| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Bakker, D. C. E., et al.
(författare)
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An update to the surface ocean CO2 atlas (SOCAT version 2)
- 2014
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Ingår i: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 6:1, s. 69-90
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Tidskriftsartikel (refereegranskat)abstract
- The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO 2 values) and extended data coverage (from 1968-2007 to 1968-2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models. © Author(s) 2014. CC Attribution 3.0 License.
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| 3. |
- Gould, A., et al.
(författare)
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MOA-2010-BLG-523:" Failed Planet"= RS CVn Star
- 2013
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Ingår i: Astrophysical Journal. - 0004-637X. ; 763:2
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Tidskriftsartikel (refereegranskat)abstract
- The Galactic bulge source MOA-2010-BLG-523S exhibited short-term deviations from a standard microlensing light curve near the peak of an A(max) similar to 265 high-magnification microlensing event. The deviations originally seemed consistent with expectations for a planetary companion to the principal lens. We combine long-term photometric monitoring with a previously published high-resolution spectrum taken near peak to demonstrate that this is an RS CVn variable, so that planetary microlensing is not required to explain the light-curve deviations. This is the first spectroscopically confirmed RS CVn star discovered in the Galactic bulge.
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| 4. |
- Frasinski, L. J., et al.
(författare)
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Dynamics of Hollow Atom Formation in Intense X-Ray Pulses Probed by Partial Covariance Mapping
- 2013
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 111:7, s. 073002-
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Tidskriftsartikel (refereegranskat)abstract
- When exposed to ultraintense x-radiation sources such as free electron lasers (FELs) the innermost electronic shell can efficiently be emptied, creating a transient hollow atom or molecule. Understanding the femtosecond dynamics of such systems is fundamental to achieving atomic resolution in flash diffraction imaging of noncrystallized complex biological samples. We demonstrate the capacity of a correlation method called partial covariance mapping'' to probe the electron dynamics of neon atoms exposed to intense 8 fs pulses of 1062 eV photons. A complete picture of ionization processes competing in hollow atom formation and decay is visualized with unprecedented ease and the map reveals hitherto unobserved nonlinear sequences of photoionization and Auger events. The technique is particularly well suited to the high counting rate inherent in FEL experiments.
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| 5. |
- Leymarie, N., et al.
(författare)
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Interlaboratory Study on Differential Analysis of Protein Glycosylation by Mass Spectrometry: The ABRF Glycoprotein Research Multi-Institutional Study 2012
- 2013
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476. ; 12:10, s. 2935-2951
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Tidskriftsartikel (refereegranskat)abstract
- One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods. T6G 2G2, Canada. [Cipollo, John F.; An, Yanming] US FDA, Ctr Biol Evaluat & Res, Bethesda, MD 20993 USA. [Desaire, Heather; Go, Eden P.] Univ Kansas, Lawrence, KS 66045 USA. [Goldman, Radoslav; Pompach, Petr; Sanda, Miloslav] Georgetown Univ, Dept Oncol, Washington, DC [Halim, Adnan; Larson, Goran; Nilsson, Jonas] Univ Gothenburg, Sahlgrenska Acad, Dept Clin Chem & [Hensbergen, Paul J.; Wuhrer, Manfred] Leiden Univ, Med Ctr, Biomol Mass Spectrometry Unit, NL- [Jabs, Wolfgang; Marx, Kristina; Resemann, Anja; Schweiger-Hufnagel, Ulrike; Suckau, Detlev] Bruker [Ly, Mellisa; Staples, Gregory O.] Agilent Technol, Agilent Labs, Santa Clara, CA 95051 USA. [Mechref, Yehia; Song, Ehwang] Texas Tech Univ, Dept Chem & Biochem, Lubbock, TX 79409 USA. [Nyalwidhe, Julius O.; Watson, Megan] Eastern Virginia Med Sch, Leroy T Canoles Jr Canc Res Ctr, Dept [Packer, Nicolle H.; Thaysen-Andersen, Morten] Macquarie Univ, Dept Chem & Biomol Sci, Biomol [Sihlbom, Carina] Gothenburg Univ, Prote Core Facil, Gothenburg, Sweden. [Tang, Haixu] Indiana Univ, Sch Informat, Bloomington, IN 47405 USA. [Valmuv, Leena] Finnish Red Cross Blood Serv, Helsinki 00310, Finland. [Wada, Yoshinao] Osaka Med Ctr Maternal & Child Hlth, Res Inst, Izumi Ku, Osaka 5941101, Japan.
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| 6. |
- Saleacuten, P., et al.
(författare)
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X-ray FEL-induced Double Core-Hole Formation in Polyatomic Molecules
- 2012
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Ingår i: Journal of Physics, Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 388:2, s. 022083-
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Tidskriftsartikel (refereegranskat)abstract
- We use extremely intense, ultrashort soft X-Ray pulses generated by the LCLS X-Ray Free Electron Laser to investigate the production of molecular double core-hole states by sequential two-photon X-Ray absorption. The effect of critical LCLS parameters such as the number of photons per pulse, the pulse duration, and the focal spot size on the photoelectron and Auger spectra is modeled in detail and the results of these simulations are used as an aid in the interpretation of the experimental spectra obtained. The emphasis is on double core-hole formation in small polyatomic molecules such as CO2.
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| 7. |
- Zhaunerchyk, Vitali, et al.
(författare)
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Using covariance mapping to investigate the dynamics of multi-photon ionization processes of Ne atoms exposed to X-FEL pulses
- 2013
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Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 46:16, s. 164034-
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Tidskriftsartikel (refereegranskat)abstract
- We report on a detailed investigation into the electron emission processes of Ne atoms exposed to intense femtosecond x-ray pulses, provided by the Linac Coherent Light Source Free Electron Laser (FEL) at Stanford. The covariance mapping technique is applied to analyse the data, and the capability of this approach to disentangle both linear and nonlinear correlation features which may be hidden on coincidence maps of the same data set is demonstrated. Different correction techniques which enable improvements on the quality of the spectral features extracted from the covariance maps are explored. Finally, a method for deriving characteristics of the x-ray FEL pulses based on covariance mapping in combination with model simulations is presented.
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| 8. |
- Bensby, Thomas, et al.
(författare)
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Chemical evolution of the Galactic bulge as traced by microlensed dwarf and subgiant stars IV. Two bulge populations
- 2011
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Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 533
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Tidskriftsartikel (refereegranskat)abstract
- Based on high-resolution (R approximate to 42 000 to 48 000) and high signal-to-noise (S/N approximate to 50 to 150) spectra obtained with UVES/VLT, we present detailed elemental abundances (O, Na, Mg, Al, Si, Ca, Ti, Cr, Fe, Ni, Zn, Y, and Ba) and stellar ages for 12 new microlensed dwarf and subgiant stars in the Galactic bulge. Including previous microlensing events, the sample of homogeneously analysed bulge dwarfs has now grown to 26. The analysis is based on equivalent width measurements and standard 1-D LTE MARCS model stellar atmospheres. We also present NLTE Li abundances based on line synthesis of the Li-7 line at 670.8 nm. The results from the 26 microlensed dwarf and subgiant stars show that the bulge metallicity distribution (MDF) is double-peaked; one peak at [Fe/H] approximate to -0.6 and one at [Fe/H] approximate to +0.3, and with a dearth of stars around solar metallicity. This is in contrast to the MDF derived from red giants in Baade's window, which peaks at this exact value. A simple significance test shows that it is extremely unlikely to have such a gap in the microlensed dwarf star MDF if the dwarf stars are drawn from the giant star MDF. To resolve this issue we discuss several possibilities, but we can not settle on a conclusive solution for the observed differences. We further find that the metal-poor bulge dwarf stars are predominantly old with ages greater than 10 Gyr, while the metal-rich bulge dwarf stars show a wide range of ages. The metal-poor bulge sample is very similar to the Galactic thick disk in terms of average metallicity, elemental abundance trends, and stellar ages. Speculatively, the metal-rich bulge population might be the manifestation of the inner thin disk. If so, the two bulge populations could support the recent findings, based on kinematics, that there are no signatures of a classical bulge and that the Milky Way is a pure-disk galaxy. Also, recent claims of a flat IMF in the bulge based on the MDF of giant stars may have to be revised based on the MDF and abundance trends probed by our microlensed dwarf stars.
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| 9. |
- Berrah, Nora, et al.
(författare)
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Double-core-hole spectroscopy for chemical analysis with an intense X-ray femtosecond laser
- 2011
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 108:41, s. 16912-16915
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Tidskriftsartikel (refereegranskat)abstract
- Theory predicts that double-core-hole (DCH) spectroscopy can provide a new powerful means of differentiating between similar chemical systems with a sensitivity not hitherto possible. Although DCH ionization on a single site in molecules was recently measured with double-and single-photon absorption, double-core holes with single vacancies on two different sites, allowing unambiguous chemical analysis, have remained elusive. Here we report that direct observation of double-core holes with single vacancies on two different sites produced via sequential two-photon absorption, using short, intense X-ray pulses from the Linac Coherent Light Source free-electron laser and compare it with theoretical modeling. The observation of DCH states, which exhibit a unique signature, and agreement with theory proves the feasibility of the method. Our findings exploit the ultrashort pulse duration of the free-electron laser to eject two core electrons on a time scale comparable to that of Auger decay and demonstrate possible future X-ray control of physical inner-shell processes.
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| 10. |
- Fang, L., et al.
(författare)
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Multiple Ionization and Double Core-hole Production in Molecules using the LCLS X-ray FEL
- 2012
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Ingår i: Journal of Physics, Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 388:3, s. 032028-
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Tidskriftsartikel (refereegranskat)abstract
- We used the world's first hard x-ray FEL to investigate the response of molecular systems to the ultra-intense, femtosecond x-ray radiation. We report sequential multiphoton ionization, frustrated absorption and double core hole production mechanisms.
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| 11. |
- Larsson, Mats, et al.
(författare)
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Double core-hole formation in small molecules at the LCLS free electron laser
- 2013
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Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 46:16, s. 164030-
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated nonlinear processes in small molecules by x-ray photoelectron spectroscopy using the Linac Coherent Light Source free electron laser, and by simulations. The main focus of the experiments was the formation of the two-site double core-hole (tsDCH) states in the molecules CO2, N2O and N-2. These experiments are described in detail and the results are compared with simulations of the photoelectron spectra. The double core-hole states, and in particular the tsDCH states, have been predicted to be highly sensitive to the chemical environment. The theory behind this chemical sensitivity is validated by the experiments. Furthermore, our simulations of the relative integrated intensities of the peaks associated with the nonlinear processes show that this type of simulation, in combination with experimental data, provides a useful tool for estimating the duration of ultra-short x-ray pulses.
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| 12. |
- Noelken, R., et al.
(författare)
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Soft and hard tissue alterations around implants placed in an alveolar ridge with a sloped configuration
- 2014
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Ingår i: Clinical Oral Implants Research. - : Wiley. - 0905-7161. ; 25:1, s. 3-9
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Tidskriftsartikel (refereegranskat)abstract
- AimThe aim of this study was to evaluate soft and hard tissue alterations around implants placed in healed, sloped ridge sites. Materials and methodsIn this prospective multi-center study, 65 patients between 20 and 74years of age and with a need for a single tooth replacement were included. All patients presented with a recipient implant site demonstrating a lingual-buccal bone height discrepancy of 2.0-5.0mm and with a neighboring tooth on its mesial aspect. Implant placement (OsseoSpeed Profile implants; Astra Tech AB, Molndal, Sweden) was performed using a non-submerged installation procedure. The implants were placed in such a way that the sloped part of the device was located at the buccal and most apical position of the osteotomy preparation. As the buccal rim of the implant was positioned at the crestal bone level, the lingual rim became situated either below or at the level of the lingual bone crest. Clinical assessments of bone levels at the buccal and lingual aspects of the implant were carried out immediately after implant installation and at a surgical re-entry procedure performed 16weeks later. Crowns were placed at 21weeks after implant placement. Radiographs were obtained immediately after implant placement, at 16 and 21weeks and at the 1-year re-examination. Clinical assessment of probing pocket depth and clinical attachment levels were carried out at 21weeks and at 1year of follow-up. ResultsThe alterations of the bone levels that occurred between implant placement and the 16-week surgical re-entry were -0.02mm (lingual) and -0.30mm (buccal). The average change in interproximal bone levels between implant placement and the 1-year re-examination was 0.54mm. Clinical attachment level changes between the 21week and the 1-year examinations varied between 0.1mm gain and 0.1mm loss. ConclusionImplant placement in an alveolar ridge with a sloped marginal configuration resulted in minor remodeling with preserved discrepancies between buccal and lingual bone levels.
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| 13. |
- Puttnam, Benjamin, et al.
(författare)
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Energy efficient modulation formats for multi-core fibers
- 2014
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Ingår i: 19th OptoElectronics and Communications Conference, OECC 2014 and the 39th Australian Conference on Optical Fibre Technology, ACOFT 2014; Melbourne, VIC; Australia; 6 - 10 Jul. 2014. - 9781922107213 ; , s. 694-696
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Konferensbidrag (refereegranskat)abstract
- We propose and experimentally investigate a family of multi-dimensional modulation formats for multi-core-fibers. Such formats can have power or spectral efficiency advantages or lower symbol energies but implementation difficulties cause an OSNR penalty.
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| 14. |
- Puttnam, Benjamin, et al.
(författare)
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Modulation formats for multi-core fiber transmission
- 2014
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Ingår i: Optics Express. - 1094-4087 .- 1094-4087. ; 22:26, s. 32457-32469
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Tidskriftsartikel (refereegranskat)abstract
- ©2014 Optical Society of America We investigate high dimensional modulation formats for multi-core fibers (MCFs) and spatial superchannels. We show that the low skew variations between MCF cores maybe exploited to generate 'multi-core' formats that offer significant advantages over independently transmitting conventional 4-dimensional formats in each core. We describe how pulse position modulation formats may be transposed to the spatial domain and then investigate a family of modulation formats referred to as core-coding, one of which has the same power and spectral efficiency as polarization switched quaternary phase shift keying but with half of the optical power, potentially improving non-linear tolerance for long distance transmission, albeit at the cost of implementation challenges. Finally, we investigate the application of set-partitioning to multi-core formats using a single-parity check bit transmitted in one quadrature of one polarization in one of the cores and polarization-division multiplexing quadrature phase shift keying data in all remaining cores. We observe that for high core counts, an advantage of almost 3 dB in asymptotic power efficiency may be obtained with negligible impact on spectral efficiency, which translates into experimentally measured reduction in the required optical signal-to-noise ratio of up to 1.8 dB at a bit-error-rate of 10-5 and the same data-rate, and additional transmission reach of up to 20%.
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| 15. |
- Puttnam, Benjamin, et al.
(författare)
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Single parity check multi-core modulation for power efficient spatial super-channels
- 2014
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Ingår i: 2014 European Conference on Optical Communication, ECOC 2014; Cannes; France; 21 September 2014 through 25 September 2014. - 9782954944401 ; , s. Art. no. 6964197-
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Konferensbidrag (refereegranskat)abstract
- We investigate multi-core modulation formats for spatial super-channels using a single parity check on PDM-QPSK symbols. Compared to per-core PDM-QPSK, we show improvements in required OSNR of up to 1.8 dB, with minimal impact on spectral efficiency.
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| 16. |
- Sahlén, Martin, et al.
(författare)
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Experimental Verification of the Chemical Sensitivity of Two-Site Double Core-Hole States Formed by an X-Ray Free-Electron Laser
- 2012
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 108:15, s. 153003-
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Tidskriftsartikel (refereegranskat)abstract
- We have performed x-ray two-photon photoelectron spectroscopy using the Linac Coherent Light Source x-ray free-electron laser in order to study double core-hole (DCH) states of CO2, N2O, and N-2. The experiment verifies the theory behind the chemical sensitivity of two-site DCH states by comparing a set of small molecules with respect to the energy shift of the two-site DCH state and by extracting the relevant parameters from this shift.
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| 17. |
- Sjödin, Martin E, 1983, et al.
(författare)
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Comparison of PS-QPSK and PM-QPSK at Different Data Rates in a 25 GHz-spaced WDM System
- 2012
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Ingår i: Optical Fiber Communication Conference, OFC 2012, Los Angeles, United States, 4-8 March 2012. - 2162-2701. - 9781557529381
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Konferensbidrag (refereegranskat)abstract
- We compare polarization-switched QPSK and polarization-multiplexed QPSK in a WDM system with 25 GHz channel spacing. We investigate experimentally the transmission distance as a function of the data rate for both modulation formats.
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| 18. |
- Sjödin, Martin E, 1983, et al.
(författare)
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Transmission of PM-QPSK and PS-QPSK with different fiber span lengths
- 2012
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Ingår i: Optics Express. - 1094-4087 .- 1094-4087. ; 20:7, s. 7544-7554
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Tidskriftsartikel (refereegranskat)abstract
- We perform experimental and numerical investigations of the transmission reach of polarization-switched QPSK (PS-QPSK) and polarization-multiplexed QPSK (PM-QPSK) for three different fiber span lengths: 83, 111 and 136 km. In the experimental comparison we investigate the performance of PS-QPSK at 20 Gbaud and PM-QPSK at the same bit rate (60 Gbit/s) and at the same symbol rate, both the single channel case and a WDM system with 9 channels on a 50 GHz grid. We show that PS-QPSK gives significant benefits in transmission reach for all span lengths. Compared to PM-QPSK, use of PS-QPSK increases the reach with more than 41 % for the same symbol rate and 21 % for the same bit rate. In the numerical simulations we use the same data rates as in the experiment. The simulation results agree well with the experimental findings, but the transmission reach is longer due to the absence of various non-ideal effects and higher back-to-back sensitivity. Apart from using data coded in the absolute phase in the simulations, we also investigate differentially coded PS-QPSK for the first time and compare with PM-QPSK with differential coding. The power efficiency advantage of PS-QPSK then increases with approximately 0.3 dB at a bit error rate of 10-3, resulting in a further relative transmission reach improvement over PM-QPSK. Both the experimental and the numerical results indicate that PS-QPSK has slightly higher tolerance to inter-channel nonlinear crosstalk than PM-QPSK.
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| 19. |
- Xu, S., et al.
(författare)
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A field-trial of on-demand integration of grid and innovative wavelength multicasting service over WSON for emerging frontier applications
- 2010
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Ingår i: 2010 14th Conference on Optical Network Design and Modeling, ONDM 2010. - 9783901882418
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- To enable the quick applications and services of new-born innovative optical network service (INS) in largescale high-end grid computing, we propose an overlay approach to integrate grid and emerging INS resources establishing the value-added optical grid network flexibly cross over multi-domain WSONs. In particular, we introduce an edge-mode approach which flexibly leverages new multifunction wavelength selective multicasting (WSM) at a special edge close to the core node. To integrate grid and innovative optical network technologies efficiently, we propose a unified platform - optical grid/INS network infrastructure (OGINI). Through field trial experiments over a developed metropolitan-scale wavelength switched optical network (WSON) test-bed, the feasibility of the proposed WSM scheme in the optical transmission systems and the totally automated value-added OGN constructions supported by the proposed OGINI have been verified successfully.
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