| 1. |
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| 2. |
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| 3. |
- Noguchi, S, et al.
(author)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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In: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Journal article (peer-reviewed)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 4. |
- Leung, J. S.-Y., et al.
(author)
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A Simulation-based Method for Correcting Mode Coupling in CMB Angular Power Spectra
- 2022
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 928:2
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Journal article (peer-reviewed)abstract
- Modern cosmic microwave background (CMB) analysis pipelines regularly employ complex time-domain filters, beam models, masking, and other techniques during the production of sky maps and their corresponding angular power spectra. However, these processes can generate couplings between multipoles from the same spectrum and from different spectra, in addition to the typical power attenuation. Within the context of pseudo-C-l based, MASTER-style analyses, the net effect of the time-domain filtering is commonly approximated by a multiplicative transfer function, F-l , that can fail to capture mode mixing and is dependent on the spectrum of the signal. To address these shortcomings, we have developed a simulation-based spectral correction approach that constructs a two-dimensional transfer matrix, J(ll'), which contains information about mode mixing in addition to mode attenuation. We demonstrate the application of this approach on data from the first flight of the Spider balloon-borne CMB experiment.
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| 5. |
- Ade, P. A. R., et al.
(author)
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A Constraint on Primordial B-modes from the First Flight of the Spider Balloon-borne Telescope
- 2022
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 927:2
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Journal article (peer-reviewed)abstract
- We present the first linear polarization measurements from the 2015 long-duration balloon flight of SPIDER, which is an experiment that is designed to map the polarization of the cosmic microwave background (CMB) on degree angular scales. The results from these measurements include maps and angular power spectra from observations of 4.8% of the sky at 95 and 150 GHz, along with the results of internal consistency tests on these data. While the polarized CMB anisotropy from primordial density perturbations is the dominant signal in this region of sky, Galactic dust emission is also detected with high significance. Galactic synchrotron emission is found to be negligible in the SPIDER bands. We employ two independent foreground-removal techniques to explore the sensitivity of the cosmological result to the assumptions made by each. The primary method uses a dust template derived from Planck data to subtract the Galactic dust signal. A second approach, which constitutes a joint analysis of SPIDER and Planck data in the harmonic domain, assumes a modified-blackbody model for the spectral energy distribution of the dust with no constraint on its spatial morphology. Using a likelihood that jointly samples the template amplitude and r parameter space, we derive 95% upper limits on the primordial tensor-to-scalar ratio from Feldman-Cousins and Bayesian constructions, finding r < 0.11 and r < 0.19, respectively. Roughly half the uncertainty in r derives from noise associated with the template subtraction. New data at 280 GHz from SPIDER´s second flight will complement the Planck polarization maps, providing powerful measurements of the polarized Galactic dust emission.
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| 6. |
- Filippini, J. P., et al.
(author)
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In-Flight Gain Monitoring of SPIDER's Transition-Edge Sensor Arrays
- 2022
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In: Journal of Low Temperature Physics. - : Springer Science and Business Media LLC. - 0022-2291 .- 1573-7357. ; 209:3-4, s. 649-657
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Journal article (peer-reviewed)abstract
- Experiments deploying large arrays of transition-edge sensors (TESs) often require a robust method to monitor gain variations with minimal loss of observing time. We propose a sensitive and non-intrusive method for monitoring variations in TES responsivity using small square waves applied to the TES bias. We construct an estimator for a TES's small-signal power response from its electrical response that is exact in the limit of strong electrothermal feedback. We discuss the application and validation of this method using flight data from SPIDER, a balloon-borne telescope that observes the polarization of the cosmic microwave background with more than 2000 TESs. This method may prove useful for future balloon- and space-based instruments, where observing time and ground control bandwidth are limited.
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| 7. |
- Gambrel, A. E., et al.
(author)
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The XFaster Power Spectrum and Likelihood Estimator for the Analysis of Cosmic Microwave Background Maps
- 2021
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 922:2
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Journal article (peer-reviewed)abstract
- We present the XFaster analysis package, a fast, iterative angular power spectrum estimator based on a diagonal approximation to the quadratic Fisher matrix estimator. It uses Monte Carlo simulations to compute noise biases and filter transfer functions and is thus a hybrid of both Monte Carlo and quadratic estimator methods. In contrast to conventional pseudo-Cℓ–based methods, the algorithm described here requires a minimal number of simulations and does not require them to be precisely representative of the data to estimate accurate covariance matrices for the bandpowers. The formalism works with polarization-sensitive observations and also data sets with identical, partially overlapping, or independent survey regions. The method was first implemented for the analysis of BOOMERanG data and also used as part of the Planck analysis. Here we describe the full, publicly available analysis package, written in Python, as developed for the analysis of data from the 2015 flight of the Spider instrument. The package includes extensions for self-consistently estimating null spectra and estimating fits for Galactic foreground contributions. We show results from the extensive validation of XFaster using simulations and its application to the Spider data set.
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| 8. |
- Ramilowski, JA, et al.
(author)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Journal article (peer-reviewed)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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| 9. |
- Paciaroni, M., et al.
(author)
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Timing of initiation of oral anticoagulants in patients with acute ischemic stroke and atrial fibrillation comparing posterior and anterior circulation strokes
- 2020
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In: European Stroke Journal. - : SAGE Publications. - 2396-9873 .- 2396-9881.
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Journal article (peer-reviewed)abstract
- Introduction: The aim of this study in patients with acute posterior ischaemic stroke (PS) and atrial fibrillation (AF) was to evaluate (1) the risks of recurrent ischaemic event and severe bleeding and (2) these risks in relation with oral anticoagulant therapy (OAT) and its timing. Materials and Methods: Patients with PS were prospectively included; the outcome events of these patients were compared with those of patients with anterior stroke (AS) which were taken from previous registries. The primary outcome was the composite of stroke recurrence, transient ischaemic attack, symptomatic systemic embolism, symptomatic cerebral bleeding and major extracranial bleeding occurring within 90 days from acute stroke. Results: A total of 2470 patients were available for the analysis: 473 (19.1%) with PS and 1997 (80.9%) with AS. Over 90 days, 213 (8.6%) primary outcome events were recorded: 175 (8.7%) in patients with AS and 38 (8.0%) in those with PS. In patients who initiated OAT within 2 days, the primary outcome occurred in 5 out of 95 patients (5.3%) with PS compared to 21 out of 373 patients (4.3%) with AS (OR 1.07; 95% CI 0.39-2.94). In patients who initiated OAT between days 3 and 7, the primary outcome occurred in 3 out of 103 patients (2.9%) with PS compared to 26 out of 490 patients (5.3%) with AS (OR 0.54; 95% CI 0.16-1.80). Discussion: our findings suggest that, when deciding the time to initiate oral anticoagulation, the location of stroke, either anterior or posterior, does not predict the risk of outcome events. Conclusions: Patients with PS or AS and AF appear to have similar risks of ischaemic or haemorrhagic events at 90 days with no difference concerning the timing of initiation of OAT.
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| 10. |
- Iacocca, Ezio, 1986, et al.
(author)
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Spin-current-mediated rapid magnon localisation and coalescence after ultrafast optical pumping of ferrimagnetic alloys
- 2019
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 10:1
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Journal article (peer-reviewed)abstract
- Sub-picosecond magnetisation manipulation via femtosecond optical pumping has attracted wide attention ever since its original discovery in 1996. However, the spatial evolution of the magnetisation is not yet well understood, in part due to the difficulty in experimentally probing such rapid dynamics. Here, we find evidence of a universal rapid magnetic order recovery in ferrimagnets with perpendicular magnetic anisotropy via nonlinear magnon processes. We identify magnon localisation and coalescence processes, whereby localised magnetic textures nucleate and subsequently interact and grow in accordance with a power law formalism. A hydrodynamic representation of the numerical simulations indicates that the appearance of noncollinear magnetisation via optical pumping establishes exchange-mediated spin currents with an equivalent 100% spin polarised charge current density of 10 7 A cm −2 . Such large spin currents precipitate rapid recovery of magnetic order after optical pumping. The magnon processes discussed here provide new insights for the stabilization of desired meta-stable states.
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| 11. |
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| 12. |
- Maznev, A. A., et al.
(author)
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Generation and detection of 50 GHz surface acoustic waves by extreme ultraviolet pulses
- 2021
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In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 119:4
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Journal article (peer-reviewed)abstract
- We use femtosecond extreme ultraviolet pulses derived from a free electron laser to excite and probe surface acoustic waves (SAWs) on the (001) surface of single crystal SrTiO3. SAWs are generated by a pair of 39.9 nm pulses crossed at the sample with the crossing angle defining the SAW wavelength at 84 nm. Detection of SAWs is performed via diffraction of a time-delayed 13.3 nm probe pulse by SAW-induced surface ripples. Despite the low reflectivity of the sample in the extreme ultraviolet range, the reflection mode detection is found to be efficient because of an increase in the diffraction efficiency for shorter wavelengths. We describe a methodology for extracting the SAW attenuation in the presence of a thermal grating, which is based on measuring the decay of oscillations at twice the SAW frequency. The proposed approach can be used to study ultrahigh frequency SAWs in a broad range of materials and will bridge the wave vector gap in surface phonon spectroscopy between Brillouin scattering and He atom scattering.
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| 13. |
- Bemmerer, D., et al.
(author)
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Feasibility of low-energy radiative-capture experiments at the LUNA underground accelerator facility
- 2005
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In: European Physical Journal A. - : Springer Science and Business Media LLC. - 1434-6001 .- 1434-601X. ; 24:2, s. 313-319
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Journal article (peer-reviewed)abstract
- The LUNA (Laboratory Underground for Nuclear Astrophysics) facility has been designed to study nuclear reactions of astrophysical interest. It is located deep underground in the Gran Sasso National Laboratory, Italy. Two electrostatic accelerators, with 50 and 400 kV maximum voltage, in combination with solid and gas target setups allowed to measure the total cross-sections of the radiative-capture reactions 2H2H(p, γ) 3He3Heand 14N14N(p, γ) 15O15Owithin their relevant Gamow peaks. We report on the gamma background in the Gran Sasso laboratory measured by germanium and bismuth germanate detectors, with and without an incident proton beam. A method to localize the sources of beam-induced background using the Doppler shift of emitted gamma rays is presented. The feasibility of radiative-capture studies at energies of astrophysical interest is discussed for several experimental scenarios. © Società Italiana di Fisica/Springer-Verlag 2005.
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| 14. |
- Costantini, H., et al.
(author)
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Recent results of the 14N(p,γ)15O measurement at LUNA
- 2005
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In: Nuclear Physics A. - : Elsevier BV. - 0375-9474 .- 1873-1554. ; 758:1-4 SPEC. ISS., s. 383C-386C
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Journal article (peer-reviewed)abstract
- The 14N(p, γ)15O reaction has been investigated by LUNA at the National Laboratory of Gran Sasso (LNGS) using two different techniques. The first study has been performed using a solid target and detecting the γ-rays coming from the single transitions with a HPGe detector in very close geometry to the target. In a second phase a windowless gas target sorrounded by a nearly 4π BGO summing crystal has been used and the total S-factor has been measured down to Eb = 80 keV. © 2005 Elsevier B.V. All rights reserved.
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| 15. |
- De La Vega Elena, Carlos D., et al.
(author)
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A rare blood group: p phenotype
- 2009
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In: Medicina. - 1648-9144. ; 69:6, s. 651-654
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Journal article (peer-reviewed)abstract
- A rare blood group: p phenotype. A rare blood group is usually defined as the absence of a high prevalence antigen or the absence of several antigens within a single blood group system. These individuals may develop clinically significant red cell antibodies to the high incidence red cell antigens they lack. A 33-year-old alloimmunized woman was referred to our center at the 12th week of her third pregnancy for evaluation and follow up. The laboratory work-up grouped her as belonging to "p" phenotype, associated with difficulties to find compatible blood for transfusion and a high incidence of recurrent miscarriage. At 36 weeks, a baby girl was born by induced labor due to fetal suffering. With a negative direct antiglobulin test but a positive elution test, she was in the neonatology ward for one week receiving luminotherapy. Homozygosity for a missense mutation at position 752 (c.752C > T) in the A4GALT gene was found to be responsible for the p phenotype. This mutation changes a proline to a leucine at codon 251 of the 4-alpha-galactosyltransferase. Recently, due to an imminent chirurgical intervention and the impossibility to have compatible blood available for transfusion. an autologous donation plan was designed to satisfy probable demand. This case showed the need for blood bank facilities capable to respond satisfactorily to these situations in Argentina. This would facilitate the storage of cryopreserved blood from individuals with rare blood groups for homologous use or to develop rare blood donors programs.
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| 16. |
- Formicola, A, et al.
(author)
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Astrophysical S-factor of 14N(p,γ)15O
- 2004
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In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 591:1-2, s. 61-68
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Journal article (peer-reviewed)abstract
- We report on a new measurement of the 14N(p,γ) 15O capture cross section at Ep=140 to 400 keV using the 400 kV LUNA accelerator facility at the Laboratori Nazionali del Gran Sasso (LNGS). The uncertainties have been reduced with respect to previous measurements and their analysis. We have analyzed the data using the R-matrix method and we find that the ground state transition accounts for about 15% of the total S-factor. The main contribution to the S-factor is given by the transition to the 6.79 MeV state. We find a total S(0)=1.7±0.2 keVb, in agreement with recent extrapolations. The result has important consequences for the solar neutrino spectrum as well as for the age of globular clusters. © 2004 Elsevier B.V. All rights reserved.
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| 17. |
- Gray, A. X., et al.
(author)
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Ultrafast terahertz field control of electronic and structural interactions in vanadium dioxide
- 2018
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In: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 98:4
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Journal article (peer-reviewed)abstract
- Vanadium dioxide (VO2), an archetypal correlated-electron material, undergoes an insulator-metal transition near room temperature that exhibits electron-correlation-driven and structurally driven physics. Using ultrafast temperature- and fluence-dependent optical spectroscopy and x-ray scattering, we show that multiple interrelated electronic and structural processes in the nonequilibrium dynamics in VO2 can be disentangled in the time domain. Specifically, following intense subpicosecond terahertz (THz) electric-field excitation, a partial collapse of the insulating gap occurs within the first picosecond. At temperatures sufficiently close to the transition temperature and for THz peak fields above a threshold of approximately 1 MV/cm, this electronic reconfiguration initiates a change in lattice symmetry taking place on a slower timescale. We identify the kinetic energy increase of electrons tunneling in the strong electric field as the driving force, illustrating a promising method to control electronic and structural interactions in correlated materials on an ultrafast timescale.
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| 18. |
- Hashimoto, K, et al.
(author)
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CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
- 2015
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 25:12, s. 1812-1824
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Journal article (peer-reviewed)abstract
- An increasing number of noncoding RNAs (ncRNAs) have been implicated in various human diseases including cancer; however, the ncRNA transcriptome of hepatocellular carcinoma (HCC) is largely unexplored. We used CAGE to map transcription start sites across various types of human and mouse HCCs with emphasis on ncRNAs distant from protein-coding genes. Here, we report that retroviral LTR promoters, expressed in healthy tissues such as testis and placenta but not liver, are widely activated in liver tumors. Despite HCC heterogeneity, a subset of LTR-derived ncRNAs were more than 10-fold up-regulated in the vast majority of samples. HCCs with a high LTR activity mostly had a viral etiology, were less differentiated, and showed higher risk of recurrence. ChIP-seq data show that MYC and MAX are associated with ncRNA deregulation. Globally, CAGE enabled us to build a mammalian promoter map for HCC, which uncovers a new layer of complexity in HCC genomics.
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| 19. |
- Henighan, T., et al.
(author)
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Generation mechanism of terahertz coherent acoustic phonons in Fe
- 2016
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In: PHYSICAL REVIEW B. - 2469-9950. ; 93:22
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Journal article (peer-reviewed)abstract
- We use femtosecond time-resolved hard x-ray scattering to detect coherent acoustic phonons generated during ultrafast laser excitation of ferromagnetic bcc Fe films grown on MgO(001). We observe the coherent longitudinal-acoustic phonons as a function of wave vector through analysis of the temporal oscillations in the x-ray scattering signal. The width of the extracted strain wave front associated with this coherent motion is similar to 100 fs. An effective electronic Gruneisen parameter is extracted within a two-temperature model. However, ab initio calculations show that the phonons are nonthermal on the time scale of the experiment, which calls into question the validity of extracting physical constants by fitting such a two-temperature model.
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| 20. |
- Imbriani, G., et al.
(author)
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S-factor of 14N(p,γ)15O at astrophysical energies
- 2005
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In: European Physical Journal A. - : Springer Science and Business Media LLC. - 1434-6001 .- 1434-601X. ; 25:3, s. 455-466
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Journal article (peer-reviewed)abstract
- The astrophysical S(E) factor of 14N(p,γ)15O has been measured for effective center-of-mass energies between E eff = 119 and 367 keV at the LUNA facility using TiN solid targets and Ge detectors. The data are in good agreement with previous and recent work at overlapping energies. R-matrix analysis reveals that due to the complex level structure of 15O the extrapolated S(0) value is model dependent and calls for additional experimental efforts to reduce the present uncertainty in S(0) to a level of a few percent as required by astrophysical calculations. © Società Italiana di Fisica / Springer-Verlag 2005.
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| 21. |
- Imbriani, G., et al.
(author)
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The bottleneck of CNO burning and the age of Globular Clusters
- 2004
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 420:2, s. 625-629
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Journal article (peer-reviewed)abstract
- The transition between the Main Sequence and the Red Giant Branch in low mass stars is powered by the onset of CNO burning, whose bottleneck is 14N(p, γ) 15O. The LUNA collaboration has recently improved the low energy measurements of the cross section of this key reaction. We analyse the impact of the revised reaction rate on the estimate of the Globular Cluster ages, as derived from the turnoff luminosity. We found that the age of the oldest Globular Clusters should be increased by about 0.7-1 Gyr with respect to the current estimates.
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| 22. |
- Trautvetter, H P, et al.
(author)
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Ground state capture in 14N(p,γ)15O studied above the 259 keV resonance at LUNA
- 2008
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In: Journal of Physics G. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 35:1
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Journal article (peer-reviewed)abstract
- We report on a new measurement of 14N(p,γ)15O for the ground state capture transition at Ep = 360, 380 and 400 keV, using the 400 kV LUNA accelerator. The true coincidence summing effect - the major source of error in the ground state capture determination - has been significantly reduced by using a Clover-type gamma detector. © 2008 IOP Publishing Ltd.
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| 23. |
- Chen, Z., et al.
(author)
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Ultrafast Self-Induced X-Ray Transparency and Loss of Magnetic Diffraction
- 2018
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In: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 121:13
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Journal article (peer-reviewed)abstract
- Using ultrafast similar or equal to 2.5 fs and similar or equal to 25 fs self-amplified spontaneous emission pulses of increasing intensity and a novel experimental scheme, we report the concurrent increase of stimulated emission in the forward direction and loss of out-of-beam diffraction contrast for a Co/Pd multilayer sample. The experimental results are quantitatively accounted for by a statistical description of the pulses in conjunction with the optical Bloch equations. The dependence of the stimulated sample response on the incident intensity, coherence time, and energy jitter of the employed pulses reveals the importance of increased control of x-ray free electron laser radiation.
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| 24. |
- Curbis, F, et al.
(author)
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HIGHLIGHTS FROM THE CONCEPTUAL DESIGN REPORT OF THE SOFT X-RAY LASER AT MAX IV
- 2021
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In: Proceedings of IPAC2021.
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Conference paper (other academic/artistic)abstract
- The SXL (Soft X-ray Laser) project developed a conceptual design for a soft X-ray Free Electron Laser (FEL) in the 1-5 nm wavelength range, driven by the existing MAX IV 3 GeV linac. In this contribution we will focus on the FEL operation modes developed for the first phase of the project based on two different linac modes. The design work was supported by the Knut and Alice Wallenberg foundation and by several Swedish universities and organizations (
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| 25. |
- Dias, J D, et al.
(author)
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Targeted cancer immunotherapy with oncolytic adenovirus coding for a fully human monoclonal antibody specific for CTLA-4
- 2012
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In: Gene Therapy. - : Springer Science and Business Media LLC. - 0969-7128 .- 1476-5462. ; 19:10, s. 988-998
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Journal article (peer-reviewed)abstract
- Promising clinical results have been achieved with monoclonal antibodies (mAbs) such as ipilimumab and tremelimumab that block cytotoxic T lymphocyte-associated antigen-4 (CTLA-4, CD152). However, systemic administration of these agents also has the potential for severe immune-related adverse events. Thus, local production might allow higher concentrations at the target while reducing systemic side effects. We generated a transductionally and transcriptionally targeted oncolytic adenovirus Ad5/3-Δ24aCTLA4 expressing complete human mAb specific for CTLA-4 and tested it in vitro, in vivo and in peripheral blood mononuclear cells (PBMCs) of normal donors and patients with advanced solid tumors. mAb expression was confirmed by western blotting and immunohistochemistry. Biological functionality was determined in a T-cell line and in PBMCs from cancer patients. T cells of patients, but not those of healthy donors, were activated by an anti-CTLA4mAb produced by Ad5/3-Δ24aCTLA4. In addition to immunological effects, a direct anti-CTLA-4-mediated pro-apoptotic effect was observed in vitro and in vivo. Local production resulted in 43-fold higher (P<0.05) tumor versus plasma anti-CTLA4mAb concentration. Plasma levels in mice remained below what has been reported safe in humans. Replication-competent Ad5/3-Δ24aCTLA4 resulted in 81-fold higher (P<0.05) tumor mAb levels as compared with a replication-deficient control. This is the first report of an oncolytic adenovirus producing a full-length human mAb. High mAb concentrations were seen at tumors with lower systemic levels. Stimulation of T cells of cancer patients by Ad5/3-Δ24aCTLA4 suggests feasibility of testing the approach in clinical trials.
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