| 1. |
- Campbell, PJ, et al.
(författare)
-
Pan-cancer analysis of whole genomes
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
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.
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Valiente-Dobon, J. J., et al.
(författare)
-
Conceptual design of the AGATA 2 pi array at LNL
- 2023
-
Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 1049
-
Tidskriftsartikel (refereegranskat)abstract
- The Advanced GAmma Tracking Array (AGATA) has been installed at Laboratori Nazionali di Legnaro (LNL), Italy. In this installation, AGATA will consist, at the beginning, of 13 AGATA triple clusters (ATCs) with an angular coverage of 1n,and progressively the number of ATCs will increase up to a 2 pi angular coverage. This setup will exploit both stable and radioactive ion beams delivered by the Tandem-PIAVE-ALPI accelerator complex and the SPES facility. The new implementation of AGATA at LNL will be used in two different configurations, firstly one coupled to the PRISMA large-acceptance magnetic spectrometer and lately a second one at Zero Degrees, along the beam line. These two configurations will allow us to cover a broad physics program, using different reaction mechanisms, such as Coulomb excitation, fusion-evaporation, transfer and fission at energies close to the Coulomb barrier. These setups have been designed to be coupled with a large variety of complementary detectors such as charged particle detectors, neutron detectors, heavy-ion detectors, high-energy gamma-ray arrays, cryogenic and gasjet targets and the plunger device for lifetime measurements. We present in this paper the conceptual design, characteristics and performance figures of this implementation of AGATA at LNL.
|
|
| 5. |
- Aharonian, F., et al.
(författare)
-
HESS observations of the 2021 periastron passage of PSR B1259-63/LS 2883
- 2024
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 687
-
Tidskriftsartikel (refereegranskat)abstract
- PSR B1259-63/LS 2883 is a gamma-ray binary system that hosts a pulsar in an eccentric orbit, with a 3.4 yr period, around an O9.5Ve star (LS 2883). At orbital phases close to periastron passages, the system radiates bright and variable non-thermal emission, for which the temporal and spectral properties of this emission are, for now, poorly understood. In this regard, very high-energy (VHE) emission is especially useful to study and constrain radiation processes and particle acceleration in the system. We report on an extensive VHE observation campaign conducted with the High Energy Stereoscopic System, comprised of approximately 100 h of data taken over five months, from t(p) - 24 days to t(p) + 127 days around the system's 2021 periastron passage (where t(p) is the time of periastron). We also present the timing and spectral analyses of the source. The VHE light curve in 2021 is consistent overall with the stacked light curve of all previous observations. Within the light curve, we report a VHE maximum at times coincident with the third X-ray peak first detected in the 2021 X-ray light curve. In the light curve - although sparsely sampled in this time period - we see no VHE enhancement during the second disc crossing. In addition, we see no correspondence to the 2021 GeV flare in the VHE light curve. The VHE spectrum obtained from the analysis of the 2021 dataset is best described by a power law of spectral index Gamma = 2.65 +/- 0.04(stat) +/- 0.04(sys), a value consistent with the spectral index obtained from the analysis of data collected with H.E.S.S. during the previous observations of the source. We report spectral variability with a difference of Delta Gamma = 0.56 +/- 0.18(stat) +/- 0.10(sys) at 95% confidence intervals, between sub-periods of the 2021 dataset. We also detail our investigation into X-ray/TeV and GeV/TeV flux correlations in the 2021 periastron passage. We find a linear correlation between contemporaneous flux values of X-ray and TeV datasets, detected mainly after t(p) + 25 days, suggesting a change in the available energy for non-thermal radiation processes. We detect no significant correlation between GeV and TeV flux points, within the uncertainties of the measurements, from similar to t(p) - 23 days to similar to t(p) + 126 days. This suggests that the GeV and TeV emission originate from different electron populations.
|
|
| 6. |
- Pasqualato, G., et al.
(författare)
-
Shape evolution in even-mass 98-104Zr isotopes via lifetime measurements using the γ γ-coincidence technique
- 2023
-
Ingår i: European Physical Journal A. - : Springer. - 1434-6001 .- 1434-601X. ; 59:11
-
Tidskriftsartikel (refereegranskat)abstract
- The Zirconium (Z = 40) isotopic chain has attracted interest for more than four decades. The abrupt lowering of the energy of the first 2(+) state and the increase in the transition strength B(E2; 2(1)(+) -> 0(1)(+) ) going from Zr-98 to Zr-100 has been the first example of "quantum phase transition" in nuclear shapes, which has few equivalents in the nuclear chart. Although a multitude of experiments have been performed to measure nuclear properties related to nuclear shapes and collectivity in the region, none of the measured lifetimes were obtained using the Recoil Distance Doppler Shift method in the gamma gamma-coincidence mode where a gate on the direct feeding transition of the state of interest allows a strict control of systematical errors. This work reports the results of lifetime measurements for the first yrast excited states in Zr98-104 carried out to extract reduced transition probabilities. The new lifetime values in gamma gamma-coincidence and gamma-single mode are compared with the results of former experiments. Recent predictions of the Interacting Boson Model with Configuration Mixing, the Symmetry Conserving Configuration Mixing model based on the Hartree-Fock- Bogoliubov approach and the Monte Carlo Shell Model are presented and compared with the experimental data.
|
|
| 7. |
- Ciemala, M., et al.
(författare)
-
Testing ab initio nuclear structure in neutron-rich nuclei : Lifetime measurements of second 2(+) state in C-16 and O-20
- 2020
-
Ingår i: Physical Review C. - : AMER PHYSICAL SOC. - 2469-9985 .- 2469-9993. ; 101:2
-
Tidskriftsartikel (refereegranskat)abstract
- To test the predictive power of ab initio nuclear structure theory, the lifetime of the second 2(+) state in neutron-rich O-20, tau(2(2)(+)) = 150(-30)(+80) fs, and an estimate for the lifetime of the second 2(+) state in C-16 have been obtained for the first time. The results were achieved via a novel Monte Carlo technique that allowed us to measure nuclear state lifetimes in the tens-to-hundreds of femtoseconds range by analyzing the Doppler-shifted gamma-transition line shapes of products of low-energy transfer and deep-inelastic processes in the reaction O-18 (7.0 MeV/u) + Ta-181. The requested sensitivity could only be reached owing to the excellent performances of the Advanced gamma-Tracking Array AGATA, coupled to the PARIS scintillator array and to the VAMOS++ magnetic spectrometer. The experimental lifetimes agree with predictions of ab initio calculations using two- and three-nucleon interactions, obtained with the valence-space in-medium similarity renormalization group for O-20 and with the no-core shell model for C-16. The present measurement shows the power of electromagnetic observables, determined with high-precision gamma spectroscopy, to assess the quality of first-principles nuclear structure calculations, complementing common benchmarks based on nuclear energies. The proposed experimental approach will be essential for short lifetime measurements in unexplored regions of the nuclear chart, including r-process nuclei, when intense beams, produced by Isotope Separation On-Line (ISOL) techniques, become available.
|
|
| 8. |
- Forstner, A. J., et al.
(författare)
-
Genome-wide association study of panic disorder reveals genetic overlap with neuroticism and depression
- 2021
-
Ingår i: Molecular Psychiatry. - : Springer Science and Business Media LLC. - 1359-4184 .- 1476-5578. ; 26, s. 4179-4190
-
Tidskriftsartikel (refereegranskat)abstract
- Panic disorder (PD) has a lifetime prevalence of 2–4% and heritability estimates of 40%. The contributory genetic variants remain largely unknown, with few and inconsistent loci having been reported. The present report describes the largest genome-wide association study (GWAS) of PD to date comprising genome-wide genotype data of 2248 clinically well-characterized PD patients and 7992 ethnically matched controls. The samples originated from four European countries (Denmark, Estonia, Germany, and Sweden). Standard GWAS quality control procedures were conducted on each individual dataset, and imputation was performed using the 1000 Genomes Project reference panel. A meta-analysis was then performed using the Ricopili pipeline. No genome-wide significant locus was identified. Leave-one-out analyses generated highly significant polygenic risk scores (PRS) (explained variance of up to 2.6%). Linkage disequilibrium (LD) score regression analysis of the GWAS data showed that the estimated heritability for PD was 28.0–34.2%. After correction for multiple testing, a significant genetic correlation was found between PD and major depressive disorder, depressive symptoms, and neuroticism. A total of 255 single-nucleotide polymorphisms (SNPs) with p < 1 × 10−4 were followed up in an independent sample of 2408 PD patients and 228,470 controls from Denmark, Iceland and the Netherlands. In the combined analysis, SNP rs144783209 showed the strongest association with PD (pcomb = 3.10 × 10−7). Sign tests revealed a significant enrichment of SNPs with a discovery p-value of <0.0001 in the combined follow up cohort (p = 0.048). The present integrative analysis represents a major step towards the elucidation of the genetic susceptibility to PD. © 2019, The Author(s), under exclusive licence to Springer Nature Limited.
|
|
| 9. |
- Girard-Alcindor, V., et al.
(författare)
-
New narrow resonances observed in the unbound nucleus F 15
- 2022
-
Ingår i: Physical Review C. - : American Physical Society (APS). - 2469-9985 .- 2469-9993. ; 105:5
-
Tidskriftsartikel (refereegranskat)abstract
- The structure of the unbound F15 nucleus is investigated using the inverse kinematics resonant scattering of a radioactive O14 beam impinging on a CH2 target. The analysis of H1(O14,p)O14 and H1(O14,2p)N13 reactions allowed the confirmation of the previously observed narrow 1/2- resonance, near the two-proton decay threshold, and the identification of two new narrow 5/2- and 3/2- resonances. The newly observed levels decay by 1p emission to the ground of O14, and by sequential 2p emission to the ground state of N13 via the 1- resonance of O14. Gamow shell model (GSM) analysis of the experimental data suggests that the wave functions of the 5/2- and 3/2- resonances may be collectivized by the continuum coupling to nearby 2p- and 1p-decay channels. The observed excitation function H1(O14,p)O14 and resonance spectrum in F15 are well reproduced in the unified framework of the GSM.
|
|
| 10. |
- Hartley, Philippa, et al.
(författare)
-
SKA Science Data Challenge 2: analysis and results
- 2023
-
Ingår i: Monthly Notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 523:2, s. 1967-1993
-
Tidskriftsartikel (refereegranskat)abstract
- The Square Kilometre Array Observatory (SKAO) will explore the radio sky to new depths in order to conduct transformational science. SKAO data products made available to astronomers will be correspondingly large and complex, requiring the application of advanced analysis techniques to extract key science findings. To this end, SKAO is conducting a series of Science Data Challenges, each designed to familiarize the scientific community with SKAO data and to drive the development of new analysis techniques. We present the results from Science Data Challenge 2 (SDC2), which invited participants to find and characterize 233 245 neutral hydrogen (H i) sources in a simulated data product representing a 2000 h SKA-Mid spectral line observation from redshifts 0.25-0.5. Through the generous support of eight international supercomputing facilities, participants were able to undertake the Challenge using dedicated computational resources. Alongside the main challenge, 'reproducibility awards' were made in recognition of those pipelines which demonstrated Open Science best practice. The Challenge saw over 100 participants develop a range of new and existing techniques, with results that highlight the strengths of multidisciplinary and collaborative effort. The winning strategy - which combined predictions from two independent machine learning techniques to yield a 20 per cent improvement in overall performance - underscores one of the main Challenge outcomes: that of method complementarity. It is likely that the combination of methods in a so-called ensemble approach will be key to exploiting very large astronomical data sets.
|
|
| 11. |
- Korenblik, R., et al.
(författare)
-
Dragon 1 Protocol Manuscript : Training, Accreditation, Implementation and Safety Evaluation of Portal and Hepatic Vein Embolization (PVE/HVE) to Accelerate Future Liver Remnant (FLR) Hypertrophy
- 2022
-
Ingår i: Cardiovascular and Interventional Radiology. - : Springer. - 0174-1551 .- 1432-086X. ; 45, s. 1391-1398
-
Tidskriftsartikel (refereegranskat)abstract
- Study Purpose The DRAGON 1 trial aims to assess training, implementation, safety and feasibility of combined portal- and hepatic-vein embolization (PVE/HVE) to accelerate future liver remnant (FLR) hypertrophy in patients with borderline resectable colorectal cancer liver metastases. Methods The DRAGON 1 trial is a worldwide multicenter prospective single arm trial. The primary endpoint is a composite of the safety of PVE/HVE, 90-day mortality, and one year accrual monitoring of each participating center. Secondary endpoints include: feasibility of resection, the used PVE and HVE techniques, FLR-hypertrophy, liver function (subset of centers), overall survival, and disease-free survival. All complications after the PVE/HVE procedure are documented. Liver volumes will be measured at week 1 and if applicable at week 3 and 6 after PVE/HVE and follow-up visits will be held at 1, 3, 6, and 12 months after the resection. Results Not applicable. Conclusion DRAGON 1 is a prospective trial to assess the safety and feasibility of PVE/HVE. Participating study centers will be trained, and procedures standardized using Work Instructions (WI) to prepare for the DRAGON 2 randomized controlled trial. Outcomes should reveal the accrual potential of centers, safety profile of combined PVE/HVE and the effect of FLR-hypertrophy induction by PVE/HVE in patients with CRLM and a small FLR.
|
|
| 12. |
- Rheinbay, E, et al.
(författare)
-
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 102-
-
Tidskriftsartikel (refereegranskat)abstract
- The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53, in the 3′ untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
|
|
| 13. |
- Sarneel, Judith M., et al.
(författare)
-
Reading tea leaves worldwide: Decoupled drivers of initial litter decomposition mass-loss rate and stabilization
- 2024
-
Ingår i: ECOLOGY LETTERS. - : John Wiley & Sons. - 1461-023X .- 1461-0248. ; 27:5
-
Tidskriftsartikel (refereegranskat)abstract
- The breakdown of plant material fuels soil functioning and biodiversity. Currently, process understanding of global decomposition patterns and the drivers of such patterns are hampered by the lack of coherent large-scale datasets. We buried 36,000 individual litterbags (tea bags) worldwide and found an overall negative correlation between initial mass-loss rates and stabilization factors of plant-derived carbon, using the Tea Bag Index (TBI). The stabilization factor quantifies the degree to which easy-to-degrade components accumulate during early-stage decomposition (e.g. by environmental limitations). However, agriculture and an interaction between moisture and temperature led to a decoupling between initial mass-loss rates and stabilization, notably in colder locations. Using TBI improved mass-loss estimates of natural litter compared to models that ignored stabilization. Ignoring the transformation of dead plant material to more recalcitrant substances during early-stage decomposition, and the environmental control of this transformation, could overestimate carbon losses during early decomposition in carbon cycle models.
|
|
| 14. |
- Yakneen, S, et al.
(författare)
-
Butler enables rapid cloud-based analysis of thousands of human genomes
- 2020
-
Ingår i: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 38:3, s. 288-
-
Tidskriftsartikel (refereegranskat)abstract
- We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data processing and analysis by 43% compared with current approaches. Butler enabled processing of a 725-terabyte cancer genome dataset from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project in a time-efficient and uniform manner.
|
|
| 15. |
|
|
| 16. |
- Zanon, I., et al.
(författare)
-
High-Precision Spectroscopy of 20O Benchmarking Ab Initio Calculations in Light Nuclei
- 2023
-
Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 131:26
-
Tidskriftsartikel (refereegranskat)abstract
- The excited states of unstable 20O were investigated via γ-ray spectroscopy following the 19O(d,p)20O reaction at 8 AMeV. By exploiting the Doppler shift attenuation method, the lifetimes of the 2+2 and 3+1 states were firmly established. From the γ-ray branching and E2/M1 mixing ratios for transitions deexciting the 2+2 and 3+1 states, the B(E2) and B(M1) were determined. Various chiral effective field theory Hamiltonians, describing the nuclear properties beyond ground states, along with a standard USDB interaction, were compared with the experimentally obtained data. Such a comparison for a large set of γ-ray transition probabilities with the valence space in medium similarity renormalization group ab initio calculations was performed for the first time in a nucleus far from stability. It was shown that the ab initio approaches using chiral effective field theory forces are challenged by detailed high-precision spectroscopic properties of nuclei. The reduced transition probabilities were found to be a very constraining test of the performance of the ab initio models.
|
|
| 17. |
- Gehlen, J., et al.
(författare)
-
First genome-wide association study of esophageal atresia identifies three genetic risk loci at CTNNA3, FOXF1/FOXC2/FOXL1, and HNF1B
- 2022
-
Ingår i: Human Genetics and Genomics Advances. - : Elsevier BV. - 2666-2477. ; 3:2
-
Tidskriftsartikel (refereegranskat)abstract
- Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) is the most common congenital malformation of the upper digestive tract. This study represents the first genome-wide association study (GWAS) to identify risk loci for EA/TEF. We used a European case-control sample comprising 764 EA/TEF patients and 5,778 controls and observed genome-wide significant associations at three loci. On chromosome 10q21 within the gene CTNNA3 (p = 2.11 × 10−8; odds ratio [OR] = 3.94; 95% confidence interval [CI], 3.10–5.00), on chromosome 16q24 next to the FOX gene cluster (p = 2.25 × 10−10; OR = 1.47; 95% CI, 1.38–1.55) and on chromosome 17q12 next to the gene HNF1B (p = 3.35 × 10−16; OR = 1.75; 95% CI, 1.64–1.87). We next carried out an esophageal/tracheal transcriptome profiling in rat embryos at four selected embryonic time points. Based on these data and on already published data, the implicated genes at all three GWAS loci are promising candidates for EA/TEF development. We also analyzed the genetic EA/TEF architecture beyond the single marker level, which revealed an estimated single-nucleotide polymorphism (SNP)-based heritability of around 37% ± 14% standard deviation. In addition, we examined the polygenicity of EA/TEF and found that EA/TEF is less polygenic than other complex genetic diseases. In conclusion, the results of our study contribute to a better understanding on the underlying genetic architecture of ET/TEF with the identification of three risk loci and candidate genes. © 2022 The Authors
|
|
| 18. |
- Oostrum, L. C., et al.
(författare)
-
Repeating fast radio bursts with WSRT/Apertif
- 2020
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 635
-
Tidskriftsartikel (refereegranskat)abstract
- Context. Repeating fast radio bursts (FRBs) present excellent opportunities to identify FRB progenitors and host environments as well as to decipher the underlying emission mechanism. Detailed studies of repeating FRBs might also hold clues as to the origin of FRBs as a population. Aims. We aim to detect bursts from the first two repeating FRBs, FRB 121102 (R1) and FRB 180814.J0422+73 (R2), and to characterise their repeat statistics. We also want to significantly improve the sky localisation of R2 and identify its host galaxy. Methods. We used the Westerbork Synthesis Radio Telescope to conduct extensive follow-up of these two repeating FRBs. The new phased-array feed system, Apertif, allows one to cover the entire sky position uncertainty of R2 with fine spatial resolution in a single pointing. The data were searched for bursts around the known dispersion measures of the two sources. We characterise the energy distribution and the clustering of detected R1 bursts. Results. We detected 30 bursts from R1. The non-Poissonian nature is clearly evident from the burst arrival times, which is consistent with earlier claims. Our measurements indicate a dispersion measure (DM) of 563.5(2) pc cm(-3), suggesting a significant increase in DM over the past few years. Assuming a constant position angle across the burst, we place an upper limit of 8% on the linear polarisation fraction for the brightest burst in our sample. We did not detect any bursts from R2. Conclusions. A single power-law might not fit the R1 burst energy distribution across the full energy range or widely separated detections. Our observations provide improved constraints on the clustering of R1 bursts. Our stringent upper limits on the linear polarisation fraction imply a significant depolarisation, either intrinsic to the emission mechanism or caused by the intervening medium at 1400 MHz, which is not observed at higher frequencies. The non-detection of any bursts from R2, despite nearly 300 h of observations, implies either a highly clustered nature of the bursts, a steep spectral index, or a combination of the two assuming that the source is still active. Another possibility is that R2 has turned off completely, either permanently or for an extended period of time.
|
|
| 19. |
- van Cappellen, W., et al.
(författare)
-
Apertif: Phased array feeds for the Westerbork Synthesis Radio Telescope: System overview and performance characteristics
- 2022
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 658
-
Tidskriftsartikel (refereegranskat)abstract
- We describe the APERture Tile In Focus (Apertif) system, a phased array feed (PAF) upgrade of the Westerbork Synthesis Radio Telescope that transforms this telescope into a high-sensitivity, wide-field-of-view L-band imaging and transient survey instrument. Using novel PAF technology, up to 40 partially overlapping beams are formed on the sky simultaneously, significantly increasing the survey speed of the telescope. With this upgraded instrument, an imaging survey covering an area of 2300 deg2 is being performed that will deliver both continuum and spectral line datasets, of which the first data have been publicly released. In addition, a time domain transient and pulsar survey covering 15 000 deg2 is in progress. An overview of the Apertif science drivers, hardware, and software of the upgraded telescope is presented, along with its key performance characteristics.
|
|
| 20. |
- Fernández, A., et al.
(författare)
-
Reinterpretation of excited states in 212Po: Shell-model multiplets rather than α-cluster states
- 2021
-
Ingår i: Physical Review C. - : American Physical Society. - 2469-9985 .- 2469-9993. ; 104:5
-
Tidskriftsartikel (refereegranskat)abstract
- A γ-ray spectroscopic study of 212Po was performed at the Grand Accélérateur National d'Ions Lourds, using the inverse kinematics α-transfer reaction 12C(208Pb,212Po)8Be and the AGATA spectrometer. A careful analysis based on γγ coincidence relations allowed us to establish 14 new excited states in the energy range between 1.9 and 3.3 MeV. None of these states, however, can be considered as candidates for the levels with spins and parities of 1− and 2− and excitation energies below 2.1 MeV, which have been predicted by recent α-cluster model calculations. A systematic comparison of the experimentally established excitation scheme of 212Po with shell-model calculations was performed. This comparison suggests that the six states with excitation energies (spins and parities) of 1744 (4−), 1751 (8−), 1787 (6−), 1946 (4−), 1986 (8−), and 2016 (6−) keV, which previously were interpreted as α-cluster states, may in fact be of positive parity and belong to low-lying shell-model multiplets. This reinterpretation of the structure of 212Po is supported by experimental information with respect to the linear polarization of γ rays, which suggests a magnetic character of the 432-keV γ ray decaying from the state at an excitation energy of 1787 keV to the 6+ yrast state, and exclusive reaction cross sections.
|
|
| 21. |
- Perez-Vidal, R. M., et al.
(författare)
-
Evidence of Partial Seniority Conservation in the pi g9/2 Shell for the N=50 Isotones
- 2022
-
Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 129:11
-
Tidskriftsartikel (refereegranskat)abstract
- The reduced transition probabilities for the 4+1 -2+1 and 2+1 -0+1 transitions in 92Mo and 94Ru and for the 4+1 -2+1 and 6+1 -4+1 transitions in 90Zr have been determined in this experiment making use of a multinucleon transfer reaction. These results have been interpreted on the basis of realistic shell-model calculations in the f5=2, p3=2, p1=2, and g9=2 proton valence space. Only the combination of extensive lifetime information and large scale shell-model calculations allowed the extent of the seniority conservation in the N = 50 g9=2 orbital to be understood. The conclusion is that seniority is largely conserved in the first 71g9=2 orbital.
|
|
| 22. |
- Siciliano, M., et al.
(författare)
-
Pairing-quadrupole interplay in the neutron-deficient tin nuclei : First lifetime measurements of low-lying states in Sn-106,Sn-108
- 2020
-
Ingår i: Physics Letters B. - : ELSEVIER. - 0370-2693 .- 1873-2445. ; 806
-
Tidskriftsartikel (refereegranskat)abstract
- The lifetimes of the low-lying excited states 2(+) and 4(+) have been directly measured in the neutron-deficient Sn-106,Sn-108 isotopes. The nuclei were populated via a deep-inelastic reaction and the lifetime measurement was performed employing a differential plunger device. The emitted gamma rays were detected by the AGATA array, while the reaction products were uniquely identified by the VAMOS++ magnetic spectrometer. Large-Scale Shell-Model calculations with realistic forces indicate that, independently of the pairing content of the interaction, the quadrupole force is dominant in the B(E2; 2(1)(+) -> 0(g.s)(+)) values and it describes well the experimental pattern for Sn104-114 ; the B(E2;(+)(4) -> 2(1)(+)) values, measured here for the first time, depend critically on a delicate pairing-quadrupole balance, disclosed by the very precise results in Sn-108.
|
|
| 23. |
- Adams, E. A. K., et al.
(författare)
-
First release of Apertif imaging survey data
- 2022
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 667
-
Tidskriftsartikel (refereegranskat)abstract
- Context. Apertif is a phased-array feed system for the Westerbork Synthesis Radio Telescope, providing forty instantaneous beams over 300 MHz of bandwidth. A dedicated survey program utilizing this upgrade started on 1 July 2019, with the last observations taken on 28 February 2022. The imaging survey component provides radio continuum, polarization, and spectral line data. Aims. Public release of data is critical for maximizing the legacy of a survey. Toward that end, we describe the release of data products from the first year of survey operations, through 30 June 2020. In particular, we focus on defining quality control metrics for the processed data products. Methods. The Apertif imaging pipeline, Apercal, automatically produces non-primary beam corrected continuum images, polarization images and cubes, and uncleaned spectral line and dirty beam cubes for each beam of an Apertif imaging observation. For this release, processed data products are considered on a beam-by-beam basis within an observation. We validate the continuum images by using metrics that identify deviations from Gaussian noise in the residual images. If the continuum image passes validation, we release all processed data products for a given beam. We apply further validation to the polarization and line data products and provide flags indicating the quality of those data products. Results. We release all raw observational data from the first year of survey observations, for a total of 221 observations of 160 independent target fields, covering approximately one thousand square degrees of sky. Images and cubes are released on a per beam basis, and 3374 beams (of 7640 considered) are released. The median noise in the continuum images is 41.4 uJy beam(-1), with a slightly lower median noise of 36.9 uJy beam(-1) in the Stokes V polarization image. The median angular resolution is 11.6 ''/sin delta. The median noise for all line cubes, with a spectral resolution of 36.6 kHz, is 1.6 mJy beam(-1), corresponding to a 3-sigma H i column density sensitivity of 1.8 x 10(20) atoms cm(-2) over 20 km s(-1) (for a median angular resolution of 24 '' x 15 ''). Line cubes at lower frequency have slightly higher noise values, consistent with the global RFI environment and overall Apertif system performance. We also provide primary beam images for each individual Apertif compound beam. The data are made accessible using a Virtual Observatory interface and can be queried using a variety of standard tools.
|
|
| 24. |
- Akdemir, KC, et al.
(författare)
-
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
- 2020
-
Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 52:3, s. 294-
-
Tidskriftsartikel (refereegranskat)abstract
- Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, and boundaries separating different domains have important roles in reinforcing the stability of these features. Indeed, domain disruptions in human cancers can lead to misregulation of gene expression. However, the frequency of domain disruptions in human cancers remains unclear. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor types, we analyzed 288,457 somatic structural variations (SVs) to understand the distributions and effects of SVs across TADs. Notably, SVs can lead to the fusion of discrete TADs, and complex rearrangements markedly change chromatin folding maps in the cancer genomes. Notably, only 14% of the boundary deletions resulted in a change in expression in nearby genes of more than twofold.
|
|
| 25. |
- Ashkir, Z., et al.
(författare)
-
Novel insights into diminished cardiac reserve in non-obstructive hypertrophic cardiomyopathy from four-dimensional flow cardiac magnetic resonance component analysis
- 2023
-
Ingår i: European Heart Journal Cardiovascular Imaging. - : OXFORD UNIV PRESS. - 2047-2404 .- 2047-2412. ; 24:9, s. 1192-1200
-
Tidskriftsartikel (refereegranskat)abstract
- Aims Hypertrophic cardiomyopathy (HCM) is characterized by hypercontractility and diastolic dysfunction, which alter blood flow haemodynamics and are linked with increased risk of adverse clinical events. Four-dimensional flow cardiac magnetic resonance (4D-flow CMR) enables comprehensive characterization of ventricular blood flow patterns. We characterized flow component changes in non-obstructive HCM and assessed their relationship with phenotypic severity and sudden cardiac death (SCD) risk. Methods and results Fifty-one participants (37 non-obstructive HCM and 14 matched controls) underwent 4D-flow CMR. Left-ventricular (LV) end-diastolic volume was separated into four components: direct flow (blood transiting the ventricle within one cycle), retained inflow (blood entering the ventricle and retained for one cycle), delayed ejection flow (retained ventricular blood ejected during systole), and residual volume (ventricular blood retained for >two cycles). Flow component distribution and component end-diastolic kinetic energy/mL were estimated. HCM patients demonstrated greater direct flow proportions compared with controls (47.9 +/- 9% vs. 39.4 +/- 6%, P = 0.002), with reduction in other components. Direct flow proportions correlated with LV mass index (r = 0.40, P = 0.004), end-diastolic volume index (r = -0.40, P = 0.017), and SCD risk (r = 0.34, P = 0.039). In contrast to controls, in HCM, stroke volume decreased with increasing direct flow proportions, indicating diminished volumetric reserve. There was no difference in component end-diastolic kinetic energy/mL. Conclusion Non-obstructive HCM possesses a distinctive flow component distribution pattern characterised by greater direct flow proportions, and direct flow-stroke volume uncoupling indicative of diminished cardiac reserve. The correlation of direct flow proportion with phenotypic severity and SCD risk highlight its potential as a novel and sensitive haemodynamic measure of cardiovascular risk in HCM.
|
|
| 26. |
- Carlevaro-Fita, J, et al.
(författare)
-
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
- 2020
-
Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1, s. 56-
-
Tidskriftsartikel (refereegranskat)abstract
- Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.
|
|
| 27. |
- Čolović, P., et al.
(författare)
-
Population of lead isotopes in binary reactions using a Rb 94 radioactive beam
- 2020
-
Ingår i: Physical Review C. - 2469-9985. ; 102:5
-
Tidskriftsartikel (refereegranskat)abstract
- We measured absolute cross sections for neutron transfer channels populated in the Rb94+Pb208 binary reaction. Cross sections have been extracted identifying directly the lead isotopes with the high efficiency MINIBALL γ-ray array coupled to a particle detector combined with a radioactive Rb94 beam delivered at Elab=6.2 MeV/nucleon by the HIE-ISOLDE facility. We observed sizable cross sections in the neutron-rich mass region, where the heavy partner acquires neutrons. A fair agreement between the measured cross sections with those from GRAZING calculations gives confidence in the cross-section predictions of more neutron-rich nuclei produced via a larger number of transferred nucleons.
|
|
| 28. |
- Gangannagaripalli, J., et al.
(författare)
-
A Standard Set of Value-Based Patient-Centered Outcomes and Measures of Overall Health in Adults
- 2022
-
Ingår i: Patient-Patient Centered Outcomes Research. - : Springer Science and Business Media LLC. - 1178-1653 .- 1178-1661. ; 15:3, s. 341-351
-
Tidskriftsartikel (refereegranskat)abstract
- Background The definition of population-specific outcomes is an essential precondition for the implementation of value-based health care. We developed a minimum standard outcome set for overall adult health (OAH) to facilitate the implementation of value-based health care in tracking, comparing, and improving overall health care outcomes of adults across multiple conditions, which would be of particular relevance for primary care and public health populations. Methods The International Consortium for Health Outcomes Measurement (ICHOM) convened an international panel (patients, clinicians, and topic experts). Following the development of a conceptual framework, a modified Delphi method (supported by public consultations) was implemented to identify, in sequence, the relevant domains, the best instruments for measuring them, the timing of measurement, and the relevant adjustment variables. Findings Outcomes were identified in relation to overall health status and the domains of physical, mental, and social health. Three instruments covering these domains were identified: PROMIS Scale v1.2-Global Health (10 items), WHO Wellbeing Index (5 items), and the WHO Disability Assessment Schedule 2.0 (12 items). Case-mix variables included a range of sociodemographic and biometric measures. Yearly measurement was proposed for all outcomes and most case-mix variables. Interpretation The ICHOM OAH Standard Set has been developed through consensus-based methods based on predefined criteria following high standards for the identification and selection of high-quality measures The involvements of a wide range of stakeholders supports the acceptability of the set, which is readily available for use and feasibility testing in clinical settings.
|
|
| 29. |
|
|
| 30. |
- Illana, A., et al.
(författare)
-
Coulomb excitation of 74,76Zn
- 2023
-
Ingår i: Physical Review C. - 2469-9985. ; 108:4
-
Tidskriftsartikel (refereegranskat)abstract
- The first experiment using radioactive beams post-accelerated by the HIE-ISOLDE facility has enabled to obtain a precise set of B(E2) transition probabilities in neutron-rich 74,76Zn isotopes. The resulting B(E2; 2+1→0+1) values are consistent with those determined in earlier REX-ISOLDE measurements. While the B(E2; 4+1→2+1) transition probability in 76Zn is also in agreement with earlier Coulomb-excitation results, the value obtained for 74Zn is considerably lower. For the first time, a spectroscopic quadrupole moment of the 2+1 state was measured for an exotic nucleus in this mass region. A detailed comparison is presented with large-scale shell-model and Monte Carlo shell-model calculations.
|
|
| 31. |
- Jin, Shoko, et al.
(författare)
-
The wide-field, multiplexed, spectroscopic facility WEAVE : Survey design, overview, and simulated implementation
- 2024
-
Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press. - 0035-8711 .- 1365-2966. ; 530:3, s. 2688-2730
-
Tidskriftsartikel (refereegranskat)abstract
- WEAVE, the new wide-field, massively multiplexed spectroscopic survey facility for the William Herschel Telescope, saw first light in late 2022. WEAVE comprises a new 2-deg field-of-view prime-focus corrector system, a nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini' integral field units (IFUs), and a single large IFU. These fibre systems feed a dual-beam spectrograph covering the wavelength range 366-959nm at R similar to 5000, or two shorter ranges at . After summarizing the design and implementation of WEAVE and its data systems, we present the organization, science drivers, and design of a five- to seven-year programme of eight individual surveys to: (i) study our Galaxy's origins by completing Gaia's phase-space information, providing metallicities to its limiting magnitude for similar to 3 million stars and detailed abundances for similar to 1.5 million brighter field and open-cluster stars; (ii) survey similar to 0.4 million Galactic-plane OBA stars, young stellar objects, and nearby gas to understand the evolution of young stars and their environments; (iii) perform an extensive spectral survey of white dwarfs; (iv) survey similar to 400 neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and kinematics of stellar populations and ionized gas in z < 0.5 cluster galaxies; (vi) survey stellar populations and kinematics in field galaxies at 0.3 less than or similar to z less than or similar to 0.7; (vii) study the cosmic evolution of accretion and star formation using >1 million spectra of LOFAR-selected radio sources; and (viii) trace structures using intergalactic/circumgalactic gas at z > 2. Finally, we describe the WEAVE Operational Rehearsals using the WEAVE Simulator.
|
|
| 32. |
- Karna, E., et al.
(författare)
-
A Multilevel Model of Older Adults' Appropriation of ICT and Acquisition of Digital Literacy
- 2022
-
Ingår i: International Journal of Environmental Research and Public Health. - : MDPI AG. - 1661-7827 .- 1660-4601. ; 19:23
-
Tidskriftsartikel (refereegranskat)abstract
- Digital literacy refers to a set of competencies related to the skilled use of computers and information technology. Low digital skills can be a barrier for older adults' full participation in a digital society, and COVID-19 has increased this risk of social exclusion. Older adults' digital inclusion is a complex process that consists of the interplay of structural and individual factors. The ACCESS project unwrapped the complexity of the process and developed an innovative, multilevel model that illustrates how societal, institutional, material and pedagogical aspects shape adults' appropriation of digital literacy. A holistic model describes factors contributing to older adults' digital literacy, acknowledging sociocultural contexts, environments, learning settings and instruction practices for learning digital literacy. Instead of seeing older adults' reasons for learning digital skills purely as individual choice, this model recognizes the interpersonal, institutional and societal aspects that implicitly or explicitly influence older adults' acquisition of digital literacy. The results offer a tool for stakeholders, the research community, companies, designers and other relevant stakeholders to consider digital skills and the given support. It demands diverse communication between different stakeholders about the things that should be discussed when organizing digital support in digitalized societies.
|
|
| 33. |
- Li, YL, et al.
(författare)
-
Patterns of somatic structural variation in human cancer genomes
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 112-
-
Tidskriftsartikel (refereegranskat)abstract
- A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1–7. Here we develop methods to group, classify and describe somatic structural variants, using data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumour types8. Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions—as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements. One prominent structure consists of 2–7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, and—in liver cancer—frequently activate the telomerase gene TERT. A wide variety of rearrangement processes are active in cancer, which generate complex configurations of the genome upon which selection can act.
|
|
| 34. |
|
|
| 35. |
- Morrison, L., et al.
(författare)
-
Dealing with contaminants in Coulomb excitation of radioactive beams
- 2020
-
Ingår i: 27th International Nuclear Physics Conference (INPC2019) 29 July - 2 August 2019, Glasgow, UK. - : IOP Publishing. - 1742-6588. ; 1643
-
Konferensbidrag (refereegranskat)abstract
- Data analysis of the Coulomb excitation experiment of the exotic 206Hg nucleus, recently performed at CERN's HIE-ISOLDE facility, needs to account for the contribution to target excitation due to the strongly-present beam contaminant 130Xe. In this paper, the contamination subtraction procedure is presented.
|
|
| 36. |
- Morrison, L., et al.
(författare)
-
Quadrupole and octupole collectivity in the semi-magic nucleus 20680Hg126
- 2023
-
Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693. ; 838
-
Tidskriftsartikel (refereegranskat)abstract
- The first low-energy Coulomb-excitation measurement of the radioactive, semi-magic, two proton-hole nucleus 206Hg, was performed at CERN's recently-commissioned HIE-ISOLDE facility. Two γ rays depopulating low-lying states in 206Hg were observed. From the data, a reduced transition strength B(E2; 2+1 → 0+1) = 4.4(6) W.u. was determined, the first such value for an N=126 nucleus south of 208Pb, which is found to be slightly lower than that predicted by shell-model calculations. In addition, a collective octupole state was identified at an excitation energy of 2705 keV, for which a reduced B(E3) transition probability of 30+10-30 W.u. was extracted. These results are crucial for understanding both quadrupole and octupole collectivity in the vicinity of the heaviest doubly-magic nucleus 208Pb, and for benchmarking a number of theoretical approaches in this key region. This is of particular importance given the paucity of data on transition strengths in this region, which could be used, in principle, to test calculations relevant to the astrophysical r-process.
|
|
| 37. |
- Morrison, L., et al.
(författare)
-
Quadrupole deformation of Xe 130 measured in a Coulomb-excitation experiment
- 2020
-
Ingår i: Physical Review C. - 2469-9985. ; 102:5
-
Tidskriftsartikel (refereegranskat)abstract
- Low-lying states in the isotope Xe130 were populated in a Coulomb-excitation experiment performed at CERN's HIE-ISOLDE facility. The magnitudes and relative signs of seven E2 matrix elements and one M1 matrix element coupling five low-lying states in Xe130 were determined using the semiclassical coupled-channel Coulomb-excitation least-squares search code gosia. The diagonal E2 matrix elements of both the 21+ and 41+ states were extracted for the first time. The reduced transition strengths are in line with those obtained from previous measurements. Experimental results were compared with the general Bohr Hamiltonian with the microscopic input from mean-field theory utilizing universal nuclear energy density functional (UNEDF0), shell-model calculations using the GCN50:82 and SN100PN interactions, and simple phenomenological models (Davydov-Filippov and γ-soft). The extracted shape parameters indicate triaxial-prolate deformation in the ground-state band. In general, good agreement between theoretical predictions and experimental values was found, while neither phenomenological model was found to provide an adequate description of Xe130.
|
|
| 38. |
- Petkevicius, K., et al.
(författare)
-
TLCD1 and TLCD2 regulate cellular phosphatidylethanolamine composition and promote the progression of non-alcoholic steatohepatitis
- 2022
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- The regulation of cellular phosphatidylethanolamine (PE) acyl chain composition is poorly understood. Here, the authors show that TLCD1 and TLCD2 proteins mediate the formation of monounsaturated fatty acid-containing PE species and promote the progression of non-alcoholic steatohepatitis. The fatty acid composition of phosphatidylethanolamine (PE) determines cellular metabolism, oxidative stress, and inflammation. However, our understanding of how cells regulate PE composition is limited. Here, we identify a genetic locus on mouse chromosome 11, containing two poorly characterized genes Tlcd1 and Tlcd2, that strongly influences PE composition. We generated Tlcd1/2 double-knockout (DKO) mice and found that they have reduced levels of hepatic monounsaturated fatty acid (MUFA)-containing PE species. Mechanistically, TLCD1/2 proteins act cell intrinsically to promote the incorporation of MUFAs into PEs. Furthermore, TLCD1/2 interact with the mitochondria in an evolutionarily conserved manner and regulate mitochondrial PE composition. Lastly, we demonstrate the biological relevance of our findings in dietary models of metabolic disease, where Tlcd1/2 DKO mice display attenuated development of non-alcoholic steatohepatitis compared to controls. Overall, we identify TLCD1/2 proteins as key regulators of cellular PE composition, with our findings having broad implications in understanding and treating disease.
|
|
| 39. |
- Rodriguez-Martin, B, et al.
(författare)
-
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
- 2020
-
Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 52:3, s. 306-
-
Tidskriftsartikel (refereegranskat)abstract
- About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage–fusion–bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of 22 L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors.
|
|
| 40. |
- Walton, Esther, et al.
(författare)
-
Brain Structure in Acutely Underweight and Partially Weight-Restored Individuals With Anorexia Nervosa : A Coordinated Analysis by the ENIGMA Eating Disorders Working Group
- 2022
-
Ingår i: Biological Psychiatry. - : Elsevier. - 0006-3223 .- 1873-2402. ; 92:9, s. 730-738
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The pattern of structural brain abnormalities in anorexia nervosa (AN) is still not well understood. While several studies report substantial deficits in gray matter volume and cortical thickness in acutely underweight patients, others find no differences, or even increases in patients compared with healthy control subjects. Recent weight regain before scanning may explain some of this heterogeneity. To clarify the extent, magnitude, and de-pendencies of gray matter changes in AN, we conducted a prospective, coordinated meta-analysis of multicenter neuroimaging data.METHODS: We analyzed T1-weighted structural magnetic resonance imaging scans assessed with standardized methods from 685 female patients with AN and 963 female healthy control subjects across 22 sites worldwide. In addition to a case-control comparison, we conducted a 3-group analysis comparing healthy control subjects with acutely underweight AN patients (n = 466) and partially weight-restored patients in treatment (n = 251).RESULTS: In AN, reductions in cortical thickness, subcortical volumes, and, to a lesser extent, cortical surface area were sizable (Cohen's d up to 0.95), widespread, and colocalized with hub regions. Highlighting the effects of un-dernutrition, these deficits were associated with lower body mass index in the AN sample and were less pronounced in partially weight-restored patients.CONCLUSIONS: The effect sizes observed for cortical thickness deficits in acute AN are the largest of any psychiatric disorder investigated in the ENIGMA (Enhancing Neuro Imaging Genetics through Meta Analysis) Consortium to date. These results confirm the importance of considering weight loss and renutrition in biomedical research on AN and underscore the importance of treatment engagement to prevent potentially long-lasting structural brain changes in this population.
|
|
| 41. |
|
|
| 42. |
- Adebahr, B., et al.
(författare)
-
Apercal - The Apertif calibration pipeline
- 2022
-
Ingår i: Astronomy and Computing. - : Elsevier BV. - 2213-1337. ; 38
-
Tidskriftsartikel (refereegranskat)abstract
- Apertif (APERture Tile In Focus) is one of the Square Kilometre Array (SKA) pathfinder facilities. The Apertif project is an upgrade to the 50-year-old Westerbork Synthesis Radio Telescope (WSRT) using phased-array feed technology. The new receivers create 40 individual beams on the sky, achieving an instantaneous sky coverage of 6.5 square degrees. The primary goal of the Apertif Imaging Survey is to perform a wide survey of 3500 square degrees (AWES) and a medium deep survey of 350 square degrees (AMES) of neutral atomic hydrogen (up to a redshift of 0.26), radio continuum emission and polarisation. Each survey pointing yields 4.6 TB of correlated data. The goal of Apercal is to process this data and fully automatically generate science ready data products for the astronomical community while keeping up with the survey observations. We make use of common astronomical software packages in combination with Python based routines and parallelisation. We use an object oriented module-based approach to ensure easy adaptation of the pipeline. A Jupyter notebook based framework allows user interaction and execution of individual modules as well as a full automatic processing of a complete survey observation. If nothing interrupts processing, we are able to reduce a single pointing survey observation on our five node cluster with 24 physical cores and 256 GB of memory each within 24 h keeping up with the speed of the surveys. The quality of the generated images is sufficient for scientific usage for 44% of the recorded data products with single images reaching dynamic ranges of several thousands. Future improvements will increase this percentage to over 80%. Our design allowed development of the pipeline in parallel to the commissioning of the Apertif system.
|
|
| 43. |
- Cederwall, B., et al.
(författare)
-
Isospin Properties of Nuclear Pair Correlations from the Level Structure of the Self-Conjugate Nucleus Ru-88
- 2020
-
Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 124:6
-
Tidskriftsartikel (refereegranskat)abstract
- The low-lying energy spectrum of the extremely neutron-deficient self-conjugate (N = Z) nuclide Ru-88(44)44 has been measured using the combination of the Advanced Gamma Tracking Array (AGATA) spectrometer, the NEDA and Neutron Wall neutron detector arrays, and the DIAMANT charged particle detector array. Excited states in Ru-88 were populated via the Fe-54(Ar-36, 2n gamma)Ru-88* fusion-evaporation reaction at the Grand Accelerateur National d'Ions Lourds (GANIL) accelerator complex. The observed gamma-ray cascade is assigned to Ru-88 using clean prompt gamma-gamma-2-neutron coincidences in anticoincidence with the detection of charged particles, confirming and extending the previously assigned sequence of low-lying excited states. It is consistent with a moderately deformed rotating system exhibiting a band crossing at a rotational frequency that is significantly higher than standard theoretical predictions with isovector pairing, as well as observations in neighboring N > Z nuclides. The direct observation of such a "delayed" rotational alignment in a deformed N = Z nucleus is in agreement with theoretical predictions related to the presence of strong isoscalar neutron-proton pair correlations.
|
|
| 44. |
- Cederwall, Bo, 1964-, et al.
(författare)
-
Isospin Properties of Nuclear Pair Correlations from the Level Structure of the Self-Conjugate Nucleus Ru 88
- 2020
-
Ingår i: Physical Review Letters. - : American Physical Society (APS). - 0031-9007 .- 1079-7114. ; 124:6
-
Tidskriftsartikel (refereegranskat)abstract
- The low-lying energy spectrum of the extremely neutron-deficient self-conjugate (N = Z) nuclide 88Ru has been measured using the combination of the Advanced Gamma Tracking Array (AGATA)spectrometer, the NEDA, and Neutron Wall neutron detector arrays, and the DIAMANT charged particle detector array. Excited states in 88 Ru were populated via the 54 Feð 36 Ar; 2nγÞ 88 Ru fusion-evaporationreaction at the Grand Accélérateur National d’Ions Lourds (GANIL) accelerator complex. The observed γ-ray cascade is assigned to 88 Ru using clean prompt γ-γ-2-neutron coincidences in anticoincidence with the detection of charged particles, confirming and extending the previously assigned sequence of low-lying excited states. It is consistent with a moderately deformed rotating system exhibiting a band crossing at a rotational frequency that is significantly higher than standard theoretical predictions with isovector pairing, as well as observations in neighboring N > Z nuclides. The direct observation of such a “delayed” rotational alignment in a deformed N 1⁄4 Z nucleus is in agreement with theoretical predictions related to the presence of strong isoscalar neutron-proton pair correlations.
|
|
| 45. |
- Clement, E., et al.
(författare)
-
Spectroscopic quadrupole moments in 124Xe
- 2023
-
Ingår i: Physical Review C. - : American Physical Society. - 2469-9985 .- 2469-9993. ; 107:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The Xe isotopic chain with four valence protons above the Z = 50 shell closure is an ideal laboratory for the study of the evolution of nuclear deformation. At the N = 82 shell closure, 136Xe presents all characteristics of a doubly closed shell nucleus with a spherical shape. In the very neutron-deficient isotopes close to N = 50, the alpha-decay chain of Xe was investigated to probe the radioactive decay properties near the drip-line and the magicity of 100Sn. Additionally, the Xe isotopes present higher order symmetries in the nuclear deformation such as the octupole degree of freedom near N = 60 and N = 90 or O(6) symmetry in stable isotopes.Purpose: The relevance of the O(6) symmetry has been investigated by measuring the spectroscopic quadrupole moment of the first excited states in 124Xe. In the O(6) symmetry limit, the spectroscopic quadrupole moment of collective states is expected to be null.Method: A stable 124Xe beam with energies of 4.03A MeV and 4.11A MeV was used to bombard a natW target at the GANIL facility. Excited states were populated via the safe Coulomb excitation reaction. The collision of the heavy ions with a large Z at low energy make this reaction sensitive to the diagonal E2 matrix element of the excited states. The recoils were detected in the VAMOS++ magnetic spectrometer and the gamma rays in the AGATA tracking array. The least squares fitting code GOSIA was used for the analysis to extract both E2 and M1 transitional and E2 diagonal matrix elements.Results: The rotational ground state band was populated up to the 8+1 state as well as the 2+2 and 4+2 states. Using high precision spectroscopic data to constrain the GOSIA fit, the spectroscopic quadrupole moments of the 2+1 , 4+1 , and 6+1 states were determined for the first time.Conclusions: The spectroscopic quadrupole moments were found to be negative, large, and constant in the ground state band underlining the prolate axially deformed ground state band of 124Xe. The present experimental data confirm that the is broken in 124Xe.
|
|
| 46. |
- Cortes-Ciriano, I, et al.
(författare)
-
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
- 2020
-
Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 52:3, s. 331-
-
Tidskriftsartikel (refereegranskat)abstract
- Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer.
|
|
| 47. |
|
|
| 48. |
|
|
| 49. |
- Denes, H., et al.
(författare)
-
Characterising the Apertif primary beam response
- 2022
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 667
-
Tidskriftsartikel (refereegranskat)abstract
- Context. Phased array feeds (PAFs) are multi-element receivers in the focal plane of a telescope that make it possible to simultaneously form multiple beams on the sky by combining the complex gains of the individual antenna elements. Recently, the Westerbork Synthesis Radio Telescope (WSRT) was upgraded with PAF receivers to carry out several observing programs, including two imaging surveys and a time-domain survey. The Apertif imaging surveys use a configuration of 40 partially overlapping compound beams (CBs) simultaneously formed on the sky and arranged in an approximately rectangular shape. Aims. This work is aimed at characterising the response of the 40 Apertif CBs to create frequency-resolved I, XX, and YY polarization empirical beam shapes. The measured CB maps can be used for the image deconvolution, primary beam correction, and mosaicking processes of Apertif imaging data. Methods. We used drift scan measurements to measure the response of each of the 40 Apertif CBs. We derived beam maps for all individual beams in I, XX, and YY polarisation in 10 or 18 frequency bins over the same bandwidth as the Apertif imaging surveys. We sampled the main lobe of the beams and the side lobes up to a radius of 0.6 degrees from the beam centres. In addition, we derived beam maps for each individual WSRT dish. Results. We present the frequency and time dependence of the beam shapes and sizes. We compared the compound beam shapes derived with the drift scan method to beam shapes derived with an independent method using a Gaussian Process Regression comparison between the Apertif continuum images and the NRAO VLA Sky Survey (NVSS) catalogue. We find a good agreement between the beam shapes derived with the two independent methods.
|
|
| 50. |
|
|
