| 1. |
- 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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| 2. |
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| 3. |
- 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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| 4. |
- Kovalev, S., et al.
(author)
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Selective THz control of magnetic order : new opportunities from superradiant undulator sources
- 2018
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In: Journal of Physics D. - : IOP Publishing. - 0022-3727 .- 1361-6463. ; 51:11
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Journal article (peer-reviewed)abstract
- Recent advancements of accelerator technology enable the generation of carrier-envelope-phase stable THz pulses with high fields at adjustable high repetition rates. The appropriate choice of THz radiator allows generation of narrow-band, spectrally dense, multicycle THz transients of tunable THz frequency which are ideally suited to selectively excite low-energy excitations such as magnons or phonons. They also allow one to study the frequency dependence of nonresonant THz-field interactions with various order parameters with high dynamic range. In this paper, we discuss the future prospects of this new type of THz light source for studying the coherent control of magnetic order based on recent results.
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| 5. |
- Andersen, J., et al.
(author)
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The soft X-ray laser project at MAX IV
- 2017
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In: IPAC 2017 - Proceedings of the 8th International Particle Accelerator Conference. - : Joint Accelerator Conferences Website - JACoW. - 9783954501823 ; , s. 2760-2762
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Conference paper (peer-reviewed)abstract
- A Soft X-ray Laser (SXL) beamline utilising FEL technology is being designed for the Short Pulse Facility (SPF) at the MAX IV Laboratory. A conceptual design study has been started following on the scientific case already prepared in collaboration between several Swedish Universities and driven by a strong (Swedish) user demand. The baseline goal of the SXL beamline is to generate intense and short pulses in the range 1-5 nm (0.2-1 keV). The system is building on the MAX IV linac system, already today providing 100 fs 3 GeV and pulses compressed to 100 fs for other applications within the SPF. As a special feature we foresee a variety of pump-probe capabilities.
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| 6. |
- Bonetti, Stefano, et al.
(author)
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THz-Driven Ultrafast Spin-Lattice Scattering in Amorphous Metallic Ferromagnets
- 2016
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 117:8
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Journal article (peer-reviewed)abstract
- We use single-cycle THz fields and the femtosecond magneto-optical Kerr effect to, respectively, excite and probe the magnetization dynamics in two thin-film ferromagnets with different lattice structures: crystalline Fe and amorphous CoFeB. We observe Landau-Lifshitz-torque magnetization dynamics of comparable magnitude in both systems, but only the amorphous sample shows ultrafast demagnetization caused by the spin-lattice depolarization of the THz-induced ultrafast spin current. Quantitative modeling shows that such spin-lattice scattering events occur on similar time scales than the conventional spin conserving electronic scattering (similar to 30 fs). This is significantly faster than optical laser-induced demagnetization. THz conductivity measurements point towards the influence of lattice disorder in amorphous CoFeB as the driving force for enhanced spin-lattice scattering.
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| 7. |
- Curbis, F., et al.
(author)
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Status of the soft X-ray laser (SXL) project at the Max IV laboratory
- 2019
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In: Proceedings of the 39th International Free-Electron Laser Conference, FEL 2019. - : JACoW Publishing. - 9783954502103 ; , s. 749-752
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Conference paper (peer-reviewed)abstract
- A Soft X-ray Laser project (the SXL) aiming to produce FEL radiation in the range of 1 to 5 nm is currently in a conceptual design phase and a report on the design is expected to be delivered by March 2021. The FEL will be driven by the existing 3 GeV linac at MAX IV laboratory, which also serves as injector for the two storage rings. The science case has been pushed by a large group of mainly Swedish users and consists of experiments ranging from AMO physics to condensed matter, chemistry and imaging in life science. In this contribution, we will present the current conceptual design of the accelerator and the FEL operation modes together with a general overview of the beamline and experimental station. In particular design options for the FEL will be discussed in conjunction with the features of the electron beam from the MAX IV linac and the connection with the proposed experiments.
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| 8. |
- 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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| 9. |
- 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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| 10. |
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