| 1. |
- Andersen, M. R., et al.
(författare)
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Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
- 2011
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 21:6, s. 885-897
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Tidskriftsartikel (refereegranskat)abstract
- The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook wholegenome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi
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| 2. |
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| 3. |
- Aguilar, J. A., et al.
(författare)
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Hardware Development for the Radio Neutrino Observatory in Greenland (RNO-G)
- 2022
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Ingår i: 37th International Cosmic Ray Conference, ICRC2021. - Trieste, Italy : Proceedings of Science.
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Konferensbidrag (refereegranskat)abstract
- The Radio Neutrino Observatory in Greenland (RNO-G) is designed to make the first observations of ultra-high energy neutrinos at energies above 10 PeV, playing a unique role in multi-messenger astrophysics as the world's largest in-ice Askaryan radio detection array. The experiment will be composed of 35 autonomous stations deployed over a 5 x 6 km grid near NSF Summit Station in Greenland. The electronics chain of each station is optimized for sensitivity and low power, incorporating 150 - 600 MHz RF antennas at both the surface and in ice boreholes, low-noise amplifiers, custom RF-over-fiber systems, and an FPGA-based phased array trigger. Each station will consume 25 W of power, allowing for a live time of 70% from a solar power system. The communications system is composed of a high-bandwidth LTE network and an ultra-low power LoRaWAN network. I will also present on the calibration and DAQ systems, as well as status of the first deployment of 10 stations in Summer 2021.
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| 4. |
- Anker, A., et al.
(författare)
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Improving sensitivity of the ARIANNA detector by rejecting thermal noise with deep learning
- 2022
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Ingår i: Journal of Instrumentation. - : IOP Publishing. - 1748-0221. ; 17:3
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Tidskriftsartikel (refereegranskat)abstract
- The ARIANNA experiment is an Askaryan detector designed to record radio signals induced by neutrino interactions in the Antarctic ice. Because of the low neutrino flux at high energies (E-nu > 10(16 )eV), the physics output is limited by statistics. Hence, an increase in sensitivity significantly improves the interpretation of data and offers the ability to probe new parameter spaces. The amplitudes of the trigger threshold are limited by the rate of triggering on unavoidable thermal noise fluctuations. We present a real-time thermal noise rejection algorithm that enables the trigger thresholds to be lowered, which increases the sensitivity to neutrinos by up to a factor of two (depending on energy) compared to the current ARIANNA capabilities. A deep learning discriminator, based on a Convolutional Neural Network (CNN), is implemented to identify and remove thermal events in real time. We describe a CNN trained on MC data that runs on the current ARIANNA microcomputer and retains 95% of the neutrino signal at a thermal noise rejection factor of 10(5), compared to a template matching procedure which reaches only 10(2) for the same signal efficiency. Then the results are verified in a lab measurement by feeding in generated neutrino-like signal pulses and thermal noise directly into the ARIANNA data acquisition system. Lastly, the same CNN is used to classify cosmic-rays events to make sure they are not rejected. The network classified 102 out of 104 cosmic-ray events as signal.
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| 5. |
- Anker, A., et al.
(författare)
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Measuring the polarization reconstruction resolution of the ARIANNA neutrino detector with cosmic rays
- 2022
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :4
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Tidskriftsartikel (refereegranskat)abstract
- The ARIANNA detector is designed to detect neutrinos with energies above 10(17) eV. Due to the similarities in generated radio signals, cosmic rays are often used as test beams for neutrino detectors. Some ARIANNA detector stations are equipped with antennas capable of detecting air showers. Since the radio emission properties of air showers are well understood, and the polarization of the radio signal can be predicted from the arrival direction, cosmic rays can be used as a proxy to assess the reconstruction capabilities of the ARIANNA neutrino detector. We report on dedicated efforts of reconstructing the polarization of cosmic-ray radio pulses. After correcting for difference in hardware, the two stations used in this study showed similar performance in terms of event rate and agreed with simulation. Subselecting high quality cosmic rays, the polarizations of these cosmic rays were reconstructed with a resolution of 2.5 degrees (68% containment), which agrees with the expected value obtained from simulation. A large fraction of this resolution originates from uncertainties in the predicted polarization because of the contribution of the subdominant Askaryan effect in addition to the dominant geomagnetic emission. Subselecting events with a zenith angle greater than 70 degrees removes most influence of the Askaryan emission, and, with limited statistics, we found the polarization uncertainty is reduced to 1.3 degrees (68% containment).
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| 6. |
- Benson, Barbara J., et al.
(författare)
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Extreme events, trends, and variability in Northern Hemisphere lake-ice phenology (1855-2005)
- 2012
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Ingår i: Climatic Change. - : Springer Science and Business Media LLC. - 0165-0009 .- 1573-1480. ; 112:2, s. 299-323
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Tidskriftsartikel (refereegranskat)abstract
- Often extreme events, more than changes in mean conditions, have the greatest impact on the environment and human well-being. Here we examine changes in the occurrence of extremes in the timing of the annual formation and disappearance of lake ice in the Northern Hemisphere. Both changes in the mean condition and in variability around the mean condition can alter the probability of extreme events. Using long-term ice phenology data covering two periods 1855-6 to 2004-5 and 1905-6 to 2004-5 for a total of 75 lakes, we examined patterns in long-term trends and variability in the context of understanding the occurrence of extreme events. We also examined patterns in trends for a 30-year subset (1975-6 to 2004-5) of the 100-year data set. Trends for ice variables in the recent 30-year period were steeper than those in the 100- and 150-year periods, and trends in the 150-year period were steeper than in the 100-year period. Ranges of rates of change (days per decade) among time periods based on linear regression were 0.3-1.6 later for freeze, 0.5-1.9 earlier for breakup, and 0.7-4.3 shorter for duration. Mostly, standard deviation did not change, or it decreased in the 150-year and 100-year periods. During the recent 50-year period, standard deviation calculated in 10-year windows increased for all ice measures. For the 150-year and 100-year periods changes in the mean ice dates rather than changes in variability most strongly influenced the significant increases in the frequency of extreme lake ice events associated with warmer conditions and decreases in the frequency of extreme events associated with cooler conditions.
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| 7. |
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| 8. |
- Hague, C F, et al.
(författare)
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Ferrimagnetic order in thin-film Fe3O4 studied by resonant inelastic X-ray scattering
- 2000
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- We have set out to use the ID21 microfocusing beamline to perform resonant inelastic x-ray scattering (RIXS) experiments on magnetic materials. For the first tests and experiments we start off with Fe oxide thin films of potential interest in new technical applications. Of main interest are thin films of Fe3O4 epitaxially grown on alumina. Note that RIXS is particularly well adapted to experiments involving samples on insulating substrates (no charging effects) prepared ex-situ (bulk sensitivity) which can be magnetized (all-photons experiment)....
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| 9. |
- Iannelli, F, et al.
(författare)
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A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks
- 2017
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8, s. 15656-
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Tidskriftsartikel (refereegranskat)abstract
- Of the many types of DNA damage, DNA double-strand breaks (DSBs) are probably the most deleterious. Mounting evidence points to an intricate relationship between DSBs and transcription. A cell system in which the impact on transcription can be investigated at precisely mapped genomic DSBs is essential to study this relationship. Here in a human cell line, we map genome-wide and at high resolution the DSBs induced by a restriction enzyme, and we characterize their impact on gene expression by four independent approaches by monitoring steady-state RNA levels, rates of RNA synthesis, transcription initiation and RNA polymerase II elongation. We consistently observe transcriptional repression in proximity to DSBs. Downregulation of transcription depends on ATM kinase activity and on the distance from the DSB. Our study couples for the first time, to the best of our knowledge, high-resolution mapping of DSBs with multilayered transcriptomics to dissect the events shaping gene expression after DSB induction at multiple endogenous sites.
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| 10. |
- Kurmaev, E. Z., et al.
(författare)
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Spectroscopic observation of polaron-lattice band structure in the conducting polymer polyaniline
- 2001
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Ingår i: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 13:17, s. 3907-3912
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Tidskriftsartikel (refereegranskat)abstract
- We present the results of soft x-ray emission measurements for undoped and protonated polyemeraldine. We show that the polaron-lattice band structure fully accounts for the observed x-ray transitions. A finite spectral intensity of C Kα and N Kα XES is observed at the Fermi level for protonated polyemeraldine, supporting the applicability of the polaronic-metal model for highly conducting polymers.
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