin Ma, Dan-Xia Xu, Martin Vachon, Boris Lamontagne, Y. Li, and N. Sabourin
- Subjects
microfluidic channel ,Materials science ,Silicon ,Instrumentation ,Microfluidics ,photonics ,wire ,chemistry.chemical_element ,Hardware_PERFORMANCEANDRELIABILITY ,fully integrated ,silicon chip ,photonic devices ,Sensor array ,Hardware_INTEGRATEDCIRCUITS ,sensor arrays ,real time ,Silicon photonics ,silicon photonics ,business.industry ,biosensors ,Chip ,Sample (graphics) ,instrumentation systems ,chemistry ,photonic wires ,Optoelectronics ,Photonics ,business - Abstract
A complete instrumentation system for interrogating silicon photonic wire waveguide sensor array chips has been built and demonstrated. The system is designed to read 16 or more photonic wire sensors on a single silicon chip simultaneously and in real time, while delivering sample fluid to the sensors through microfluidic channels fabricated monolithically on the chip. The chip can be inserted into the instrument, automatically aligned with input optics and fluid connection, and be ready for measurement in a few minutes. © 2011 IEEE., 8th IEEE International Conference on Group IV Photonics, GFP 2011, 14 September 2011 through 16 September 2011, London
- Published
- 2011
39. Silicon-chip-based real-time dispersion monitoring for 640 Gbit/s DPSK signals
- Author
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Jochen Schröder, Siegfried Janz, Trung D. Vo, Adam Densmore, Mark Pelusi, Bill Corcoran, Dan-Xia Xu, David J. Moss, Rubin Ma, and Benjamin J. Eggleton
- Subjects
optical signal processing ,optical planar waveguides ,Computer science ,Cross-phase modulation ,Bandwidth (signal processing) ,nonlinear optics ,Nonlinear optics ,Keying ,Atomic and Molecular Physics, and Optics ,spectral analysis ,CMOS ,optical performance monitoring (OPM) ,Gigabit ,Dispersion (optics) ,Electronic engineering ,Terabit - Abstract
We demonstrate silicon-chip-based instantaneous chromatic dispersion monitoring (GVD) for an ultrahigh bandwidth 640 Gbit/s differential phase-shift keying (DPSK) signal. This monitoring scheme is based on cross-phase modulation in a highly nonlinear silicon nanowire. We show that two-photon absorption and free-carrier-related effects do not compromise the GVD monitoring performance, making our scheme a reliable on-chip CMOS-compatible, all-optical, and real-time impairment monitoring approach for up to Terabit/s DPSK signals.
- Published
- 2011
40. Silicon photonic wire biosensors: Sensing, instrumentation, and applications
- Author
-
Rubin Ma, Jean Lapointe, Heping Ding, G. Lopinski, W. Sinclair, Adam Densmore, Boris Lamontagne, R. MacKenzie, Robert Halir, Dan-Xia Xu, H. McIntosh, Martin Vachon, T. Mischki, Y. Li, D. Desrosiers, N. Sabourin, E. Post, Pavel Cheben, Andre Delage, Siegfried Janz, Q. Y. Liu, Jens H. Schmid, and Íñigo Molina-Fernández
- Subjects
optical couplings ,patterned structure ,Materials science ,sensor chips ,molecular binding ,photonics ,wire ,ease-of-use ,Integrated circuit design ,Grating ,sensors ,label free ,Optics ,label-free molecular detection ,silicon waveguide ,propagation lengths ,Fluidics ,sub-wavelength ,Silicon photonics ,silicon photonics ,business.industry ,grating couplers ,biosensors ,Chip ,on chips ,sensor platform ,molecular sensing ,instruments ,photonic wires ,Optoelectronics ,Millimeter ,evanescent fields ,Square Millimeter ,Photonics ,business ,fluidics - Abstract
Photonic wire evanescent field (PWEF) sensor chips have been developed for multiplexed label free molecular detection. The sensors are made using 260 nm ×450 nm cross-section silicon waveguides folded into spirals less than 200 μm in diameter, but with an overall sensor length of more than a millimeter. The long propagation length gives a response to molecular binding much better than currently available tools for label-free molecular sensing. These sensors can be arrayed at densities up to ten or more per square millimeter. This talk reviews our ongoing work on the photonic wire sensor chip design and layout, on-chip integrated fluidics, optical coupling, and chip interrogation using arrays of grating couplers formed using sub-wavelength patterned structures. The goal is to develop a commercially viable sensor platform by addressing cost-of-instrumentation, cost per measurement, ease-of-use, and by increasing the number of sensors that can be simultaneously monitored. © 2011 IEEE., 2011 ICO International Conference on Information Photonics, IP 2011, 18 May 2011 through 20 May 2011, Ottawa, ON
- Published
- 2011
41. Subwavelength and diffractive waveguide structures and their applications in nanophotonics and sensing
- Author
-
Jean Lapointe, André Delâge, Przemek J. Bock, Boris Lamontagne, Adam Densmore, Jens H. Schmid, Rubin Ma, Siegfried Janz, Robert Halir, Dan-Xia Xu, Trevor J. Hall, Íñigo Molina-Fernández, J-M. Fedeli, and Pavel Cheben
- Subjects
fiber optic sensors ,organic polymers ,light refraction ,diffraction ,photonics ,Nanophotonics ,integration ,silicon-on-insulator waveguide ,optical waveguides ,law.invention ,waveguide core ,optical materials ,Planar ,law ,telecom wavelengths ,waveguide crossings ,sub-wavelength ,refractive index ,surface grating coupler and evanescent field sensor ,fibre-chip microphotonic coupler ,Wavelength ,waveguide structure ,integrated optics ,nanophotonics ,Optoelectronics ,device sizes ,tuning mechanism ,silicon compounds ,diffractive structures ,biological sensors ,Materials science ,surfaces ,Grating ,Multiplexer ,subwavelength grating ,Optics ,nanostructures ,microphotonic waveguides ,wavelength dependence ,wavelength ranges ,Diffraction grating ,diffractive surfaces ,two-materials ,business.industry ,planar waveguides ,diffraction gratings ,lithographic patterning ,biosensors ,silicon oxides ,operation bandwidth ,evanescent fields ,constituent materials ,refractometers ,business ,Waveguide ,Refractive index - Abstract
We review recent advances in subwavelength and diffractive structures in planar waveguides. First, we present a new type of microphotonic waveguide, exploiting the subwavelength grating (SWG) effect. We demonstrate several examples of subwavelength grating waveguides and components made of silicon, operating at telecom wavelengths. The SWG technique allows for engineering of the refractive index of a waveguide core over a range as broad as 1.5-3.5 simply by lithographic patterning using only two materials, for example Si and SiO2. This circumvents an important limitation in integrated optics, which is the fixed value of the refractive indices of the constituent materials in the absence of an active tuning mechanism. A subwavelength grating fibre-chip microphotonic coupler is presented with a loss as low as 0.9 dB and with minimal wavelength dependence over a broad wavelength range exceeding 200 nm. It is shown that the SWG waveguides can be used to make efficient waveguide crossings with minimal loss and negligible crosstalk. We also present a diffractive surface grating coupler with subwavelength nanostructure, that has been implemented in a Si-wire evanescent field biological sensor. Furthermore, we discuss a new type of planar waveguide multiplexer with a SWG engineered nanostructure, yielding an operation bandwidth exceeding 170 nm for a device size of only 160 μm × 100 μm., Integrated Optics: Devices, Materials, and Technologies XV, January 24-26, 2011, San Francisco, CA, USA, Series: Proceedings of SPIE; no. 7941
- Published
- 2011
42. Silicon photonic wire evanescent field sensors: sensor arrays and instrumentation
- Author
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Boris Lamontagne, T. Mischki, Y. Li, Íñigo Molina-Fernández, N. Sabourin, André Delâge, R. MacKenzie, Rubin Ma, Robert Halir, Jens H. Schmid, G. Lopinski, Jean Lapointe, Martin Vachon, Adam Densmore, E. Post, W. Sinclair, Siegfried Janz, Pavel Cheben, Dan-Xia Xu, and Q. Y. Liu
- Subjects
affinity binding ,Waveguide (electromagnetism) ,Materials science ,wire ,Grating ,optical waveguides ,photonic devices ,Sensor array ,sensor arrays ,Fluidics ,Silicon photonics ,silicon photonics ,business.industry ,optical resonators ,label-free sensors ,waveguides ,biosensors ,Chip ,ring resonators ,instruments ,photonic wires ,Optoelectronics ,Photonics ,Square Millimeter ,business ,fluidics ,nanosensors - Abstract
We are developing a photonic wire evanescent field (PWEF) sensor chip using 260 nm x 450 nm cross-section silicon photonic wire waveguides. The waveguide mode is strongly localized near the silicon surface, so that light interacts strongly with molecules bound to the waveguide surface. The millimeter long sensor waveguides can be folded into tight spiral structures less than 200 micrometers in diameter, which can be arrayed at densities up to ten or more independent sensors per square millimeter. The long propagation length in each sensor element gives a response to molecular binding much better than currently available tools for label-free molecular sensing. Cost of instrumentation, cost per measurement, ease-of-use, and the number of sensors that can be simultaneously monitored on a sensor array chip are equally important in determining whether an instrument is practical for the end user and hence commercially viable. The objective of our recent work on PWEF sensor array chips and the associated instrumentation is to address all of these issues. This conference paper reviews our ongoing work on the photonic wire sensor chip design and layout, on-chip integrated fluidics, optical coupling, and chip interrogation using arrays of grating couplers formed using sub-wavelength patterned structures. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE)., SPIE BiOS, January 22-23, 2011, San Francisco, CA, USA, Series: Proceedings of SPIE; no. 7888
- Published
- 2011
43. Athermal silicon waveguides using the subwavelength grating effect
- Author
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Winnie N. Ye, Jean Lapointe, Pavel Cheben, Marc Ibrahim, Rubin Ma, Dan-Xia Xu, Jens H. Schmid, Przemek J. Bock, Adam Densmore, and Siegfried Janz
- Subjects
chemistry.chemical_classification ,Waveguide (electromagnetism) ,Materials science ,Silicon ,business.industry ,Temperature independent ,chemistry.chemical_element ,Physics::Optics ,Polymer ,Grating ,Optics ,chemistry ,Optoelectronics ,Photonics ,business ,Electron-beam lithography - Abstract
We present a method for designing temperature independent silicon waveguide devices using the subwavelength grating effect. Photonic wire waveguides are patterned with periodic gaps and filled with SU-8 polymer to cancel the silicon thermo-optic effect., Integrated Photonics Research, Silicon and Nanophotonics, 12–15 June 2011, Toronto, ON, Canada
- Published
- 2011
44. Single etch fibre-to-chip grating couplers for high-volume production in SOI
- Author
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Pavel Cheben, Dan-Xia Xu, Rubin Ma, Íñigo Molina-Fernández, J-M. Fedeli, Robert Halir, Adam Densmore, Siegfried Janz, and Jens H. Schmid
- Subjects
Fiber gratings ,Fabrication ,Materials science ,sub-wave length grating ,business.industry ,Volume (computing) ,photonics ,Silicon on insulator ,grating couplers ,Grating ,Chip ,effective medium ,high-volume production ,Optics ,DUV lithography ,Optoelectronics ,sub-wavelength structures ,business ,effective media ,single etch ,Lithography - Abstract
Fibre-to-chip grating couplers are an efficient means for injecting and extracting light from silicon-wire waveguides. Here we present the design of single-etch couplers, based on effective media implemented with sub-wavelength gratings. We show that the pitch of these sub-wavelength structures can be increased to make their fabrication compatible with deep-ultraviolet lithography, without compromising their effective medium behavior. We experimentally demonstrate fully-etched grating couplers fabricated with DUV lithography. © 2011 IEEE., 2011 ICO International Conference on Information Photonics, IP 2011, 18 May 2011 through 20 May 2011, Ottawa, ON
- Published
- 2011
45. Engineering light at the sub-wavelength scale using silicon photonics
- Author
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Martin Vachon, André Delâge, W. Sinclair, Jean Lapointe, Siegfried Janz, Robert Halir, Dan-Xia Xu, Przemek J. Bock, Jens H. Schmid, Pavel Cheben, E. Post, Adam Densmore, Boris Lamontagne, Rubin Ma, and Íñigo Molina-Fernández
- Subjects
optical properties ,Materials science ,Semiconductor device fabrication ,molecular monolayer ,Nanophotonics ,photonics ,Physics::Optics ,high-index contrast waveguides ,Grating ,Waveguide (optics) ,electric fields ,optical structures ,photonic devices ,waveguide core ,Optics ,optical materials ,optical bio-sensors ,semiconductor devices ,length scale ,etch depth ,sub-wavelength ,electric field profiles ,semi-conductor fabrication ,Silicon photonics ,segmented waveguides ,silicon photonics ,business.industry ,optical instruments ,cladding layer ,Metamaterial ,grating couplers ,waveguides ,Cladding (fiber optics) ,lithographic patterning ,biosensors ,metamaterials ,monolayers ,integrated optics ,Optoelectronics ,nanophotonics ,Photonics ,business ,light - Abstract
As a result of the evolution semiconductor fabrication tools and methods over several decades, it now possible to routinely design and make optical devices with features comparable to or smaller than the wavelength of the light that propagates through these structures. This paper will review some silicon optical structures with critical features at these extremely short length scales. For example it becomes possible to create segmented waveguide structures with optical properties that can be tuned continuously between those of the cladding and waveguide core, using lithographic patterning rather than varying etch depth. Using thin high index contrast waveguides and the correct polarization, the optical electric field profiles can be shaped to maximize the coupling to molecular monolayers or cladding layers with specific functionality. Examples are given from our recent work on optical biosensors chips which employ grating couplers made by sub-wavelength digital patterning, and use waveguides optimized for coupling to molecular monolayers., Silicon Photonics VI, January 23-26, 2011, San Francisco, CA, USA, Series: Proceedings of SPIE; no. 7943
- Published
- 2011
46. Silicon photonic wire devices for biosensing and communications
- Author
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Jens H. Schmid, Rubin Ma, Andre Delage, Dan-Xia Xu, Adam Densmore, Y. Li, Siegfried Janz, G. Lopinski, Robert Halir, Martin Vachon, Pavel Cheben, Jean Lapointe, and Íñigo Molina-Fernández
- Subjects
Materials science ,Silicon photonics ,Optical fiber ,business.industry ,Physics::Optics ,Grating ,Waveguide (optics) ,law.invention ,Resonator ,Optics ,Sensor array ,law ,Optoelectronics ,business ,Optical filter ,Diffraction grating - Abstract
We review our work on silicon wire devices designed for evanescent field sensor arrays and ultra-compact dense optical comb filters, both taking advantage of a spiral cavity resonator design. Two sensor array configurations are described, and monitoring of biomolecular binding is demonstrated with a detection limit of 0.3 pg/mm2. On-chip temperature drift compensation is achieved by using a reference resonator. A novel grating coupler using subwavelength structures facilitates the coupling of light between the optical fiber and waveguide chips.
- Published
- 2010
47. Integration of vertical grating couplers and microfluidic channels with silicon photonic wire biosensor arrays
- Author
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Jens H. Schmid, Adam Densmore, Y. Li, Andre Delage, Robert Halir, G. Lopinski, Martin Vachon, D. Bedard, Rubin Ma, Dan-Xia Xu, Pavel Cheben, Íñigo Molina-Fernández, and Siegfried Janz
- Subjects
Resonator ,Silicon photonics ,Optics ,Materials science ,business.industry ,Microfluidics ,Physics::Optics ,Photonics ,Grating ,business ,Diffraction grating ,Biosensor ,Photonic crystal - Abstract
We describe a new label-free biosensor array chip developed for the real-time, simultaneous monitoring of multiple molecular binding reactions. It is composed of monolithically integrated grating couplers, microfluidic channels and spiral cavity silicon photonic wire sensors. The grating couplers use a novel design for coupling to the transverse magnetic mode of a silicon photonic wire. They contain arrays of subwavelength dimension holes, which allow the local refractive index to be engineered in the grating region. They can be fabricated with the photonic wires in a single etch step, an important advantage over other vertical couplers. The coiled waveguides are configured as ring resonators with extended cavity length for high sensitivity and small footprint for compatibility with microarray spotting. For analyte delivery, microfluidic channels were formed in an SU-8 overlayer.
- Published
- 2010
48. Silicon nanowire based radio-frequency spectrum analyser
- Author
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Christelle Monat, Mark Pelusi, Bill Corcoran, Benjamin J. Eggleton, Rubin Ma, David J. Moss, Tony Vo, Siegfried Janz, Adam Densmore, and D.-X. Xu
- Subjects
Spectrum analyzer ,3D optical data storage ,Materials science ,Silicon ,business.industry ,Cross-phase modulation ,Bandwidth (signal processing) ,Analyser ,Optical communication ,Nanophotonics ,Nanowire ,Physics::Optics ,chemistry.chemical_element ,Radio spectrum ,Optics ,chemistry ,Dispersion (optics) ,Radio frequency ,business - Abstract
We demonstrate a silicon nanowire based radio frequency spectrum analyser based on cross-phase modulation. We show that the device is accurate, with cross-chirp from photogenerated free-carriers negligible and measure RF spectra for 640Gbaud on-off-keyed data., 2010 36th European Conference and Exhibition on Optical Communication, ECOC 2010, September 19-23, 2010, Torino, Italy
- Published
- 2010
49. Detection of lead contamination of water and VOC contamination of air using SOI micro-optical devices
- Author
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Marian A. Dreher, Martin Vachon, Pavel Cheben, Jack A. Barnes, Hans-Peter Loock, Andre Delage, Adam Densmore, Cathleen M. Crudden, John Saunders, Rubin Ma, Dan-Xia Xu, Jens H. Schmid, Siegfried Janz, Jean Lapointe, and Jenny Du
- Subjects
Detection limit ,Materials science ,Polydimethylsiloxane ,business.industry ,Analytical chemistry ,Silicon on insulator ,BTEX ,engineering.material ,Contamination ,Solid-phase microextraction ,chemistry.chemical_compound ,Coating ,chemistry ,engineering ,Optoelectronics ,business ,Mesoporous material - Abstract
Micro-photonic SOI Mach-Zehnder interferometers were coated with solid-phase micro-extraction materials derived from polydimethylsiloxane to enable sensing of volatile organic compounds of the BTEX class in air. A different coating based on functionalized mesoporous silicates is used to detect lead Pb(II) with a detection limit of < 100 ppb in water.
- Published
- 2010
50. Quantum dot multiwavelength comb lasers with Si ring resonator
- Author
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Jiaren Liu, Rubin Ma, D.-X. Xu, Siegfried Janz, Philip J. Poole, Z. G. Lu, Martin Vachon, Jean Lapointe, Daniel Poitras, Pedro Barrios, and W. Y. Li
- Subjects
Materials science ,Extinction ratio ,business.industry ,Laser ,Semiconductor laser theory ,law.invention ,chemistry.chemical_compound ,Resonator ,Optics ,chemistry ,Quantum dot laser ,Quantum dot ,law ,Optoelectronics ,Photonics ,Indium arsenide ,business - Abstract
The gain media of the quantum dot lasers consist of InAs QDs in an InGaAsP matrix on an InP substrate. The quantum dot lasers have different free spacing ranges (FSRs) corresponding to Fabry-Perot (F-P) cavity lengths. A silicon ring resonator and a QD laser have been combined to form comb laser. The output characteristics of the combined comb laser were investigated. The measured FSR was about 2.8nm and the extinction ratio was about 10(dB) when the FSR of the QD laser was about 0.4nm and the FSR of the ring resonator was about 0.47nm. The experimental results show that the ring resonator had a strong control on the FSR and extinction ratio of the comb laser.
- Published
- 2010
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