| 1. |
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| 2. |
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| 3. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 4. |
- Bousquet, J, et al.
(författare)
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Nrf2-interacting nutrients and COVID-19: time for research to develop adaptation strategies
- 2020
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Ingår i: Clinical and translational allergy. - : Wiley. - 2045-7022. ; 10:1, s. 58-
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Tidskriftsartikel (refereegranskat)abstract
- There are large between- and within-country variations in COVID-19 death rates. Some very low death rate settings such as Eastern Asia, Central Europe, the Balkans and Africa have a common feature of eating large quantities of fermented foods whose intake is associated with the activation of the Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) anti-oxidant transcription factor. There are many Nrf2-interacting nutrients (berberine, curcumin, epigallocatechin gallate, genistein, quercetin, resveratrol, sulforaphane) that all act similarly to reduce insulin resistance, endothelial damage, lung injury and cytokine storm. They also act on the same mechanisms (mTOR: Mammalian target of rapamycin, PPARγ:Peroxisome proliferator-activated receptor, NFκB: Nuclear factor kappa B, ERK: Extracellular signal-regulated kinases and eIF2α:Elongation initiation factor 2α). They may as a result be important in mitigating the severity of COVID-19, acting through the endoplasmic reticulum stress or ACE-Angiotensin-II-AT1R axis (AT1R) pathway. Many Nrf2-interacting nutrients are also interacting with TRPA1 and/or TRPV1. Interestingly, geographical areas with very low COVID-19 mortality are those with the lowest prevalence of obesity (Sub-Saharan Africa and Asia). It is tempting to propose that Nrf2-interacting foods and nutrients can re-balance insulin resistance and have a significant effect on COVID-19 severity. It is therefore possible that the intake of these foods may restore an optimal natural balance for the Nrf2 pathway and may be of interest in the mitigation of COVID-19 severity.
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| 5. |
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| 6. |
- Adcox, K, et al.
(författare)
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Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC: Experimental evaluation by the PHENIX Collaboration
- 2005
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Ingår i: Nuclear Physics, Section A. - : Elsevier BV. - 0375-9474. ; 757:1-2, s. 184-283
-
Forskningsöversikt (refereegranskat)abstract
- Extensive experimental data from high-energy nucleus-nucleus collisions were recorded using the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). The comprehensive set of measurements from the first three years of RHIC operation includes charged particle multiplicities, transverse energy, yield ratios and spectra of identified hadrons in a wide range of transverse momenta (PT), elliptic flow, two-particle correlations, nonstatistical fluctuations, and suppression of particle production at high PT. The results are examined with an emphasis on implications for the formation of a new state of dense matter. We find that the state of matter created at RHIC cannot be described in terms of ordinary color neutral hadrons.
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| 7. |
- Adcox, K, et al.
(författare)
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PHENIX detector overview
- 2003
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 499:2-3, s. 469-479
-
Tidskriftsartikel (refereegranskat)abstract
- The PHENIX detector is designed to perform a broad study of A-A, p-A, and p-p collisions to investigate nuclear matter under extreme conditions. A wide variety of probes, sensitive to all timescales, are used to study systematic variations with species and energy as well as to measure the spin structure of the nucleon. Designing for the needs of the heavy-ion and polarized-proton programs has produced a detector with unparalleled capabilities. PHENIX measures electron and muon pairs, photons, and hadrons with excellent energy and momentum resolution. The detector consists of a large number of subsystems that are discussed in other papers in this volume. The overall design parameters of the detector are presented. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 8. |
- Chumak, A. V., et al.
(författare)
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Advances in Magnetics Roadmap on Spin-Wave Computing
- 2022
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Ingår i: IEEE Transactions on Magnetics. - 0018-9464. ; 58:6
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Tidskriftsartikel (refereegranskat)abstract
- Magnonics addresses the physical properties of spin waves and utilizes them for data processing. Scalability down to atomic dimensions, operation in the GHz-to-THz frequency range, utilization of nonlinear and nonreciprocal phenomena, and compatibility with CMOS are just a few of many advantages offered by magnons. Although magnonics is still primarily positioned in the academic domain, the scientific and technological challenges of the field are being extensively investigated, and many proof-of-concept prototypes have already been realized in laboratories. This roadmap is a product of the collective work of many authors that covers versatile spin-wave computing approaches, conceptual building blocks, and underlying physical phenomena. In particular, the roadmap discusses the computation operations with Boolean digital data, unconventional approaches like neuromorphic computing, and the progress towards magnon-based quantum computing. The article is organized as a collection of sub-sections grouped into seven large thematic sections. Each sub-section is prepared by one or a group of authors and concludes with a brief description of current challenges and the outlook of further development for each research direction. Author
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| 9. |
- Adcox, K, et al.
(författare)
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Flow Measurements via Two-Particle Azimuthal Correlations in Au+Au Collisions at sqrt[sNN]=130 GeV
- 2002
-
Ingår i: Physical Review Letters. - 1079-7114. ; 89
-
Tidskriftsartikel (refereegranskat)abstract
- Two-particle azimuthal correlation functions are presented for charged hadrons produced in Au+Au collisions at the Relativistic Heavy Ion Collider (sqrt[sNN]=130 GeV). The measurements permit determination of elliptic flow without event-by-event estimation of the reaction plane. The extracted elliptic flow values (v2) show significant sensitivity to both the collision centrality and the transverse momenta of emitted hadrons, suggesting rapid thermalization and relatively strong velocity fields. When scaled by the eccentricity of the collision zone ε, the scaled elliptic flow shows little or no dependence on centrality for charged hadrons with relatively low pT. A breakdown of this ε scaling is observed for charged hadrons with pT >1.0 GeV/c.
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| 10. |
- Adcox, K, et al.
(författare)
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Transverse-mass dependence of two-pion correlations in Au+Au collisions at root(NN)-N-S=130 GeV
- 2002
-
Ingår i: Physical Review Letters. - 1079-7114. ; 88:19
-
Tidskriftsartikel (refereegranskat)abstract
- Two-pion correlations in roots(NN) = 130 GeV Au+Au collisions at RHIC have been measured over a broad range of pair transverse momentum k(T) by the PHENIX experiment at RHIC. The k(T) dependent transverse radii are similar to results from heavy-ion collisions at roots(NN) = 4.1 , 4.9, and 17.3 GeV, whereas the longitudinal radius increases monotonically with beam energy. The ratio of the outwards to sidewards transverse radii (R-out/R-side) is consistent with unity and independent of k(T) .
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| 11. |
- Adcox, K, et al.
(författare)
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Centrality dependence of the high (PT) charged hadron suppression in Au+Au collisions at root s(NN)=130 GeV
- 2003
-
Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 561:1-2, s. 82-92
-
Tidskriftsartikel (refereegranskat)abstract
- PHENIX has measured the centrality dependence of charged hadron p(T) spectra from Au +An collisions at root(s)NN = 130 GeV The truncated mean p(T) decreases with centrality for p(T) > 2 GeV/c, indicating an apparent reduction of the contribution from hard scattering to high p(T) hadrdn production. For central collisions the yield at high p(T) is shown to be suppressed compared to binary nucleon-nucleon collision scaling of p + p, data. This suppression is monotonically increasing with centrality, but most of the change occurs below 30% centrality, i.e., for collisions with less than similar to140 participating nucleons. The observed p(T) and centrality dependence is consistent with the particle production predicted by models including hard scattering and subsequent energy loss of the scattered partons in the dense matter created in the collisions. (C) 2003 Published by Elsevier Science B.V.
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| 12. |
- Adcox, K, et al.
(författare)
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Event-by-event fluctuations in mean p(T) and mean E(T) in root s(NN)=130 GeVAu+Au collisions
- 2002
-
Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 66:2
-
Tidskriftsartikel (refereegranskat)abstract
- Distributions of event-by-event fluctuations of the mean transverse momentum and mean transverse energy near mid-rapidity have been measured in Au+Au collisions at roots(NN)=130 GeV at the Relativistic Heavy-Ion Collider. By comparing the distributions to what is expected for statistically independent particle emission, the magnitude of nonstatistical fluctuations in mean transverse momentum is determined to be consistent with zero. Also, no significant nonrandom fluctuations in mean transverse energy are observed. By constructing a fluctuation model with two event classes that preserve the mean and variance of the semi-inclusive p(T) or e(T) spectra, we exclude a region of fluctuations in roots(NN)=130 GeV Au+Au collisions.
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| 13. |
- Adcox, K, et al.
(författare)
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Measurement of Lambda and (Lambda)over-bar particles in Au plus Au collisions at root s(NN)=130 GeV
- 2002
-
Ingår i: Physical Review Letters. - 1079-7114. ; 89:9
-
Tidskriftsartikel (refereegranskat)abstract
- We present results on the measurement of Lambda and (&ULambda;) over bar production in Au+Au collisions at roots(NN)=130 GeV with the PHENIX detector at the Relativistic Heavy Ion Collider. The transverse momentum spectra were measured for minimum bias and for the 5% most central events. The (&ULambda;) over bar/Lambda ratios are constant as a function of p(T) and the number of participants. The measured net Lambda density is significantly larger than predicted by models based on hadronic strings (e.g., HIJING) but in approximate agreement with models which include the gluon-junction mechanism.
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| 14. |
- Adcox, K, et al.
(författare)
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Measurement of single electrons and implications for charm production in Au+Au collisions at root(NN)-N-S=130 GeV
- 2002
-
Ingår i: Physical Review Letters. - 1079-7114. ; 88:19
-
Tidskriftsartikel (refereegranskat)abstract
- Transverse momentum spectra of electrons from Au+Au collisions at roots(NN) = 130 GeV have been measured at midrapidity by the PHENIX experiment at the Relativistic Heavy Ion Collider. The spectra show an excess above the background from photon conversions and light hadron decays. The electron signal is consistent with that expected from semileptonic decays of charm. The yield of the electron signal dN(e)/dy for p(T) > 0.8 GeV/c is 0.025 +/- 0.004(stat) +/- 0.010( syst) in central collisions, and the corresponding charm cross section is 380 +/- 60(stat) +/- 200(syst ) mub per binary nucleon-nucleon collision.
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| 15. |
- Adcox, K, et al.
(författare)
-
Net charge fluctuations in Au+Au interactions root s(NN)=130 GeV
- 2002
-
Ingår i: Physical Review Letters. - 1079-7114. ; 89
-
Tidskriftsartikel (refereegranskat)abstract
- Data from Au+ Au interactions at s(NN)=130 GeV, obtained with the PHENIX detector at the Relativistic Heavy-Ion Collider, are used to investigate local net charge fluctuations among particles produced near midrapidity. According to recent suggestions, such fluctuations may carry information from the quark-gluon plasma. This analysis shows that the fluctuations are dominated by a stochastic distribution of particles, but are also sensitive to other effects, like global charge conservation and resonance decays.
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| 16. |
- Adcox, K, et al.
(författare)
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Suppression of hadrons with large transverse momentum in central Au+Au collisions at root s(NN)=130 GeV
- 2002
-
Ingår i: Physical Review Letters. - 1079-7114. ; 88:2
-
Tidskriftsartikel (refereegranskat)abstract
- Transverse momentum spectra for charged hadrons and for neutral pions in the range 1 Gev/c < P-T < 5 GeV/c have been measured by the PHENIX experiment at RHIC in Au + Au collisions at rootS(NN) = 130 GeV. At high p(T) the spectra from peripheral nuclear collisions are consistent with scaling the spectra from p + p collisions by the average number of binary nucleon-nucleon collisions. The spectra from central collisions are significantly suppressed when compared to the binary-scaled p + p expectation, and also when compared to similarly binary-scaled peripheral collisions, indicating a novel nuclear-medium effect in central nuclear collisions at RHIC energies.
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| 17. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
-
Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 18. |
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| 19. |
- Mlecnik, B, et al.
(författare)
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Clinical Performance of the Consensus Immunoscore in Colon Cancer in the Asian Population from the Multicenter International SITC Study
- 2022
-
Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 14:18
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: In this study, we evaluated the prognostic value of Immunoscore in patients with stage I–III colon cancer (CC) in the Asian population. These patients were originally included in an international study led by the Society for Immunotherapy of Cancer (SITC) on 2681 patients with AJCC/UICC-TNM stages I–III CC. METHODS: CD3+ and cytotoxic CD8+ T-lymphocyte densities were quantified in the tumor and invasive margin by digital pathology. The association of Immunoscore with prognosis was evaluated for time to recurrence (TTR), disease-free survival (DFS), and overall survival (OS). RESULTS: Immunoscore stratified Asian patients (n = 423) into different risk categories and was not impacted by age. Recurrence-free rates at 3 years were 78.5%, 85.2%, and 98.3% for a Low, Intermediate, and High Immunoscore, respectively (HR[Low-vs-High] = 7.26 (95% CI 1.75−30.19); p = 0.0064). A High Immunoscore showed a significant association with prolonged TTR, OS, and DFS (p < 0.05). In Cox multivariable analysis stratified by center, Immunoscore association with TTR was independent (HR[Low-vs-Int+High] = 2.22 (95% CI 1.10–4.55) p = 0.0269) of the patient’s gender, T-stage, N-stage, sidedness, and MSI status. A significant association of a High Immunoscore with prolonged TTR was also found among MSS (HR[Low-vs-Int+High] = 4.58 (95% CI 2.27−9.23); p ≤ 0.0001), stage II (HR[Low-vs-Int+High] = 2.72 (95% CI 1.35−5.51); p = 0.0052), low-risk stage-II (HR[Low-vs-Int+High] = 2.62 (95% CI 1.21−5.68); p = 0.0146), and high-risk stage II patients (HR[Low-vs-Int+High] = 3.11 (95% CI 1.39−6.91); p = 0.0055). CONCLUSION: A High Immunoscore is significantly associated with the prolonged survival of CC patients within the Asian population.
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| 20. |
- Okada, Yukinori, et al.
(författare)
-
Genetics of rheumatoid arthritis contributes to biology and drug discovery
- 2014
-
Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 506:7488, s. 376-381
-
Tidskriftsartikel (refereegranskat)abstract
- A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA)(1). Here we performed a genome-wide association study meta-analysis in a total of >100,000 subjects of European and Asian ancestries (29,880 RA cases and 73,758 controls), by evaluating similar to 10 million single-nucleotide polymorphisms. We discovered 42 novel RA risk loci at a genome-wide level of significance, bringing the total to 101 (refs 2-4). We devised an in silico pipeline using established bioinformatics methods based on functional annotation(5), cis-acting expression quantitative trait loci(6) and pathway analyses(7-9)-as well as novel methods based on genetic overlap with human primary immunodeficiency, haematological cancer somatic mutations and knockout mouse phenotypes-to identify 98 biological candidate genes at these 101 risk loci. We demonstrate that these genes are the targets of approved therapies for RA, and further suggest that drugs approved for other indications may be repurposed for the treatment of RA. Together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to RA pathogenesis, and provides empirical evidence that the genetics of RA can provide important information for drug discovery.
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| 21. |
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| 22. |
- Barthelmi, K., et al.
(författare)
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Atomistic defects as single-photon emitters in atomically thin MoS2
- 2020
-
Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 117:7
-
Tidskriftsartikel (refereegranskat)abstract
- Precisely positioned and scalable single-photon emitters (SPEs) are highly desirable for applications in quantum technology. This Perspective discusses single-photon-emitting atomistic defects in monolayers of MoS2 that can be generated by focused He-ion irradiation with few nanometers positioning accuracy. We present the optical properties of the emitters and the possibilities to implement them into photonic and optoelectronic devices. We showcase the advantages of the presented emitters with respect to atomistic positioning, scalability, long (microsecond) lifetime, and a homogeneous emission energy within ensembles of the emitters. Moreover, we demonstrate that the emitters are stable in energy on a timescale exceeding several weeks and that temperature cycling narrows the ensembles' emission energy distribution.
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| 23. |
- Dub, S. N., et al.
(författare)
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Theoretical shear strength and the onset of plasticity in nanodeformation of cubic boron nitride
- 2017
-
Ingår i: Journal of Superhard Materials. - 1063-4576. ; 39:2, s. 88-98
-
Tidskriftsartikel (refereegranskat)abstract
- The nanoindentation in the continuous stiffness measurement mode was used to investigate the onset of plasticity at the nanodeformation of cubic boron nitride (cBN). This technique allows us to reveal an elastic-plastic transition in the contact and to measure the yield strength of cBN at the nanoscale. An abrupt elastoplastic transition (a pop-in) was observed in the (111) cBN single crystal as a result of a homogeneous or heterogeneous nucleation of dislocations in the previously dislocations-free region under the contact. The analysis of the data obtained at the homogeneous nucleation of dislocations in the contact region made it possible to experimentally estimate the theoretical shear strength of cBN and its ideal (elastic) hardness. In a sample of the fine-grained cBN with a nanotwinned substructure a smooth elastoplastic transition was observed in consequence of the propagation and multiplication of already existing dislocations in the contact region.
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| 24. |
- Geach, J. E., et al.
(författare)
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ALMA OBSERVATIONS OF Ly alpha BLOB 1 : HALO SUBSTRUCTURE ILLUMINATED FROM WITHIN
- 2016
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 832:1
-
Tidskriftsartikel (refereegranskat)abstract
- We present new Atacama Large Millimeter/Submillimeter Array (ALMA) 850 mu m continuum observations of the original Ly alpha Blob (LAB) in the SSA22 field at z = 3.1 (SSA22-LAB01). The ALMA map resolves the previously identified submillimeter source into three components with a total flux density of S-850 = 1.68 +/- 0.06 mJy, corresponding to a star-formation rate of similar to 150M(circle dot) yr(-1). The submillimeter sources are associated with several faint (m approximate to 27 mag) rest-frame ultraviolet sources identified in Hubble Space Telescope Imaging Spectrograph (STIS) clear filter imaging (lambda approximate to 5850 angstrom). One of these companions is spectroscopically confirmed with the Keck Multi-Object Spectrometer For Infra-Red Exploration to lie within 20 projected kpc and 250 km s(-1) of one of the ALMA components. We postulate that some of these STIS sources represent a population of low-mass star-forming satellites surrounding the central submillimeter sources, potentially contributing to their growth and activity through accretion. Using a high-resolution cosmological zoom simulation of a 10(13)M(circle dot) halo at z = 3, including stellar, dust, and Ly alpha radiative transfer, we can model the ALMA + STIS observations and demonstrate that Ly alpha photons escaping from the central submillimeter sources are expected to resonantly scatter in neutral hydrogen, the majority of which is predicted to be associated with halo substructure. We show how this process gives rise to extended Ly alpha emission with similar surface brightness and morphology to observed giant LABs.
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| 25. |
- Brem, Samuel, 1991, et al.
(författare)
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Intrinsic lifetime of higher excitonic states in tungsten diselenide monolayers
- 2019
-
Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3372 .- 2040-3364. ; 11:25, s. 12381-12387
-
Tidskriftsartikel (refereegranskat)abstract
- © 2019 The Royal Society of Chemistry. The reduced dielectric screening in atomically thin transition metal dichalcogenides allows to study the hydrogen-like series of higher exciton states in optical spectra even at room temperature. The width of excitonic peaks provides information about the radiative decay and phonon-assisted scattering channels limiting the lifetime of these quasi-particles. While linewidth studies so far have been limited to the exciton ground state, encapsulation with hBN has recently enabled quantitative measurements of the broadening of excited exciton resonances. Here, we present a joint experiment-theory study combining microscopic calculations with spectroscopic measurements on the intrinsic linewidth and lifetime of higher exciton states in hBN-encapsulated WSe2 monolayers. Surprisingly, despite the increased number of scattering channels, we find both in theory and experiment that the linewidth of higher excitonic states is similar or even smaller compared to the ground state. Our microscopic calculations ascribe this behavior to a reduced exciton-phonon scattering efficiency for higher excitons due to spatially extended orbital functions.
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| 26. |
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| 27. |
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| 28. |
- Ito, H., et al.
(författare)
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Comparison of analytical methods for profiling N- and O-linked glycans from cultured cell lines
- 2016
-
Ingår i: Glycoconjugate Journal. - : Springer Science and Business Media LLC. - 0282-0080 .- 1573-4986. ; 33:3, s. 405-415
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Tidskriftsartikel (refereegranskat)abstract
- The Human Disease Glycomics/Proteome Initiative (HGPI) is an activity in the Human Proteome Organization (HUPO) supported by leading researchers from international institutes and aims at development of disease-related glycomics/glycoproteomics analysis techniques. Since 2004, the initiative has conducted three pilot studies. The first two were N- and O-glycan analyses of purified transferrin and immunoglobulin-G and assessed the most appropriate analytical approach employed at the time. This paper describes the third study, which was conducted to compare different approaches for quantitation of N- and O-linked glycans attached to proteins in crude biological samples. The preliminary analysis on cell pellets resulted in wildly varied glycan profiles, which was probably the consequence of variations in the pre-processing sample preparation methodologies. However, the reproducibility of the data was not improved dramatically in the subsequent analysis on cell lysate fractions prepared in a specified method by one lab. The study demonstrated the difficulty of carrying out a complete analysis of the glycome in crude samples by any single technology and the importance of rigorous optimization of the course of analysis from preprocessing to data interpretation. It suggests that another collaborative study employing the latest technologies in this rapidly evolving field will help to realize the requirements of carrying out the large-scale analysis of glycoproteins in complex cell samples.
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| 29. |
- Mobasher, B., et al.
(författare)
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Photometric redshifts of galaxies in COSMOS
- 2007
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Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 172:1, s. 117-131
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Tidskriftsartikel (refereegranskat)abstract
- We present photometric redshifts for the COSMOS survey derived from a new code, optimized to yield accurate and reliable redshifts and spectral types of galaxies down to faint magnitudes and redshifts out to z similar to 1.2. The technique uses chi (2) template fitting, combined with luminosity function priors and with the option to estimate the internal extinction [ or E( B-V)]. The median most probable redshift, best-fit spectral type and reddening, absolute magnitude, and stellarmass are derived in addition to the full redshift probability distributions. Using simulations with sampling and noise similar to those in COSMOS, the accuracy and reliability is estimated for the photometric redshifts as a function of the magnitude limits of the sample, S/N ratios, and the number of bands used. We find from the simulations that the ratio of derived 95% confidence interval in the chi (2) probability distribution to the estimated photometric redshift (D-95) can be used to identify and exclude the catastrophic failures in the photometric redshift estimates. To evaluate the reliability of the photometric redshifts, we compare the derived redshifts with high-reliability spectroscopic redshifts for a sample of 868 normal galaxies with z < 1: 2 from zCOSMOS. Considering different scenarios, depending on using prior, no prior, and/or extinction, we compare the photometric and spectroscopic redshifts for this sample. The rms scatter between the estimated photometric redshifts and known spectroscopic redshifts is sigma(Delta( z))= 0. 031, where Delta(z) ( z(phot) - z(spec))/( 1+ z(spec)) with a small fraction of outliers (< 2.5%) [ outliers are defined as objects with Delta( z) > 3 sigma(Delta( z)), where sigma(Delta(z)) is the rms scatter in Delta( z)]. We also find good agreement [sigma(Delta(z))= 0.10] between photometric and spectroscopic redshifts for type II AGNs. We compare results fromour photometric redshift procedure with three other independent codes and find them in excellent agreement. We show preliminary results, based on photometric redshifts for the entire COSMOS sample ( to i < 25 mag).
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| 30. |
- Raja, A., et al.
(författare)
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Dielectric disorder in two-dimensional materials
- 2019
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Ingår i: Nature Nanotechnology. - : Springer Science and Business Media LLC. - 1748-3387 .- 1748-3395. ; 14:9, s. 832-837
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Tidskriftsartikel (refereegranskat)abstract
- Understanding and controlling disorder is key to nanotechnology and materials science. Traditionally, disorder is attributed to local fluctuations of inherent material properties such as chemical and structural composition, doping or strain. Here, we present a fundamentally new source of disorder in nanoscale systems that is based entirely on the local changes of the Coulomb interaction due to fluctuations of the external dielectric environment. Using two-dimensional semiconductors as prototypes, we experimentally monitor dielectric disorder by probing the statistics and correlations of the exciton resonances, and theoretically analyse the influence of external screening and phonon scattering. Even moderate fluctuations of the dielectric environment are shown to induce large variations of the bandgap and exciton binding energies up to the 100 meV range, often making it a dominant source of inhomogeneities. As a consequence, dielectric disorder has strong implications for both the optical and transport properties of nanoscale materials and their heterostructures.
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| 31. |
- Rosati, Roberto, 1984, et al.
(författare)
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Temporal Evolution of Low-Temperature Phonon Sidebands in Transition Metal Dichalcogenides
- 2020
-
Ingår i: ACS Photonics. - : American Chemical Society (ACS). - 2330-4022. ; 7:10, s. 2756-2764
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Tidskriftsartikel (refereegranskat)abstract
- Low-temperature photoluminescence (PL) of hBN-encapsulated monolayer tungsten diselenide (WSe2) shows a multitude of sharp emission peaks below the bright exciton. Some of them have been recently identified as phonon sidebands of momentum-dark states. However, the exciton dynamics behind the emergence of these sidebands has not been revealed yet. In this joint theory-experiment study, we theoretically predict and experimentally observe time-resolved PL, providing microscopic insights into the thermalization of hot excitons formed after optical excitation. In very good agreement between theory and experiment, we demonstrate a spectral red-shift of phonon sidebands on a time scale of tens of picoseconds, reflecting the phonon-driven thermalization of hot excitons in momentum-dark states. Furthermore, we predict the emergence of a transient phonon sideband that vanishes in the stationary PL. The obtained microscopic insights are applicable to a broad class of 2D materials with multiple exciton valleys.
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| 32. |
- Solis, Jorge, 1976-, et al.
(författare)
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Musical Skills of the Waseda Flutist Robot WF-4RIV
- 2007
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Ingår i: Intelligent Robots and Systems, 2007. IROS 2007. IEEE/RSJ International Conference on. - : IEEE Computer Society. ; , s. 2570-2571
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Konferensbidrag (refereegranskat)
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| 33. |
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| 34. |
- Taniguchi, Y, et al.
(författare)
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Notch receptor cleavage depends on but is not directly executed by presenilins
- 2002
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 99:6, s. 4014-4019
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Tidskriftsartikel (refereegranskat)abstract
- Notch receptors undergo three distinct proteolytic cleavages during maturation and activation. The third cleavage occurs within the plasma membrane and results in the release and translocation of the intracellular domain into the nucleus to execute Notch signaling. This so-called γ-secretase cleavage is under the control of presenilins, but it is not known whether presenilins themselves carry out the cleavage or whether they act by means of yet-unidentified γ-secretase(s). In this article, we show that Notch intracellular cleavage in intact cells completely depends on presenilins. In contrast, partial purification of the Notch cleavage activity reveals an activity, which is present only in protein extracts from presenilin-containing cells, and which does not comigrate with presenilin. This finding provides evidence for the existence of a specific Notch-processing activity, which is physically distinct from presenilins. We conclude from these experiments that presenilins are critically required for Notch intracellular cleavage but are not themselves directly mediating the cleavage.
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| 35. |
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| 36. |
- Ao, Y., et al.
(författare)
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Deep Submillimeter and Radio Observations in the SSA22 Field. I. Powering Sources and the Ly alpha Escape Fraction of Ly alpha Blobs
- 2017
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 850:2
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Tidskriftsartikel (refereegranskat)abstract
- We study the heating mechanisms and Ly alpha escape fractions of 35 Ly alpha blobs (LABs) at z approximate to 3.1 in the SSA22 field. Dust continuum sources have been identified in 11 of the 35 LABs, all with star formation rates (SFRs) above 100M(circle dot) yr(-1). Likely radio counterparts are detected in 9 out of 29 investigated LABs. The detection of submillimeter dust emission is more linked to the physical size of the Ly alpha emission than to the Ly alpha luminosities of the LABs. A radio excess in the submillimeter/ radio-detected LABs is common, hinting at the presence of active galactic nuclei. Most radio sources without X-ray counterparts are located at the centers of the LABs. However, all X-ray counterparts avoid the central regions. This may be explained by absorption due to exceptionally large column densities along the line-of-sight or by LAB morphologies, which are highly orientation dependent. The median Lya escape fraction is about 3% among the submillimeter-detected LABs, which is lower than a lower limit of 11% for the submillimeter-undetected LABs. We suspect that the large difference is due to the high dust attenuation supported by the large SFRs, the dense large-scale environment as well as large uncertainties in the extinction corrections required to apply when interpreting optical data.
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| 37. |
- Binggeli, Christian, et al.
(författare)
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A puzzling non-detection of [O III] and [C II] from a z ≈ 7.7 galaxy observed with ALMA
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 646
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Tidskriftsartikel (refereegranskat)abstract
- Context. Characterizing the galaxy population in the early Universe holds the key to understanding the evolution of these objects and the role they played in cosmic reionization. However, there have been very few observations at the very highest redshifts to date. Aims. In order to shed light on the properties of galaxies in the high-redshift Universe and their interstellar media, we observe the Lyman-α emitting galaxy z7_GSD_3811 at z = 7.664 with bands 6 and 8 at the Atacama Large Millimeter/submillimeter Array (ALMA). Methods. We target the far-infrared [O iii] 88 µm and [C ii] 158 µm emission lines and dust continuum in the star-forming galaxy z7_GSD_3811 with ALMA. We combine these measurements with earlier observations in the rest-frame ultraviolet (UV) in order to characterize the object and compare the results to those of earlier studies that observed [O iii] and [C ii] emission in high-redshift galaxies. Results. The [O iii] 88 µm and [C ii] 158 µm emission lines are undetected at the position of z7_GSD_3811, with 3σ upper limits of 1.6 × 108 L and 4.0 × 107 L, respectively. We do not detect any dust continuum in band 6 nor band 8. The measured rms in the band 8 and band 6 continua are 26 and 9.9 µJy beam−1, respectively. Similar to several other high-redshift galaxies, z7_GSD_3811 exhibits low [C ii] emission for its star formation rate compared to local galaxies. Furthermore, our upper limit on the [O iii] line luminosity is lower than the previously observed [O iii] lines in high-redshift galaxies with similar UV luminosities. Our ALMA band 6 and 8 dust continuum observations imply that z7_GSD_3811 likely has a low dust content, and our non-detections of the [O iii] and [C ii] lines could indicate that z7_GSD_3811 has a low metallicity (Z. 0.1 Z).
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| 38. |
- Bommer, Jouri D. S., et al.
(författare)
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Spin-Orbit Protection of Induced Superconductivity in Majorana Nanowires
- 2019
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Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 122:18
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Tidskriftsartikel (refereegranskat)abstract
- Spin-orbit interaction (SOI) plays a key role in creating Majorana zero modes in semiconductor nanowires proximity coupled to a superconductor. We track the evolution of the induced superconducting gap in InSb nanowires coupled to a NbTiN superconductor in a large range of magnetic field strengths and orientations. Based on realistic simulations of our devices, we reveal SOI with a strength of 0.15-0.35 eV angstrom. Our approach identifies the direction of the spin-orbit field, which is strongly affected by the superconductor geometry and electrostatic gates.
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| 39. |
- Casey, Caitlin M., et al.
(författare)
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Physical Characterization of an Unlensed, Dusty Star-forming Galaxy at z = 5.85
- 2019
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 887:1
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Tidskriftsartikel (refereegranskat)abstract
- We present a physical characterization of MM J100026.36+021527.9 (a.k.a. "Mambo-9"), a dusty star-forming galaxy (DSFG) at z = 5.850 ± 0.001. This is the highest-redshift unlensed DSFG (and fourth most distant overall) found to date and is the first source identified in a new 2 mm blank-field map in the COSMOS field. Though identified in prior samples of DSFGs at 850 μm to 1.2 mm with unknown redshift, the detection at 2 mm prompted further follow-up as it indicated a much higher probability that the source was likely to sit at z > 4. Deep observations from the Atacama Large Millimeter and submillimeter Array (ALMA) presented here confirm the redshift through the secure detection of 12CO(J = 6→5) and p-H2O (21,1 → 20,2). Mambo-9 is composed of a pair of galaxies separated by 6 kpc with corresponding star formation rates of 590 M o˙ yr-1 and 220 M o˙ yr-1, total molecular hydrogen gas mass of (1.7 ± 0.4) × 1011 M o˙, dust mass of (1.3 ± 0.3) × 109 M o˙, and stellar mass of (3.2-1.5+1.0) × 109 M o˙. The total halo mass, (3.3 ± 0.8) × 1012 M o˙, is predicted to exceed 1015 M o˙ by z = 0. The system is undergoing a merger-driven starburst that will increase the stellar mass of the system tenfold in τ depl = 40-80 Myr, converting its large molecular gas reservoir (gas fraction of 96-2+1) into stars. Mambo-9 evaded firm spectroscopic identification for a decade, following a pattern that has emerged for some of the highest-redshift DSFGs found. And yet, the systematic identification of unlensed DSFGs like Mambo-9 is key to measuring the global contribution of obscured star formation to the star formation rate density at z ⪆ 4, the formation of the first massive galaxies, and the formation of interstellar dust at early times (≲1 Gyr).
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| 40. |
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| 41. |
- Hashimoto, Takuya, et al.
(författare)
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Big Three Dragons: A z=7.15 Lyman-break galaxy detected in [Oiii] 88 mu m, [Cii] 158 mu m, and dust continuum with ALMA
- 2019
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Ingår i: Publication of the Astronomical Society of Japan. - : Oxford University Press (OUP). - 2053-051X .- 0004-6264. ; 71:4
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Tidskriftsartikel (refereegranskat)abstract
- We present new ALMA observations and physical properties of a Lyman break galaxy at z = 7.15. Our target, B14-65666, has a bright ultra-violet (UV) absolute magnitude, M-UV approximate to -22.4, and has been spectroscopically identified in Ly alpha with a small rest-frame equivalent width of approximate to 4 angstrom. A previous Hubble Space TElescope (HST) image has shown that the target is composed of two spatially separated clumps in the rest-frame UV. With ALMA, we have newly detected spatially resolved [Oiii] 88 mu m, [Cii] 158 mu m, and their underlying dust continuum emission. In the whole system of B14-65666, the [Oiii] and [Cii] lines have consistent redshifts of 7.1520 +/- 0.0003, and the [Oiii] luminosity, (34.4 +/- 4.1)x 10(8)L(circle dot), is about three times higher than the [Cii] luminosity, (11.0 +/- 1.4) x 10(8)L(circle dot). With our two continuum flux densities, the dust temperature is constrained to be T-d approximate to 50-60K under the assumption of a dust emissivity index of beta(d) = 2.0-1.5, leading to a large total infrared luminosity of L-TIR approximate to 1 x 10(12)L(circle dot). Owing to our high spatial resolution data, we show that the [Oiii] and [Cii] emission can be spatially decomposed into two clumps associated with the two rest-frame UV clumps whose spectra are kinematically separated by approximate to 200kms(-1). We also find these two clumps have comparable UV, infrared, [Oiii], and [Cii] luminosities. Based on these results, we argue that B14-65666 is a starburst galaxy induced by a major merger. The merger interpretation is also supported by the large specific star formation rate (defined as the star formation rate per unit stellar mass), sSFR Gyr(-1), inferred from our SED fitting. Probably, a strong UV radiation field caused by intense star formation contributes to its high dust temperature and the [Oiii]-to-[Cii] luminosity ratio.
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| 42. |
- Izumi, Takuma, et al.
(författare)
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Submillimeter ALMA Observations of the Dense Gas in the Low-Luminosity Type-1 Active Nucleus of NGC 1097
- 2013
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Ingår i: Publications of the Astronomical society of Japan. - : Oxford University Press (OUP). - 0004-6264 .- 2053-051X. ; 65:5
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Tidskriftsartikel (refereegranskat)abstract
- We present the first 100 pc scale view of the dense molecular gas in the central similar to 1.3 kpc of the type-1 Seyfert NGC 1097, traced by HCN (J = 4-3) and HCO+ (J = 4-3) lines afforded with ALMA band 7. This galaxy shows significant HCN enhancement with respect to HCO+ and CO in the low-J transitions, which seems to be a common characteristic in AGN environments. Using the ALMA data, we consider the characteristics of the dense gas around this AGN, and search for the mechanism of HCN enhancement. We find a high HCN (J = 4-3) to HCO+ (J = 4-3) line ratio in the nucleus. The upper limit of the brightness temperature ratio of HCN (nu(2) = 1(1f), J = 4-3) to HCN (J = 4-3) is 0.08, which indicates that IR pumping does not significantly affect the pure rotational population in this nucleus. We also find a higher HCN (J = 4-3) to CS (J = 7-6) line ratio in NGC 1097 than in starburst galaxies, which is more than 12.7 on the brightness temperature scale. Combined with similar observations from other galaxies, we tentatively suggest that this ratio appears to be higher in AGN-host galaxies than in pure starburst ones, similar to the widely used HCN to HCO+ ratio. LTE and non-LTE modeling of the observed HCN and HCO+ lines using J = 4-3 and 1-0 data from ALMA, and J = 3-2 data from SMA, reveals a high HCN to HCO+ abundance ratio (5 <= [HCN]/[HCO+] <= 20: non-LTE analysis) in the nucleus, and that the high-J lines (J = 4-3 and 3-2) are emitted from dense (10(4.5) cm(-3) <= n(H2) <= 10(6) cm(-3)), hot (70 K <= T-kin <= 550 K) regions. Finally we propose that high-temperature chemistry is more plausible to explain the observed enhanced HCN emission in NGC 1097 than pure gas-phase PDR/XDR chemistry.
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| 43. |
- Jones, Alfred J. H., et al.
(författare)
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Visualizing band structure hybridization and superlattice effects in twisted MoS2/WS2 heterobilayers
- 2022
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Ingår i: Current Opinion in Chemical Engineering. - : IOP Publishing Ltd. - 2211-3398. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- A mismatch of atomic registries between single-layer transition metal dichalcogenides (TMDs) in a two-dimensional (2D) van der Waals heterostructure produces a moire superlattice with a periodic potential, which can be fine-tuned by introducing a twist angle between the materials. This approach is promising both for controlling the interactions between the TMDs and for engineering their electronic band structures, yet direct observation of the changes to the electronic structure introduced with varying twist angle has so far been missing. Here, we probe heterobilayers comprised of single-layer MoS2 and WS2 with twist angles ranging from 2 degrees to 20 degrees and determine the twist angle-dependent evolution of the electronic band structure using micro-focused angle-resolved photoemission spectroscopy. We find strong interlayer hybridization between MoS2 and WS2 electronic states at the (Gamma) over bar -point of the Brillouin zone, leading to a shift of the valence band maximum in the heterostructure. Replicas of the hybridized states are observed at the center of twist angle-dependent moire mini Brillouin zones. We confirm that these replica features arise from the inherent moire potential by comparing our experimental observations with density functional theory calculations of the superlattice dispersion. Our direct visualization of these features underscores the potential of using twisted heterobilayer semiconductors to engineer hybrid electronic states and superlattices that alter the electronic and optical properties of 2D heterostructures for a wide range of twist angles.
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| 44. |
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| 45. |
- Kato, Yuta, et al.
(författare)
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A high dust emissivity index beta for a CO-faint galaxy in a filamentary Ly alpha nebula at z=3.1
- 2018
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Ingår i: Publications of the Astronomical Society of Japan. - : Oxford University Press (OUP). - 0004-6264 .- 2053-051X. ; 70:5
-
Tidskriftsartikel (refereegranskat)abstract
- We present CO J = 4-3 line and 3 mm dust continuum observations of a 100 kpc-scale filamentary Ly alpha nebula (SSA22 LAB18) at z = 3.1 using the Atacama Large Millimeter/submillimeter Array (ALMA). We detected the CO J = 4-3 line at a systemic z(CO) = 3.093 +/- 0.001 at 11 sigma from one of the ALMA continuum sources associated with the Ly alpha filament. We estimated the CO J = 4-3 luminosity of L'(CO(4-3)) = (2.3 +/- 0.2) x 10(9) Kkms(-1) pc(2) for this CO source, which is one order of magnitude smaller than those of typical z > 1 dusty star-forming galaxies (DSFGs) of similar far-infrared luminosity L-IR similar to 10(12) L-circle dot. We derived a molecular gas mass of M-gas = (4.4(-0.6)(+0.9)) x 10(9) M-circle dot and a star-formation rate of SFR = 270 +/- 160M(circle dot) yr(-1). We also estimated a gas depletion time of tau(dep) = 17 +/- 10 Myr, which is shorter than those of typical DSFGs. It is suggested that this source is in the transition phase from DSFG to a gas-poor, early-type galaxy. From ALMA to Herschel multi-band dust continuum observations, we measured a dust emissivity index beta = 2.3 +/- 0.2, which is similar to those of local gas-poor, early-type galaxies. From recent laboratory experiments, the specific chemical compositions needed to reproduce such a high beta for interstellar dust at the submillimeter wavelengths. ALMA CO and multi-band dust continuum observations can constrain the evolutionary stage of high-redshift galaxies through tau(dep) and beta, and thus we can investigate the chemical composition of dust even in the early Universe.
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| 46. |
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| 47. |
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| 48. |
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| 49. |
- Pasquale, Gabriele, et al.
(författare)
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Flat-Band-Induced Many-Body Interactions and Exciton Complexes in a Layered Semiconductor
- 2022
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 22:22, s. 8883-8891
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Tidskriftsartikel (refereegranskat)abstract
- Interactions among a collection of particles generate many-body effects in solids that result in striking modifications of material properties. The heavy carrier mass that yields strong interactions and gate control of carrier density over a wide range makes two-dimensional semiconductors an exciting playground to explore many-body physics. The family of III-VI metal monochalcogenides emerges as a new platform for this purpose because of its excellent optical properties and the flat valence band dispersion. In this work, we present a complete study of charge-tunable excitons in few-layer InSe by photoluminescence spectroscopy. From the optical spectra, we establish that free excitons in InSe are more likely to be captured by ionized donors leading to the formation of bound exciton complexes. Surprisingly, a pronounced red shift of the exciton energy accompanied by a decrease of the exciton binding energy upon hole-doping reveals a significant band gap renormalization induced by the presence of the Fermi reservoir.
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| 50. |
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