| 1. |
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- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Adrian-Martinez, S., et al.
(författare)
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A first search for coincident gravitational waves and high energy neutrinos using LIGO, Virgo and ANTARES data from 2007
- 2013
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :6
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Tidskriftsartikel (refereegranskat)abstract
- We present the results of the first search for gravitational wave bursts associated with high energy neutrinos. Together, these messengers could reveal new, hidden sources that are not observed by conventional photon astronomy, particularly at high energy. Our search uses neutrinos detected by the underwater neutrino telescope ANTARES in its 5 line configuration during the period January - September 2007, which coincided with the fifth and first science runs of LIGO and Virgo, respectively. The LIGO-Virgo data were analysed for candidate gravitational-wave signals coincident in time and direction with the neutrino events. No significant coincident events were observed. We place limits on the density of joint high energy neutrino - gravitational wave emission events in the local universe, and compare them with densities of merger and core-collapse events.
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| 3. |
- Abadie, J., et al.
(författare)
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Implementation and testing of the first prompt search for gravitational wave transients with electromagnetic counterparts
- 2012
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Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 539
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Tidskriftsartikel (refereegranskat)abstract
- Aims. A transient astrophysical event observed in both gravitational wave (GW) and electromagnetic (EM) channels would yield rich scientific rewards. A first program initiating EM follow-ups to possible transient GW events has been developed and exercised by the LIGO and Virgo community in association with several partners. In this paper, we describe and evaluate the methods used to promptly identify and localize GW event candidates and to request images of targeted sky locations. Methods. During two observing periods (Dec. 17, 2009 to Jan. 8, 2010 and Sep. 2 to Oct. 20, 2010), a low-latency analysis pipeline was used to identify GW event candidates and to reconstruct maps of possible sky locations. A catalog of nearby galaxies and Milky Way globular clusters was used to select the most promising sky positions to be imaged, and this directional information was delivered to EM observatories with time lags of about thirty minutes. A Monte Carlo simulation has been used to evaluate the low-latency GW pipeline's ability to reconstruct source positions correctly. Results. For signals near the detection threshold, our low-latency algorithms often localized simulated GW burst signals to tens of square degrees, while neutron star/neutron star inspirals and neutron star/black hole inspirals were localized to a few hundred square degrees. Localization precision improves for moderately stronger signals. The correct sky location of signals well above threshold and originating from nearby galaxies may be observed with similar to 50% or better probability with a few pointings of wide-field telescopes.
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| 4. |
- Abadie, J., et al.
(författare)
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All-sky search for periodic gravitational waves in the full S5 LIGO data
- 2012
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 85:2
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Tidskriftsartikel (refereegranskat)abstract
- We report on an all-sky search for periodic gravitational waves in the frequency band 50-800 Hz and with the frequency time derivative in the range of 0 through -6 x 10(-9) Hz/s. Such a signal could be produced by a nearby spinning and slightly nonaxisymmetric isolated neutron star in our Galaxy. After recent improvements in the search program that yielded a 10x increase in computational efficiency, we have searched in two years of data collected during LIGO's fifth science run and have obtained the most sensitive all-sky upper limits on gravitational-wave strain to date. Near 150 Hz our upper limit on worst-case linearly polarized strain amplitude h(0) is 1 x 10(-24), while at the high end of our frequency range we achieve a worst-case upper limit of 3.8 x 10(-24) for all polarizations and sky locations. These results constitute a factor of 2 improvement upon previously published data. A new detection pipeline utilizing a loosely coherent algorithm was able to follow up weaker outliers, increasing the volume of space where signals can be detected by a factor of 10, but has not revealed any gravitational-wave signals. The pipeline has been tested for robustness with respect to deviations from the model of an isolated neutron star, such as caused by a low-mass or long-period binary companion.
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| 5. |
- Abadie, J., et al.
(författare)
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Search for gravitational waves from low mass compact binary coalescence in LIGO's sixth science run and Virgo's science runs 2 and 3
- 2012
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 85:8
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Tidskriftsartikel (refereegranskat)abstract
- We report on a search for gravitational waves from coalescing compact binaries using LIGO and Virgo observations between July 7, 2009, and October 20, 2010. We searched for signals from binaries with total mass between 2 and 25M(circle dot); this includes binary neutron stars, binary black holes, and binaries consisting of a black hole and neutron star. The detectors were sensitive to systems up to 40 Mpc distant for binary neutron stars, and further for higher mass systems. No gravitational-wave signals were detected. We report upper limits on the rate of compact binary coalescence as a function of total mass, including the results from previous LIGO and Virgo observations. The cumulative 90% confidence rate upper limits of the binary coalescence of binary neutron star, neutron star-black hole, and binary black hole systems are 1.3 x 10(-4), 3.1 x 10(-5), and 6.4 x 10(-6) Mpc(-3) yr(-1), respectively. These upper limits are up to a factor 1.4 lower than previously derived limits. We also report on results from a blind injection challenge.
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| 6. |
- Abadie, J., et al.
(författare)
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Search for Gravitational Waves Associated with Gamma-Ray Bursts during LIGO Science Run 6 and Virgo Science Runs 2 and 3
- 2012
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Ingår i: Astrophysical Journal. - 0004-637X. ; 760:1
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Tidskriftsartikel (refereegranskat)abstract
- We present the results of a search for gravitational waves associated with 154 gamma-ray bursts (GRBs) that were detected by satellite-based gamma-ray experiments in 2009-2010, during the sixth LIGO science run and the second and third Virgo science runs. We perform two distinct searches: a modeled search for coalescences of either two neutron stars or a neutron star and black hole, and a search for generic, unmodeled gravitational-wave bursts. We find no evidence for gravitational-wave counterparts, either with any individual GRB in this sample or with the population as a whole. For all GRBs we place lower bounds on the distance to the progenitor, under the optimistic assumption of a gravitational-wave emission energy of 10(-2) M-circle dot c(2) at 150 Hz, with a median limit of 17 Mpc. For short-hard GRBs we place exclusion distances on binary neutron star and neutron-star-black-hole progenitors, using astrophysically motivated priors on the source parameters, with median values of 16 Mpc and 28 Mpc, respectively. These distance limits, while significantly larger than for a search that is not aided by GRB satellite observations, are not large enough to expect a coincidence with a GRB. However, projecting these exclusions to the sensitivities of Advanced LIGO and Virgo, which should begin operation in 2015, we find that the detection of gravitational waves associated with GRBs will become quite possible.
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| 7. |
- Abadie, J., et al.
(författare)
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All-sky search for gravitational-wave bursts in the second joint LIGO-Virgo run
- 2012
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 85:12
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Tidskriftsartikel (refereegranskat)abstract
- We present results from a search for gravitational-wave bursts in the data collected by the LIGO and Virgo detectors between July 7, 2009 and October 20, 2010: data are analyzed when at least two of the three LIGO-Virgo detectors are in coincident operation, with a total observation time of 207 days. The analysis searches for transients of duration less than or similar to 1 s over the frequency band 64-5000 Hz, without other assumptions on the signal waveform, polarization, direction or occurrence time. All identified events are consistent with the expected accidental background. We set frequentist upper limits on the rate of gravitational-wave bursts by combining this search with the previous LIGO-Virgo search on the data collected between November 2005 and October 2007. The upper limit on the rate of strong gravitational-wave bursts at the Earth is 1.3 events per year at 90% confidence. We also present upper limits on source rate density per year and Mpc(3) for sample populations of standard-candle sources. As in the previous joint run, typical sensitivities of the search in terms of the root-sum-squared strain amplitude for these waveforms lie in the range similar to 5 x 10(-22) Hz(-1/2) to similar to 1 x 10(-20) Hz(-1/2). The combination of the two joint runs entails the most sensitive all-sky search for generic gravitational-wave bursts and synthesizes the results achieved by the initial generation of interferometric detectors.
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| 8. |
- Abadie, J., et al.
(författare)
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First low-latency LIGO plus Virgo search for binary inspirals and their electromagnetic counterparts
- 2012
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Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 541
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Tidskriftsartikel (refereegranskat)abstract
- Aims. The detection and measurement of gravitational-waves from coalescing neutron-star binary systems is an important science goal for ground-based gravitational-wave detectors. In addition to emitting gravitational-waves at frequencies that span the most sensitive bands of the LIGO and Virgo detectors, these sources are also amongst the most likely to produce an electromagnetic counterpart to the gravitational-wave emission. A joint detection of the gravitational-wave and electromagnetic signals would provide a powerful new probe for astronomy. Methods. During the period between September 19 and October 20, 2010, the first low-latency search for gravitational-waves from binary inspirals in LIGO and Virgo data was conducted. The resulting triggers were sent to electromagnetic observatories for followup. We describe the generation and processing of the low-latency gravitational-wave triggers. The results of the electromagnetic image analysis will be described elsewhere. Results. Over the course of the science run, three gravitational-wave triggers passed all of the low-latency selection cuts. Of these, one was followed up by several of our observational partners. Analysis of the gravitational-wave data leads to an estimated false alarm rate of once every 6.4 days, falling far short of the requirement for a detection based solely on gravitational-wave data.
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| 9. |
- Abadie, J., et al.
(författare)
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Upper limits on a stochastic gravitational-wave background using LIGO and Virgo interferometers at 600-1000 Hz
- 2012
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 85:12
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Tidskriftsartikel (refereegranskat)abstract
- A stochastic background of gravitational waves is expected to arise from a superposition of many incoherent sources of gravitational waves, of either cosmological or astrophysical origin. This background is a target for the current generation of ground-based detectors. In this article we present the first joint search for a stochastic background using data from the LIGO and Virgo interferometers. In a frequency band of 600-1000 Hz, we obtained a 95% upper limit on the amplitude of Omega(GW)(f) = Omega(3)(f/900 Hz)(3), of Omega(3) < 0.32, assuming a value of the Hubble parameter of h(100) = 0.71. These new limits are a factor of seven better than the previous best in this frequency band.
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| 10. |
- Evans, P. A., et al.
(författare)
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Swift Follow-up Observations of Candidate Gravitational-wave Transient Events
- 2012
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Ingår i: The Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 203:2
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Tidskriftsartikel (refereegranskat)abstract
- We present the first multi-wavelength follow-up observations of two candidate gravitational-wave (GW) transient events recorded by LIGO and Virgo in their 2009-2010 science run. The events were selected with low latency by the network of GW detectors (within less than 10 minutes) and their candidate sky locations were observed by the Swift observatory (within 12 hr). Image transient detection was used to analyze the collected electromagnetic data, which were found to be consistent with background. Off-line analysis of the GW data alone has also established that the selected GW events show no evidence of an astrophysical origin; one of them is consistent with background and the other one was a test, part of a "blind injection challenge." With this work we demonstrate the feasibility of rapid follow-ups of GW transients and establish the sensitivity improvement joint electromagnetic and GW observations could bring. This is a first step toward an electromagnetic follow-up program in the regime of routine detections with the advanced GW instruments expected within this decade. In that regime, multi-wavelength observations will play a significant role in completing the astrophysical identification of GW sources. We present the methods and results from this first combined analysis and discuss its implications in terms of sensitivity for the present and future instruments.
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| 11. |
- Aasi, J., et al.
(författare)
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Parameter estimation for compact binary coalescence signals with the first generation gravitational-wave detector network
- 2013
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 88:6
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Tidskriftsartikel (refereegranskat)abstract
- Compact binary systems with neutron stars or black holes are one of the most promising sources for ground-based gravitational-wave detectors. Gravitational radiation encodes rich information about source physics; thus parameter estimation and model selection are crucial analysis steps for any detection candidate events. Detailed models of the anticipated waveforms enable inference on several parameters, such as component masses, spins, sky location and distance, that are essential for new astrophysical studies of these sources. However, accurate measurements of these parameters and discrimination of models describing the underlying physics are complicated by artifacts in the data, uncertainties in the waveform models and in the calibration of the detectors. Here we report such measurements on a selection of simulated signals added either in hardware or software to the data collected by the two LIGO instruments and the Virgo detector during their most recent joint science run, including a "blind injection'' where the signal was not initially revealed to the collaboration. We exemplify the ability to extract information about the source physics on signals that cover the neutron-star and black-hole binary parameter space over the component mass range 1M(circle dot)-25M(circle dot) and the full range of spin parameters. The cases reported in this study provide a snapshot of the status of parameter estimation in preparation for the operation of advanced detectors.
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| 12. |
- Aasi, J., et al.
(författare)
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Search for gravitational waves from binary black hole inspiral, merger, and ringdown in LIGO-Virgo data from 2009-2010
- 2013
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 87:2
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Tidskriftsartikel (refereegranskat)abstract
- We report a search for gravitational waves from the inspiral, merger and ringdown of binary black holes (BBH) with total mass between 25 and 100 solar masses, in data taken at the LIGO and Virgo observatories between July 7, 2009 and October 20, 2010. The maximum sensitive distance of the detectors over this period for a (20, 20)M-circle dot coalescence was 300 Mpc. No gravitational wave signals were found. We thus report upper limits on the astrophysical coalescence rates of BBH as a function of the component masses for nonspinning components, and also evaluate the dependence of the search sensitivity on component spins aligned with the orbital angular momentum. We find an upper limit at 90% confidence on the coalescence rate of BBH with nonspinning components of mass between 19 and 28M(circle dot) of 3:3 x 10(-7) mergers Mpc(-3) yr(-1).
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| 13. |
- Aasi, J., et al.
(författare)
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The characterization of Virgo data and its impact on gravitational-wave searches
- 2012
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Ingår i: Classical and Quantum Gravity. - : IOP Publishing. - 1361-6382 .- 0264-9381. ; 29:15
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Tidskriftsartikel (refereegranskat)abstract
- Between 2007 and 2010 Virgo collected data in coincidence with the LIGO and GEO gravitational-wave (GW) detectors. These data have been searched for GWs emitted by cataclysmic phenomena in the universe, by non-axisymmetric rotating neutron stars or from a stochastic background in the frequency band of the detectors. The sensitivity of GW searches is limited by noise produced by the detector or its environment. It is therefore crucial to characterize the various noise sources in a GW detector. This paper reviews the Virgo detector noise sources, noise propagation, and conversion mechanisms which were identified in the three first Virgo observing runs. In many cases, these investigations allowed us to mitigate noise sources in the detector, or to selectively flag noise events and discard them from the data. We present examples from the joint LIGO-GEO-Virgo GW searches to show how well noise transients and narrow spectral lines have been identified and excluded from the Virgo data. We also discuss how detector characterization can improve the astrophysical reach of GW searches.
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| 14. |
- Abadie, J., et al.
(författare)
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Search for gravitational waves from intermediate mass binary black holes
- 2012
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 85:10
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Tidskriftsartikel (refereegranskat)abstract
- We present the results of a weakly modeled burst search for gravitational waves from mergers of nonspinning intermediate mass black holes in the total mass range 100-450 M-circle dot and with the component mass ratios between 1: and 4:1. The search was conducted on data collected by the LIGO and Virgo detectors between November of 2005 and October of 2007. No plausible signals were observed by the search which constrains the astrophysical rates of the intermediate mass black holes mergers as a function of the component masses. In the most efficiently detected bin centered on 88 + 88 M-circle dot, for nonspinning sources, the rate density upper limit is 0.13 per Mpc(3) per Myr at the 90% confidence level.
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| 15. |
- Aasi, J., et al.
(författare)
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Einstein@Home all-sky search for periodic gravitational waves in LIGO S5 data
- 2013
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 87:4
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents results of an all-sky search for periodic gravitational waves in the frequency range [50, 1190] Hz and with frequency derivative range of similar to[-20, 1.1] x 10(-10) Hz s(-1) for the fifth LIGO science run (S5). The search uses a noncoherent Hough-transform method to combine the information from coherent searches on time scales of about one day. Because these searches are very computationally intensive, they have been carried out with the Einstein@Home volunteer distributed computing project. Postprocessing identifies eight candidate signals; deeper follow-up studies rule them out. Hence, since no gravitational wave signals have been found, we report upper limits on the intrinsic gravitational wave strain amplitude h(0). For example, in the 0.5 Hz-wide band at 152.5 Hz, we can exclude the presence of signals with h(0) greater than 7.6 x 10(-25) at a 90% confidence level. This search is about a factor 3 more sensitive than the previous Einstein@Home search of early S5 LIGO data.
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| 16. |
- Pfaller, M.A., et al.
(författare)
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Twelve years of fluconazole in clinical practice : Global-trends in species distribution and fluconazole susceptibility of bloodstream isolates of Candida
- 2004
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Ingår i: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X .- 1469-0691. ; 10:SUPPL. 1, s. 11-23
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Tidskriftsartikel (refereegranskat)abstract
- We determined the species distribution and in-vitro susceptibility of 6082 bloodstream infection (BSI) isolates of Candida spp. collected from 250 medical centres in 32 nations over a 10-year period from 1992 through 2001. The species included 3401 C. albicans, 984 C. glabrata, 796 C. parapsilosis, 585 C. tropicalis, 153 C. krusei, 67 C. lusitaniae, 48 C. guilliermondii, 10 C. famata, 10 C. kefyr, six C. pelliculosa, five C. rugosa, four C. lipolytica, three C. dubliniensis, three C. inconspicua, two C. sake and one isolate each of C. lambica, C. norvegensis and C. zeylanoides. Minimum inhibitory concentration determinations were made using the National Committee for Clinical Laboratory Standards reference broth microdilution method. Variation in the rank order and frequency of the different species of Candida was observed over time and by geographic area. The proportion of BSI due to C. albicans and C. glabrata increased and C. parapsilosis decreased over time in Canada, the USA and Europe. C. glabrata was an infrequent cause of BSI in Latin America and the Asia-Pacific region. Very little variation in fluconazole susceptibility was observed among isolates of C. albicans, C. tropicalis and C. parapsilosis. These species accounted for 78% of all BSI and remained highly susceptible (91-100% susceptible) to fluconazole from 1992 to 2001 irrespective of geographic origin. The prevalence of fluconazole resistance among C. glabrata isolates was variable both over time and among the various countries and regions. Resistance to fluconazole among C. glabrata isolates was greatest in the USA and varied by US census region (range 0-23%). These observations are generally encouraging relative to the sustained usefulness of fluconazole as a systemically active antifungal agent for the treatment of candida BSI. © 2004 Copyright by the European Society of Clinical Microbiology and Infectious Diseases.
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| 17. |
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| 18. |
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| 19. |
- Carmona-Gutierrez, D., et al.
(författare)
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Guidelines and recommendations on yeast cell death nomenclature
- 2018
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Ingår i: Microbial Cell. - : Shared Science Publishers OG. - 2311-2638. ; 5:1, s. 4-31
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Forskningsöversikt (refereegranskat)abstract
- Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research.
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| 20. |
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| 21. |
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| 22. |
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| 23. |
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| 24. |
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| 25. |
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| 26. |
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| 27. |
- Cavalieri, A L, et al.
(författare)
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Clocking femtosecond X rays.
- 2005
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Ingår i: Phys Rev Lett. - 0031-9007. ; 94:11
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Tidskriftsartikel (refereegranskat)abstract
- Linear-accelerator-based sources will revolutionize ultrafast x-ray science due to their unprecedented brightness and short pulse duration. However, time-resolved studies at the resolution of the x-ray pulse duration are hampered by the inability to precisely synchronize an external laser to the accelerator. At the Sub-Picosecond Pulse Source at the Stanford Linear-Accelerator Center we solved this problem by measuring the arrival time of each high energy electron bunch with electro-optic sampling. This measurement indirectly determined the arrival time of each x-ray pulse relative to an external pump laser pulse with a time resolution of better than 60 fs rms.
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| 28. |
- Chasman, Daniel I., et al.
(författare)
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Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function
- 2012
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 21:24, s. 5329-5343
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Tidskriftsartikel (refereegranskat)abstract
- In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P 5.6 10(9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 10(4)2.2 10(7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.
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| 29. |
- Köttgen, Anna, et al.
(författare)
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New loci associated with kidney function and chronic kidney disease
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:5, s. 376-384
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Tidskriftsartikel (refereegranskat)abstract
- Chronic kidney disease (CKD) is a significant public health problem, and recent genetic studies have identified common CKD susceptibility variants. The CKDGen consortium performed a meta-analysis of genome-wide association data in 67,093 individuals of European ancestry from 20 predominantly population-based studies in order to identify new susceptibility loci for reduced renal function as estimated by serum creatinine (eGFRcrea), serum cystatin c (eGFRcys) and CKD (eGFRcrea < 60 ml/min/1.73 m2; n = 5,807 individuals with CKD (cases)). Follow-up of the 23 new genome-wide–significant loci (P < 5 × 10−8) in 22,982 replication samples identified 13 new loci affecting renal function and CKD (in or near LASS2, GCKR, ALMS1, TFDP2, DAB2, SLC34A1, VEGFA, PRKAG2, PIP5K1B, ATXN2, DACH1, UBE2Q2 and SLC7A9) and 7 loci suspected to affect creatinine production and secretion (CPS1, SLC22A2, TMEM60, WDR37, SLC6A13, WDR72 and BCAS3). These results further our understanding of the biologic mechanisms of kidney function by identifying loci that potentially influence nephrogenesis, podocyte function, angiogenesis, solute transport and metabolic functions of the kidney.
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| 30. |
- Pattaro, Cristian, et al.
(författare)
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Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.
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| 31. |
- Pattaro, Cristian, et al.
(författare)
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Genome-Wide Association and Functional Follow-Up Reveals New Loci for Kidney Function
- 2012
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 8:3, s. e1002584-
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Tidskriftsartikel (refereegranskat)abstract
- Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genomewide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.
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| 32. |
- Fritz, D. M., et al.
(författare)
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Ultrafast bond softening in bismuth : Mapping a solid's interatomic potential with X-rays
- 2007
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 315:5812, s. 633-636
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Tidskriftsartikel (refereegranskat)abstract
- Intense femtosecond laser excitation can produce transient states of matter that would otherwise be inaccessible to laboratory investigation. At high excitation densities, the interatomic forces that bind solids and determine many of their properties can be substantially altered. Here, we present the detailed mapping of the carrier density-dependent interatomic potential of bismuth approaching a solid-solid phase transition. Our experiments combine stroboscopic techniques that use a high-brightness linear electron accelerator-based x-ray source with pulse-by-pulse timing reconstruction for femtosecond resolution, allowing quantitative characterization of the interatomic potential energy surface of the highly excited solid.
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| 33. |
- Gaffney, K J, et al.
(författare)
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Observation of structural anisotropy and the onset of liquidlike motion during the nonthermal melting of InSb
- 2005
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 95:12
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Tidskriftsartikel (refereegranskat)abstract
- The melting dynamics of laser excited InSb have been studied with femtosecond x-ray diffraction. These measurements observe the delayed onset of diffusive atomic motion, signaling the appearance of liquidlike dynamics. They also demonstrate that the root-mean-squared displacement in the [111] direction increases faster than in the [110] direction after the first 500 fs. This structural anisotropy indicates that the initially generated fluid differs significantly from the equilibrium liquid.
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| 34. |
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| 35. |
- Hillyard, P. B., et al.
(författare)
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Carrier-density-dependent lattice stability in InSb
- 2007
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 98:12, s. 125501-
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Tidskriftsartikel (refereegranskat)abstract
- The ultrafast decay of the x-ray diffraction intensity following laser excitation of an InSb crystal has been utilized to observe carrier dependent changes in the potential energy surface. For the first time, an abrupt carrier dependent onset for potential energy surface softening and the appearance of accelerated atomic disordering for a very high average carrier density have been observed. Inertial dynamics dominate the early stages of crystal disordering for a wide range of carrier densities between the onset of crystal softening and the appearance of accelerated atomic disordering.
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| 36. |
- Lindenberg, AM, et al.
(författare)
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Atomic-scale visualization of inertial dynamics
- 2005
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 308:5720, s. 392-395
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Tidskriftsartikel (refereegranskat)abstract
- The motion of atoms on interatomic potential energy surfaces is fundamental to the dynamics of liquids and solids. An accelerator-based source of femtosecond x-ray pulses allowed us to follow directly atomic displacements on an optically modified energy landscape, leading eventually to the transition from crystalline solid to disordered liquid. We show that, to first order in time, the dynamics are inertial, and we place constraints on the shape and curvature of the transition-state potential energy surface. Our measurements point toward analogies between this nonequilibrium phase transition and the short-time dynamics intrinsic to equilibrium liquids.
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| 37. |
- Lindenberg, A. M., et al.
(författare)
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X-ray diffuse scattering measurements of nucleation dynamics at femtosecond resolution.
- 2008
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 100:13, s. 135502-1-135502-5
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Tidskriftsartikel (refereegranskat)abstract
- Femtosecond time-resolved small and wide angle x-ray diffuse scattering techniques are applied to investigate the ultrafast nucleation processes that occur during the ablation process in semiconducting materials. Following intense optical excitation, a transient liquid state of high compressibility characterized by large-amplitude density fluctuations is observed and the buildup of these fluctuations is measured in real time. Small-angle scattering measurements reveal snapshots of the spontaneous nucleation of nanoscale voids within a metastable liquid and support theoretical predictions of the ablation process.
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| 38. |
- Morra, Pierluigi
(författare)
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Modelling and control of turbulent and transitional flows
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The dynamics of fluid motion can accurately be described by the Navier– Stokes equations. Manipulating these equations to reduce their complexity but preserving their main characteristics has always been a key research activity in the field of fluid mechanics. Effort has been made to provide high-fidelity models for wall-bounded turbulent flows or reduced-order models for applications such as drag reduction, lift enhancement, or noise suppression. Model order reduction has also been employed for studying the dynamics of the Navier-Stokes equations. In this PhD thesis, the emphasis is on providing computationally inexpensive methods for industrial applications.Numerical simulations are performed to tackle model order reduction for flow control of transitional boundary-layer flows for drag reduction. It is assumed that localized wall sensors and actuators are available, and that only the time signals accessible in experiments are provided. Thus, a method to include unknown high-dimensional input disturbances in a reduced-order model of a transitional boundary-layer flow is presented. The method is applied for the design of an optimal controller for drag reduction through delay of transition. Moreover, the role of the actuator is discussed and a comparison between realistic actuators and actuators computed using optimization methods is presented. Here, the emphasis is on the effectiveness of the actuators for the studied flow control cases.Numerical simulations are also performed to tackle high-fidelity modeling in wall-bounded turbulent flows. The accuracy of the resolvent analysis in predicting the most energetic flow structures in a wall-bounded turbulent flow is quantified for different temporal frequencies. A direct comparison between the predictions from the resolvent analysis and the flow structures identified in DNS data is presented. Moreover, the beneficial effects attained with the inclusion of the Reynolds-stresses via an eddy-viscosity model are clarified for flows with friction Reynolds number up to 1007.
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| 39. |
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| 40. |
- Morra, Pierluigi, et al.
(författare)
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The colour of forcing statistics in resolvent analyses of turbulent channel flows
- 2020
-
Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 907
-
Tidskriftsartikel (refereegranskat)abstract
- In resolvent analyses of turbulent channel flows it has been common practice to neglect or model the nonlinear forcing term that forms the input of the resolvent. However, the spatiotemporal structure of this term is mostly unknown. Here, this nonlinear forcing term is quantified. The Fourier transform of its two-point space-time correlation, its cross-spectral density (CSD), is computed. The CSD is evaluated for two channel flows at friction Reynolds numbers Re-tau = 179 and Re-tau = 543 via direct numerical simulations (DNS). The CSDs are computed for energetic structures typical of buffer-layer and large-scale motions, for different temporal frequencies. It is found that the forcing is structured and that its solenoidal part, which is the only one affecting the velocity field, is the combination of an oblique streamwise vortical forcing and a streamwise component that counteract each other, as in a destructive interference. It is shown that a rank-2 approximation of the forcing, with only the most energetic spectral proper orthogonal decomposition (SPOD) modes, leads to the bulk of the response. Moreover, it is found that the nonlinear forcing term has a non-negligible projection onto the linear sub-optimal forcings of resolvent analysis, which demonstrates that the linear optimal forcing is not representative of the nonlinear forcing. Finally, it is clarified that the Cess eddy-viscosity-modelled forcing improves the accuracy of resolvent analysis prediction because the modelled forcing projects onto the linear sub-optimal forcings similarly to DNS data.
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| 41. |
- Nogueira, Petronio A. S., et al.
(författare)
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Forcing statistics in resolvent analysis : application in minimal turbulent Couette flow
- 2021
-
Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 908
-
Tidskriftsartikel (refereegranskat)abstract
- An analysis of the statistics of the nonlinear terms in resolvent analysis is performed in this work for turbulent Couette flow at Reynolds number 400. Data from a direct numerical simulation of a minimal flow unit is used to compute the covariance matrix of the velocity. From the same data, we computed the nonlinear terms of the Navier-Stokes equations (treated as forcing), which allowed us to compute the covariance matrix of the forcing. The quantitative relation between the two covariances via the resolvent operator is confirmed here for the first time, accounting for relevant signal processing issues related to the windowing procedure for frequency-domain quantities. Such exact correspondence allowed the eduction of the most relevant force components for the dominant structures in this flow, which participate in the self-sustaining cycle of turbulence: (i) streamwise vortices and streaks, and (ii) spanwise-coherent fluctuations of spanwise velocity. The results show a dominance by a subset of the nonlinear terms for the prediction of the full statistics of streamwise vortices and streaks; a single term is seen to be dominant for spanwise motions. A relevant feature observed in these cases is that the forcing covariance is dominated by its first eigenfunction, showing that nonlinear terms also have a coherent structure at low frequencies in this flow. Different forcing components are also coherent between them, which leads to constructive and destructive interferences that greatly modify the flow response. These are key features of forcing 'colour' for the present flow.
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| 42. |
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| 43. |
- Nogueira, P. A. S., et al.
(författare)
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Resolvent analysis in unbounded flows : role of free-stream modes
- 2020
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Ingår i: Theoretical and Computational Fluid Dynamics. - : Springer. - 0935-4964 .- 1432-2250. ; 34:1-2, s. 163-176
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Tidskriftsartikel (refereegranskat)abstract
- The problem of finding optimal forcing and response for unbounded base flows, exemplified by the Blasius boundary layer, is assessed by means of a locally parallel resolvent analysis. A new analysis of previous results in the literature, which stated that a maximum resolvent gain occurs for spanwise wavenumber kz≈ 0.2 , revealed that this result was not domain converged, and larger domains lead to peak amplification for kz→ 0 ; this result is seen to depend strongly on domain size. It is seen that forcing and response modes for low frequency and wavenumber tend to be extended throughout the computational domain, with substantial support in the free stream. Free-stream modes and their gains are found analytically by considering the resolvent operator for uniform flow, and it is seen that low frequencies and wavenumbers lead to a dominance of such free-stream modes in the resolvent analysis of boundary layers. The lack of domain convergence is explained by the analysis, as gains scale with the square of the domain height. We then propose a new approach to evaluate the resolvent gains for this kind of unbounded flows, by means of a weighting function for the chosen norm that neglects response modes above a cut-off height yp, typically placed outside the boundary layer thickness; this ensures that relevant responses will only be sought in a region of interest, which here corresponds to the boundary layer. The method proved to solve the problem raised by the presence of free-stream modes, resulting in domain-converged forcing and response modes with the shape of streamwise vortices and streaks, respectively. The results were also shown to be independent of the choice of the filter parameters, leading to converged gains for the whole spectrum.
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| 44. |
- Nogueira, P. A. S., et al.
(författare)
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Resolvent-based control of streaks in boundary layers
- 2018
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Ingår i: 31st Congress of the International Council of the Aeronautical Sciences, ICAS 2018. - : International Council of the Aeronautical Sciences. - 9783932182884
-
Konferensbidrag (refereegranskat)abstract
- In the present work, we investigate efficient placement of sensors and actuators for closed-loop control of boundary-layer flows. The focus of this work is on the transitional flow cases where perturbation field is dominated by streaks. This is done using a reduced-order model based on resolvent analysis, an approach that also allows us to analyse the sensitivity of the flow response to control. A numerical sensitivity analysis was performed in this first approach, leading to conclusions about best choices of velocity components to be sensed and directions to be forced. Afterwards, we compared the performance between gaussian and shear sensors at the wall, focusing on the damping of the first resolvent gain using these devices. We close the work with the analysis of a plasma actuator, a configuration closer to standard choices for this kind of problem in both simulations and experiments.
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| 45. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 46. |
- Abreu, L. I., et al.
(författare)
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Reduced-order models to analyse coherent structures in turbulent pipe flow
- 2019
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Ingår i: 11th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2019. - : International Symposium on Turbulence and Shear Flow Phenomena, TSFP.
-
Konferensbidrag (refereegranskat)abstract
- Fully resolved direct numerical simulations, performed with a high-order spectral-element method, are used to study coherent structures in turbulent pipe flow at friction Reynolds numbers Reτ = 180 and 550 (El Khoury et al., 2013). The database was analysed using spectral proper orthogonal decomposition (SPOD) so as to identify dominant coherent structures, most of which are of streaky shape. As a reduced-order model for such structures, the linearised flow response to harmonic forcing was computed, and the analysed singular modes of the resolvent operator were analysed. For turbulent flows, this approach amounts to considering the non-linear terms in the Navier–Stokes system as an unknown forcing, treated convenienty as external. Resolvent analysis then allows an identification of the optimal forcing and most amplified flow response; the latter may be related to observed relevant structures obtained by SPOD, especially if the gain between forcing and response is much larger than what is found for suboptimal forcings or if the non-linear forcing is white noise. Results from SPOD and resolvent analysis were extracted for several combinations of frequencies, streamwise and azimuthal wavenumbers. For both Reynolds numbers, good agreement between SPOD and resolvent modes was observed for parameter combinations where the lift-up mechanism is present: optimal forcing from resolvent analysis represents streamwise vortices and the associated response are streaky structures.
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| 47. |
- Abreu, Leandra, I, et al.
(författare)
-
Resolvent modelling of near-wall coherent structures in turbulent channel flow
- 2020
-
Ingår i: International Journal of Heat and Fluid Flow. - : ELSEVIER SCIENCE INC. - 0142-727X .- 1879-2278. ; 85
-
Tidskriftsartikel (refereegranskat)abstract
- Turbulent channel flow was analysed using direct numerical simulations at friction Reynolds numbers Re-tau = 180 and 550. The databases were studied using spectral proper orthogonal decomposition (SPOD) to identify dominant near-wall coherent structures, most of which turn out to be streaks and streamwise vortices. Resolvent analysis was used as a theoretical approach to model such structures, as it allows the identification of the optimal forcing and most amplified flow response; the latter may be related to the observed relevant structures obtained by SPOD, especially if the gain between forcing and response is much larger than what is found for suboptimal forcings or if the non-linear forcing is white noise. Results from SPOD and resolvent analysis were compared for several combinations of frequencies and wavenumbers. For both Reynolds numbers, the best agreement between SPOD and resolvent modes was observed for the cases where the lift-up mechanism from resolvent analysis is present, which are also the cases where the optimal resolvent gain is dominant. These results confirm the outcomes in our previous studies (Abreu et al., 2019; Abreu et al., 2020), where we used a DNS database of a pipe flow for the same Reynolds numbers.
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| 48. |
- Abreu, Leandra, I, et al.
(författare)
-
Spanwise-coherent hydrodynamic waves around flat plates and airfoils
- 2021
-
Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 927
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Tidskriftsartikel (refereegranskat)abstract
- We investigate spanwise-coherent structures in the turbulent flow around airfoils, motivated by their connection with trailing-edge noise. We analyse well-resolved large-eddy simulations (LES) of the flow around NACA 0012 and NACA 4412 airfoils, both at a Reynolds number of 400 000 based on the chord length. Spectral proper orthogonal decomposition performed on the data reveals that the most energetic coherent structures are hydrodynamic waves, extending over the turbulent boundary layers around the airfoils with significant amplitudes near the trailing edge. Resolvent analysis was used to model such structures, using the mean field as a base flow. We then focus on evaluating the dependence of such structures on the domain size, to ensure that they are not an artefact of periodic boundary conditions in small computational boxes. To this end, we performed incompressible LES of a zero-pressure-gradient turbulent boundary layer, for three different spanwise sizes, with the momentum-thickness Reynolds number matching those near the airfoils trailing edge. The same coherent hydrodynamic waves were observed for the three domains. Such waves are accurately modelled as the most amplified flow response from resolvent analysis. The signature of such wide structures is seen in non-premultiplied spanwise wavenumber spectra, which collapse for the three computational domains. These results suggest that the spanwise-elongated structures are not domain-size dependent for the studied simulations, indicating thus the presence of very wide structures in wall-bounded turbulent flows.
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| 49. |
- Abreu, Leandra, I, et al.
(författare)
-
Spectral proper orthogonal decomposition and resolvent analysis of near-wall coherent structures in turbulent pipe flows
- 2020
-
Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 900
-
Tidskriftsartikel (refereegranskat)abstract
- Direct numerical simulations, performed with a high-order spectral-element method, are used to study coherent structures in turbulent pipe flow at friction Reynolds numbers Re-tau = 180 and 550. The database was analysed using spectral proper orthogonal decomposition (SPOD) to identify energetically dominant coherent structures, most of which turn out to be streaks and quasi-streamwise vortices. To understand how such structures can be modelled, the linear flow responses to harmonic forcing were computed using the singular value decomposition of the resolvent operator, using the mean field as a base flow. The SPOD and resolvent analysis were calculated for several combinations of frequencies and wavenumbers, allowing the mapping out of similarities between SPOD modes and optimal responses for a wide range of relevant scales in turbulent pipe flows. In order to explore physical reasons behind the agreement between both methods, an indicator of lift-up mechanism in the resolvent analysis was introduced, activated when optimal forcing is dominated by the wall-normal and azimuthal components, and associated response corresponds to streaks of streamwise velocity. Good agreement between leading SPOD and resolvent modes is observed in a large region of parameter space. In this region, a significant gain separation is found in resolvent analysis, which may be attributed to the strong amplification associated with the lift-up mechanism, here understood as nonlinear forcing terms leading to the appearance of streamwise vortices, which in turn form high-amplitude streaks. For both Reynolds numbers, the observed concordances were generally for structures with large energy in the buffer layer. The results highlight resolvent analysis as a pertinent reduced-order model for coherent structures in wall-bounded turbulence, particularly for streamwise elongated structures corresponding to near-wall streamwise vortices and streaks.
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| 50. |
- Abreu, L. I., et al.
(författare)
-
Wavepackets in turbulent flow over a NACA 4412 airfoil
- 2018
-
Ingår i: 31st Congress of the International Council of the Aeronautical Sciences, ICAS 2018. - : International Council of the Aeronautical Sciences. - 9783932182884
-
Konferensbidrag (refereegranskat)abstract
- Turbulent flow over a NACA 4412 airfoil with an angle of attack AoA = 5◦ was analysed using an incompressible direct numerical simulation (DNS) at chord Reynolds number of Rec = 4 · 105. Snapshots of the flow field were analysed using the method of Spectral Proper Orthogonal Decomposition (SPOD) in frequency domain, in order to extract the dominant coherent structures of the flow. Focus is given to two-dimensional disturbances, known to be most relevant for aeroacoustics. The leading SPOD modes show coherent structures forming a wavepacket, with significant amplitudes in the trailing-edge boundary layer and in the wake. To model coherent structures in the turbulent boundary layer, the optimal harmonic forcing and the associated linear response of the flow were obtained using the singular value decomposition of the linear resolvent operator. The resolvent analysis shows that the leading SPOD modes can be associated to most amplified, linearised flow responses. Furthermore, coherent structures in the wake are modelled as the Kelvin-Helmholtz mode from linear stability theory (LST).
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