| 1. |
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| 2. |
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| 3. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 4. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 5. |
- Glasbey, JC, et al.
(author)
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- 2021
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swepub:Mat__t
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| 6. |
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| 7. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)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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| 8. |
- Singh, B., et al.
(author)
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Study of doubly strange systems using stored antiprotons
- 2016
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In: Nuclear Physics A. - : Elsevier. - 0375-9474 .- 1873-1554. ; 954, s. 323-340
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Journal article (peer-reviewed)abstract
- Bound nuclear systems with two units of strangeness are still poorly known despite their importance for many strong interaction phenomena. Stored antiprotons beams in the GeV range represent an unparalleled factory for various hyperon-antihyperon pairs. Their outstanding large production probability in antiproton collisions will open the floodgates for a series of new studies of systems which contain two or even more units of strangeness at the PANDA experiment at FAIR. For the first time, high resolution gamma-spectroscopy of doubly strange Lambda Lambda-hypernuclei will be performed, thus complementing measurements of ground state decays of Lambda Lambda-hypernuclei at J-PARC or possible decays of particle unstable hypernuclei in heavy ion reactions. High resolution spectroscopy of multistrange Xi(-) -atoms will be feasible and even the production of Omega(-) -atoms will be within reach. The latter might open the door to the vertical bar S vertical bar = 3 world in strangeness nuclear physics, by the study of the hadronic Omega(-) -nucleus interaction. For the first time it will be possible to study the behavior of Xi(+) in nuclear systems under well controlled conditions.
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| 9. |
- Collaboration, The PANDA, et al.
(author)
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Feasibility studies of time-like proton electromagnetic form factors at PANDA at FAIR
- 2016
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In: European Physical Journal A. - : Springer Publishing Company. - 1434-6001 .- 1434-601X. ; 52:10
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Journal article (peer-reviewed)abstract
- Simulation results for future measurements of electromagnetic proton form factors at P ¯ ANDA (FAIR) within the PandaRoot software framework are reported. The statistical precision with which the proton form factors can be determined is estimated. The signal channel p¯ p→ e+e- is studied on the basis of two different but consistent procedures. The suppression of the main background channel, i.e.p¯ p→ π+π-, is studied. Furthermore, the background versus signal efficiency, statistical and systematical uncertainties on the extracted proton form factors are evaluated using two different procedures. The results are consistent with those of a previous simulation study using an older, simplified framework. However, a slightly better precision is achieved in the PandaRoot study in a large range of momentum transfer, assuming the nominal beam conditions and detector performance.
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| 10. |
- Singh, B., et al.
(author)
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Feasibility study for the measurement of pi N transition distribution amplitudes at (P)over-barANDA in (P)over-barp -> J/psi pi(0)
- 2017
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In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 95:3
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Journal article (peer-reviewed)abstract
- The exclusive charmonium production process in (P) over barp annihilation with an associated pi 0 meson (p) over barp -> J/psi pi(0) is studied in the framework of QCD collinear factorization. The feasibility of measuring this reaction through the J/psi -> e(+) e(-) decay channel with the AntiProton ANnihilation at DArmstadt ((P) over bar ANDA) experiment is investigated. Simulations on signal reconstruction efficiency as well as the background rejection from various sources including the (P) over barp -> pi(+)pi(-)pi(0) and (p) over barp -> J/psi pi(0)pi(0) reactions are performed with PANDAROOT, the simulation and analysis software framework of the (P) over bar ANDA experiment. It is shown that the measurement can be done at (P) over bar ANDA with significant constraining power under the assumption of an integrated luminosity attainable in four to five months of data taking at the maximum design luminosity.
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| 11. |
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| 12. |
- Barucca, G., et al.
(author)
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Study of excited Ξ baryons with the P¯ ANDA detector
- 2021
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In: European Physical Journal A. - : Springer Nature. - 1434-6001 .- 1434-601X. ; 57:4
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Journal article (peer-reviewed)abstract
- The study of baryon excitation spectra provides insight into the inner structure of baryons. So far, most of the world-wide efforts have been directed towards N∗ and Δ spectroscopy. Nevertheless, the study of the double and triple strange baryon spectrum provides independent information to the N∗ and Δ spectra. The future antiproton experiment P¯ANDA will provide direct access to final states containing a Ξ¯ Ξ pair, for which production cross sections up to μb are expected in p¯p reactions. With a luminosity of L= 10 31 cm- 2 s- 1 in the first phase of the experiment, the expected cross sections correspond to a production rate of ∼106events/day. With a nearly 4 π detector acceptance, P¯ANDA will thus be a hyperon factory. In this study, reactions of the type p¯p → Ξ¯ +Ξ∗ - as well as p¯p → Ξ¯ ∗ +Ξ- with various decay modes are investigated. For the exclusive reconstruction of the signal events a full decay tree fit is used, resulting in reconstruction efficiencies between 3 and 5%. This allows high statistics data to be collected within a few weeks of data taking.
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| 13. |
- Barucca, G., et al.
(author)
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The potential of Λ and Ξ- studies with PANDA at FAIR
- 2021
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In: European Physical Journal A. - : Springer Nature. - 1434-6001 .- 1434-601X. ; 57:4
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Journal article (peer-reviewed)abstract
- The antiproton experiment PANDA at FAIR is designed to bring hadron physics to a new level in terms of scope, precision and accuracy. In this work, its unique capability for studies of hyperons is outlined. We discuss ground-state hyperons as diagnostic tools to study non-perturbative aspects of the strong interaction, and fundamental symmetries. New simulation studies have been carried out for two benchmark hyperon-antihyperon production channels: p¯ p→ Λ¯ Λ and p¯ p→ Ξ¯ +Ξ-. The results, presented in detail in this paper, show that hyperon-antihyperon pairs from these reactions can be exclusively reconstructed with high efficiency and very low background contamination. In addition, the polarisation and spin correlations have been studied, exploiting the weak, self-analysing decay of hyperons and antihyperons. Two independent approaches to the finite efficiency have been applied and evaluated: one standard multidimensional efficiency correction approach, and one efficiency independent approach. The applicability of the latter was thoroughly evaluated for all channels, beam momenta and observables. The standard method yields good results in all cases, and shows that spin observables can be studied with high precision and accuracy already in the first phase of data taking with PANDA.
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| 14. |
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| 15. |
- Beral, V, et al.
(author)
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Alcohol, tobacco and breast cancer - collaborative reanalysis of individual data from 53 epidemiological studies, including 58515 women with breast cancer and 95067 women without the disease
- 2002
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In: British Journal of Cancer. - : Springer Science and Business Media LLC. - 1532-1827 .- 0007-0920. ; 87, s. 1234-45
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Journal article (peer-reviewed)abstract
- Alcohol and tobacco consumption are closely correlated and published results on their association with breast cancer have not always allowed adequately for confounding between these exposures. Over 80% of the relevant information worldwide on alcohol and tobacco consumption and breast cancer were collated, checked and analysed centrally. Analyses included 58515 women with invasive breast cancer and 95067 controls from 53 studies. Relative risks of breast cancer were estimated, after stratifying by study, age, parity and, where appropriate, women's age when their first child was born and consumption of alcohol and tobacco. The average consumption of alcohol reported by controls from developed countries was 6.0 g per day, i.e. about half a unit/drink of alcohol per day, and was greater in ever-smokers than never-smokers, (8.4 g per day and 5.0 g per day, respectively). Compared with women who reported drinking no alcohol, the relative risk of breast cancer was 1.32 (1.19 - 1.45, P < 0.00001) for an intake of 35 - 44 g per day alcohol, and 1.46 (1.33 - 1.61, P < 0.00001) for greater than or equal to 45 g per day alcohol. The relative risk of breast cancer increased by 7.1% (95% CI 5.5-8.7%; P<0.00001) for each additional 10 g per day intake of alcohol, i.e. for each extra unit or drink of alcohol consumed on a daily basis. This increase was the same in ever-smokers and never-smokers (7.1 % per 10 g per day, P < 0.00001, in each group). By contrast, the relationship between smoking and breast cancer was substantially confounded by the effect of alcohol. When analyses were restricted to 22 255 women with breast cancer and 40 832 controls who reported drinking no alcohol, smoking was not associated with breast cancer (compared to never-smokers, relative risk for ever-smokers= 1.03, 95% CI 0.98 - 1.07, and for current smokers=0.99, 0.92 - 1.05). The results for alcohol and for tobacco did not vary substantially across studies, study designs, or according to 15 personal characteristics of the women; nor were the findings materially confounded by any of these factors. If the observed relationship for alcohol is causal, these results suggest that about 4% of the breast cancers in developed countries are attributable to alcohol. In developing countries, where alcohol consumption among controls averaged only 0.4 g per day, alcohol would have a negligible effect on the incidence of breast cancer. In conclusion, smoking has little or no independent effect on the risk of developing breast cancer; the effect of alcohol on breast cancer needs to be interpreted in the context of its beneficial effects, in moderation, on cardiovascular disease and its harmful effects on cirrhosis and cancers of the mouth, larynx, oesophagus and liver. (C) 2002 Cancer Research UK.
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| 16. |
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| 17. |
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| 18. |
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| 19. |
- Abdoullaye, Doukary, et al.
(author)
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Permanent genetic resources added to molecular ecology resources database 1 August 2009 - 30 September 2009
- 2010
-
In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:1, s. 232-236
-
Journal article (peer-reviewed)abstract
- This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.
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| 20. |
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| 21. |
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| 22. |
- Turkington, RC, et al.
(author)
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Immune activation by DNA damage predicts response to chemotherapy and survival in oesophageal adenocarcinoma
- 2019
-
In: Gut. - : BMJ. - 1468-3288 .- 0017-5749. ; 68:11, s. 1918-1927
-
Journal article (peer-reviewed)abstract
- Current strategies to guide selection of neoadjuvant therapy in oesophageal adenocarcinoma (OAC) are inadequate. We assessed the ability of a DNA damage immune response (DDIR) assay to predict response following neoadjuvant chemotherapy in OAC.DesignTranscriptional profiling of 273 formalin-fixed paraffin-embedded prechemotherapy endoscopic OAC biopsies was performed. All patients were treated with platinum-based neoadjuvant chemotherapy and resection between 2003 and 2014 at four centres in the Oesophageal Cancer Clinical and Molecular Stratification consortium. CD8 and programmed death ligand 1 (PD-L1) immunohistochemical staining was assessed in matched resection specimens from 126 cases. Kaplan-Meier and Cox proportional hazards regression analysis were applied according to DDIR status for recurrence-free survival (RFS) and overall survival (OS).ResultsA total of 66 OAC samples (24%) were DDIR positive with the remaining 207 samples (76%) being DDIR negative. DDIR assay positivity was associated with improved RFS (HR: 0.61; 95% CI 0.38 to 0.98; p=0.042) and OS (HR: 0.52; 95% CI 0.31 to 0.88; p=0.015) following multivariate analysis. DDIR-positive patients had a higher pathological response rate (p=0.033), lower nodal burden (p=0.026) and reduced circumferential margin involvement (p=0.007). No difference in OS was observed according to DDIR status in an independent surgery-alone dataset.DDIR-positive OAC tumours were also associated with the presence of CD8+ lymphocytes (intratumoural: p<0.001; stromal: p=0.026) as well as PD-L1 expression (intratumoural: p=0.047; stromal: p=0.025).ConclusionThe DDIR assay is strongly predictive of benefit from DNA-damaging neoadjuvant chemotherapy followed by surgical resection and is associated with a proinflammatory microenvironment in OAC.
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| 23. |
- Antonarakis, S. E., et al.
(author)
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Factor VIII gene inversions in severe hemophilia A : Results of an international consortium study
- 1995
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In: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 86:6, s. 2206-2212
-
Journal article (peer-reviewed)abstract
- Twenty-two molecular diagnostic laboratories from 14 countries participated in a consortium study to estimate the impact of Factor VIII gene inversions in severe hemophilia A. A total of 2,093 patients with severe hemophilia A were studied; of those, 740 (35%) had a type 1 (distal) factor VIII inversion, and 140 (7%) showed a type 2 (proximal) inversion. In 25 cases, the molecular analysis showed additional abnormal or polymorphic patterns. Ninety-eight percent of 532 mothers of patients with inversions were carriers of the abnormal factor VIII gene; when only mothers of nonfamilial cases were studied, 9 de novo inversions in maternal germ cells ware observed among 225 cases (≃ 1 de novo maternal origin of the inversion in 25 mothers of sporadic cases). When the maternal grandparental origin was examined, the inversions occurred de novo in male germ cells in 69 cases and female germ cells in 1 case. The presence of factor VIII inversions is not a major predisposing factor for the development of factor VIII inhibitors; however, slightly more patients with severe hemophilia A and factor VIII inversions develop inhibitors (130 of 642 [20%]) than patients with severe hemophilia A without inversions (131 of 821 [16%]).
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| 24. |
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| 25. |
- Marcaide, J. M., et al.
(author)
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Discovery of shell-like radio-structure in SN1993J
- 1995
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In: Nature. - London : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 373:6509, s. 44-45
-
Journal article (peer-reviewed)abstract
- SUPERNOVA explosions are poorly understood, partly because of difficulties in modelling them theoretically(1), and partly because there have been no supernovae observed in our Galaxy since the invention of the telescope. But the recent discovery(2) of supernova SN1993J in the nearby galaxy M81 offers an opportunity to investigate the evolution of the remnant, and its interaction with the surrounding interstellar medium, at high resolution. Here we present radio observations of SN1993J, made using very-long-baseline interferometry, which show the development of a shell structure. This 8-month-old radio shell is the youngest ever discovered in a supernova. The data suggest that the supernova explosion and the expanding shell of the remnant have nearly spherical symmetry, with small deviations where some parts of the shell are brighter than others. If these deviations arise because of variations in the density of the shell, this may reconcile earlier reports of symmetric radio emission(3) with the observed optical asymmetry(4,5), as the density variations could easily cause the latter. We infer that the radio emission is generated at the interface(6-9), where the surrounding gas is shocked by the ejecta.
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| 26. |
- Mourikis, TP, et al.
(author)
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Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma
- 2019
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 3101-
-
Journal article (peer-reviewed)abstract
- The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously. Analysing 261 EACs from the OCCAMS Consortium, we discover helper genes that, alongside well-known drivers, promote cancer. We confirm the robustness of our approach in 107 additional EACs. Unlike recurrent alterations of known drivers, these cancer helper genes are rare or patient-specific. However, they converge towards perturbations of well-known cancer processes. Recurrence of the same process perturbations, rather than individual genes, divides EACs into six clusters differing in their molecular and clinical features. Experimentally mimicking the alterations of predicted helper genes in cancer and pre-cancer cells validates their contribution to disease progression, while reverting their alterations reveals EAC acquired dependencies that can be exploited in therapy.
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| 27. |
- Ness, A. R., et al.
(author)
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Centralization of cleft care in the UK. Part 6 : a tale of two studies
- 2015
-
In: Orthod Craniofac Res. - 1601-6343 (Electronic) 1601-6335 (Linking) ; 18 Suppl 2, s. 56-62
-
Journal article (peer-reviewed)abstract
- OBJECTIVES: We summarize and critique the methodology and outcomes from a substantial study which has investigated the impact of reconfigured cleft care in the United Kingdom (UK) 15 years after the UK government started to implement the centralization of cleft care in response to an earlier survey in 1998, the Clinical Standards Advisory Group (CSAG). SETTING AND SAMPLE POPULATION: A UK multicentre cross-sectional study of 5-year-olds born with non-syndromic unilateral cleft lip and palate. Data were collected from children born in the UK with a unilateral cleft lip and palate between 1 April 2005 and 31 March 2007. MATERIALS AND METHODS: We discuss and contextualize the outcomes from speech recordings, hearing, photographs, models, oral health and psychosocial factors in the current study. We refer to the earlier survey and other relevant studies. RESULTS: We present arguments for centralization of cleft care in healthcare systems, and we evidence this with improvements seen over a period of 15 years in the UK. We also make recommendations on how future audit and research may configure. CONCLUSIONS: Outcomes for children with a unilateral cleft lip and palate have improved after the introduction of a centralized multidisciplinary service, and other countries may benefit from this model. Predictors of early outcomes are still needed, and repeated cross-sectional studies, larger longitudinal studies and adequately powered trials are required to create a research-led evidence-based (centralized) service.
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| 28. |
- Persson, Martin, 1971-, et al.
(author)
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A cross-sectional survey of 5-year-old children with non-syndromic unilateral cleft lip and palate : the Cleft Care UK study. Part 1
- 2015
-
In: Orthod Craniofac Res. - 1601-6343 (Electronic) 1601-6335 (Linking) ; 18 Suppl 2, s. 1-13
-
Journal article (peer-reviewed)abstract
- OBJECTIVES: We describe the methodology for a major study investigating the impact of reconfigured cleft care in the United Kingdom (UK) 15 years after an initial survey, detailed in the Clinical Standards Advisory Group (CSAG) report in 1998, had informed government recommendations on centralization. SETTING AND SAMPLE POPULATION: This is a UK multicentre cross-sectional study of 5-year-olds born with non-syndromic unilateral cleft lip and palate. Children born between 1 April 2005 and 31 March 2007 were seen in cleft centre audit clinics. MATERIALS AND METHODS: Consent was obtained for the collection of routine clinical measures (speech recordings, hearing, photographs, models, oral health, psychosocial factors) and anthropometric measures (height, weight, head circumference). The methodology for each clinical measure followed those of the earlier survey as closely as possible. RESULTS: We identified 359 eligible children and recruited 268 (74.7%) to the study. Eleven separate records for each child were collected at the audit clinics. In total, 2666 (90.4%) were collected from a potential 2948 records. The response rates for the self-reported questionnaires, completed at home, were 52.6% for the Health and Lifestyle Questionnaire and 52.2% for the Satisfaction with Service Questionnaire. CONCLUSIONS: Response rates and measures were similar to those achieved in the previous survey. There are practical, administrative and methodological challenges in repeating cross-sectional surveys 15 years apart and producing comparable data.
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| 29. |
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| 30. |
- Marcaide, J. M., et al.
(author)
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The quasars 1038+528 A and B
- 1985
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In: Astronomy and Astrophysics. - Les Ulis : EDP Sciences. - 0004-6361 .- 1432-0746. ; 142:1, s. 71-84
-
Journal article (peer-reviewed)abstract
- The results of VLBI observations of the quasars 1038 + 528 A and B at 2.8, 3.6, 13, and 18 cm at various times between November 1979 and March 1981 are reported. The observations and data calibration are described, as are the mapping and astrometric techniques applied in the study. Both quasars are found to have 'core-jet' morphologies. The core of the A quasar dominates its morphology at centrimetric wavelengths with the brightness temperature of its 400 pc long jet being about 1/100 that of the core. By contrast, the 'jet' in the B quasar is very short (about 70 pc); the tail of this jet has the steepest spectral index found to date in extragalactic compact sources, indicating that high electron losses are responsible for the shortness of the jet. No evidence for appreciable morphological change in the B quasar was found over the time span of the study, whereas a new feature may be emerging from the A quasar core at superluminal speed.
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| 31. |
- Myers, L. S., et al.
(author)
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Compton scattering from C-12 using tagged photons in the energy range 65-115 MeV
- 2014
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 89:3
-
Journal article (peer-reviewed)abstract
- Elastic scattering of photons from C-12 has been investigated using quasimonoenergetic tagged photons with energies in the range 65-115 MeV at laboratory angles of 60 degrees, 120 degrees, and 150 degrees. at the Tagged-Photon Facility at the MAX IV Laboratory in Lund, Sweden. A phenomenological model was employed to provide an estimate of the sensitivity of the C-12(gamma,gamma)C-12 cross section to the bound- nucleon polarizabilities.
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| 32. |
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| 33. |
- Sztuk-Dambietz, J., et al.
(author)
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Operational experience with Adaptive Gain Integrating Pixel Detectors at European XFEL
- 2024
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In: Frontiers in Physics. - : Frontiers Media SA. - 2296-424X. ; 11
-
Research review (peer-reviewed)abstract
- The European X-ray Free Electron Laser (European XFEL) is a cutting-edge user facility that generates per second up to 27,000 ultra-short, spatially coherent X-ray pulses within an energy range of 0.26 to more than 20 keV. Specialized instrumentation, including various 2D X-ray detectors capable of handling the unique time structure of the beam, is required. The one-megapixel AGIPD (AGIPD1M) detectors, developed for the European XFEL by the AGIPD Consortium, are the primary detectors used for user experiments at the SPB/SFX and MID instruments. The first AGIPD1M detector was installed at SPB/SFX when the facility began operation in 2017, and the second one was installed at MID in November 2018. The AGIPD detector systems require a dedicated infrastructure, well-defined safety systems, and high-level control procedures to ensure stable and safe operation. As of now, the AGIPD1M detectors installed at the SPB/SFX and MID experimental end stations are fully integrated into the European XFEL environment, including mechanical integration, vacuum, power, control, data acquisition, and data processing systems. Specific high-level procedures allow facilitated detector control, and dedicated interlock systems based on Programmable Logic Controllers ensure detector safety in case of power, vacuum, or cooling failure. The first 6 years of operation have clearly demonstrated that the AGIPD1M detectors provide high-quality scientific results. The collected data, along with additional dedicated studies, have also enabled the identification and quantification of issues related to detector performance, ensuring stable operation. Characterization and calibration of detectors are among the most critical and challenging aspects of operation due to their complex nature. A methodology has been developed to enable detector characterization and data correction, both in near real-time (online) and offline mode. The calibration process optimizes detector performance and ensures the highest quality of experimental results. Overall, the experience gained from integrating and operating the AGIPD detectors at the European XFEL, along with the developed methodology for detector characterization and calibration, provides valuable insights for the development of next-generation detectors for Free Electron Laser X-ray sources.
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| 34. |
- Azulay, R., et al.
(author)
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Dynamical masses of the low-mass stellar binary AB Doradus B
- 2015
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 578, s. Art. no. A16-
-
Journal article (peer-reviewed)abstract
- Context. AB Doradus is the main system of the AB Doradus moving group. It is a quadruple system formed by two widely separated binaries of pre-main-sequence (PMS) stars: AB Dor A/C and AB Dor Ba/Bb. The pair AB Dor A/C has been extensively studied and its dynamical masses have been determined with high precision, thus making AB Dor C a benchmark for calibrating PMS stellar models. If the orbit and dynamical masses of the pair AB Dor Ba/Bb could be determined, they could play a similar role to that of AB Dor C in calibrating PMS models, and would also help to better understand the dynamics of the whole AB Doradus system. Aims. We aim to determine the individual masses of the pair AB Dor Ba/Bb using VLBI observations and archive infrared data as part of a larger program that monitors binary systems in the AB Doradus moving group. Methods. We observed the system AB Dor B between 2007 and 2013 with the Australian Long Baseline Array (LBA) at a frequency of 8.4 GHz in phase-reference mode. Results. We detected, for the first time, compact radio emission from both stars in the binary, AB Dor Ba and AB Dor Bb. This result allowed us to determine the orbital parameters of both the relative and absolute orbits and, consequently, their individual dynamical masses: 0.28 ± 0.05 M⊙ and 0.25 ± 0.05 M⊙, respectively. Conclusions. Comparisons of the dynamical masses with the prediction of PMS evolutionary models show that the models underpredict the dynamical masses of the binary components Ba and Bb by 10-30% and 10-40%, respectively, although they still agree at the 2σ level. Some of the stellar models considered favor an age between 50 and 100 Myr for this system, while others predict older ages. We also discuss the evolutionary status of AB Dor Ba/Bb in terms of an earlier double-double star scenario that might explain the strong radio emission detected in both components.
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| 35. |
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| 36. |
- Hu, F.Z., et al.
(author)
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Mapping of an autosomal dominant gene for Dupuytren's contracture to chromosome 16q in a Swedish family
- 2005
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In: Clinical Genetics. - Oxford : Wiley. - 0009-9163 .- 1399-0004. ; 68:5, s. 424-429
-
Journal article (peer-reviewed)abstract
- Dupuytren's contracture (DC) (OMIM 126900) is the most common connective tissue disease of mankind and has both heritable and sporadic forms. The inherited form is most frequently observed among the xanthochroi peoples of Northern Europe where its most common manifestations are thickening of the palmar fascia and contracture of the fingers. We ascertained a five-generation Swedish family in which DC is inherited in an autosomal dominant manner with high, but incomplete, penetrance by the end of the fifth decade. Blood was collected from all affected and informative unaffected family members for the performance of a genome-wide scan at a resolution of approximately 8 cM for all autosomes. Linkage was established to a single 6 cM region between markers D 16S419 and D 16S3032 on chromosome 16. A maximal two-point logarithm of odds (LOD) score of 3.18 was achieved at microsatellite marker D16S415 with four other markers in the region producing LODs of > 1.5. © Blackwell Munksgaard, 2005.
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| 37. |
- Ma, C. R., et al.
(author)
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Addition of a Genetic Risk Score for Identification of Men with a Low Prostate-specific Antigen Level in Midlife at Risk of Developing Lethal Prostate Cancer
- 2023
-
In: European Urology Open Science. - : Elsevier BV. - 2666-1691 .- 2666-1683. ; 50, s. 27-30
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Journal article (peer-reviewed)abstract
- Men with a low prostate-specific antigen (PSA) level (<1 ng/ml) in midlife may extend the rescreening interval (if aged 40-59 yr) or forgo future PSA screening (if aged >60 yr) owing to their low risk of aggressive prostate cancer (PCa). However, there is a subset of men who develop lethal PCa despite low baseline PSA. We investigated how a PCa polygenic risk score (PRS) in addition to baseline PSA impacts the prediction of lethal PCa among 483 men aged 40-70 yr from the Physicians' Health Study followed over a median of 33 yr. We examined the association of the PRS with the risk of lethal PCa (lethal cases vs controls) using logistic regression adjusted for baseline PSA. The PCa PRS was associated with risk of lethal PCa (odds ratio per 1 standard deviation in PRS [OR] 1.79, 95% confidence interval [CI] 1.28-2.49). The association between the PRS and lethal PCa was stronger for those with PSA <1 ng/ml (OR 2.23, 95% CI 1.19-4.21) than for men with PSA >= 1 ng/ml (OR 1.61, 95% CI 1.07-2.42). Our PCa PRS improved the identification of men with PSA <1 ng/ml at greater risk of future lethal PCa who should consider ongoing PSA testing. Patient summary: A subset of men develop fatal prostate cancer despite having low prostate-specific antigen (PSA) levels in middle age. A risk score based on multiple genes can help in predicting men who may be at risk of developing lethal prostate cancer and who should be advised to have regular PSA measurements. (c) 2023 The Authors.
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| 38. |
- Mason, R Preston, et al.
(author)
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Loss of arterial and renal nitric oxide bioavailability in hypertensive rats with diabetes : effect of beta-blockers
- 2009
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In: American Journal of Hypertension. - : Oxford University Press (OUP). - 0895-7061 .- 1941-7225. ; 22:11, s. 1160-1166
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Journal article (peer-reviewed)abstract
- BACKGROUND: Endothelial cell (EC) dysfunction contributes to hypertension and mechanisms of atherosclerosis. Agents that improve EC function may provide vascular protection, especially in patients with multiple risk factors. In this study, we examined the effects of beta(1)-selective antagonists, nebivolol and metoprolol, on vascular and renal EC function in spontaneously hypertensive (SH) rats with diabetes. METHODS: Male SH rats were treated with streptozotocin (STZ) to induce type 2 diabetes, followed by treatment with nebivolol or metoprolol at 2 mg/kg/day (vs. vehicle). After 4 weeks, aortic and glomerular ECs were isolated, stimulated with calcium ionophore (CaI), and assayed for nitric oxide (NO), and peroxynitrite (ONOO(-)) release using amperometric approaches. RESULTS: Glucose and mean blood pressure (BP) levels were significantly elevated in diabetic SH rats. In aortic ECs isolated from diabetic SH rats, NO production decreased by 20% whereas ONOO(-) increased by 16%, an effect linked to NAD(P)H oxidase and endothelial NO synthase (eNOS) uncoupling. Nebivolol treatment reduced glucose and BP levels and restored aortic EC function in diabetic SH rats, as indicated by a 30% increase and 23% decrease in NO and ONOO(-) levels, respectively. The NO/ONOO(-) ratio increased by more than twofold with nebivolol treatment in aortic and glomerular ECs. Despite similar reductions in glucose and mean BP levels, metoprolol had a smaller effect on the NO/ONOO(-) ratio in glomerular ECs but no effect in aortic ECs. CONCLUSIONS: Vascular and renal NO was significantly reduced in diabetic hypertensive rats and correlated with metabolic changes. Nebivolol reversed these effects in a manner consistent with enhanced endothelial function.
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| 39. |
- Preston, M. F., et al.
(author)
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Tests of the Monte Carlo Simulation of the Photon-Tagger Focal-Plane Electronics at the MAX IV Laboratory
- 2014
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In: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - : Elsevier BV. - 0167-5087 .- 0168-9002. ; 744, s. 17-17
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Journal article (peer-reviewed)abstract
- Rate-dependent effects in the electronics used to instrument the tagger focal plane at the MAX IV Laboratory were recently investigated using the novel approach of Monte Carlo simulation to allow for normalization of high-rate experimental data acquired with single-hit time-to-digital converters (TDCs). The instrumentation of the tagger focal plane has now been expanded to include multi-hit TDCs. The agreement between results obtained from data taken using single-hit and multi-hit TDCs demonstrate a thorough understanding of the behavior of the detector system.
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| 40. |
- Rosendaal, Frits R., et al.
(author)
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Geographic distribution of the 20210 G to A prothrombin variant
- 1998
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In: Thrombosis and Haemostasis. - 0340-6245. ; 79:4, s. 8-706
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Journal article (peer-reviewed)abstract
- A variant in prothrombin (clotting factor II), a G to A transition at nucleotide position 20210, has recently been shown to be associated with the prothrombin plasma levels and the risk of both venous and arterial thrombosis. The purpose of this study was to investigate the prevalence of carriership of this mutation in various populations. We combined data from 11 centres in nine countries, where tests for this mutation had been performed in groups representing the general population. We calculated an overall prevalence estimate, by a precision-weighted method, and, since the distribution of the prevalences did not appear homogeneous, by an unweighted average of the prevalences. We examined differences in the prevalences by geographical location and ethnic background as a possible explanation for the heterogeneity. Among a total of 5527 individuals who had been tested, 111 heterozygous carriers of the 20210A mutation were found. The prevalence estimates varied from 0.7 to 4.0 between the centres. The overall prevalence estimate was 2.0 percent (CI95 1.4-2.6%). The variation around the summary estimate appeared more than was expected by chance alone, and this heterogeneity could be explained by geographic differences. In southern Europe, the prevalence was 3.0 percent (CI95 2.3 to 3.7%), nearly twice as high as the prevalence in northern Europe (1.7%, CI95 1.3 to 2.2%). The prothrombin variant appeared very rare in individuals from Asian and African descent. The 20210A prothrombin variant is a common abnormality, with a prevalence of carriership between one and four percent. It is more common in southern than in northern Europe. Since this distribution within Europe is very different to that of another prothrombotic mutation (factor V Leiden or factor V R506Q), founder effects are the most likely explanation for the geographical distribution of both mutations.
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| 41. |
- Strandberg, B., et al.
(author)
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Compton scattering from the deuteron above pion-production threshold
- 2018
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In: Physical Review C. - 2469-9985. ; 98:1
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Journal article (peer-reviewed)abstract
- The electromagnetic polarizabilities of the nucleon are fundamental nucleon-structure observables that characterize its response to external electromagnetic fields. The neutron polarizabilities can be accessed from Compton-scattering data on light nuclear targets. Recent measurements of the differential cross section for Compton scattering on the deuteron below the pion-production threshold have decreased the uncertainties in the neutron polarizabilities, yet the proton polarizabilities remain known substantially more accurately. As the sensitivity of the cross section to the polarizabilities increases with incident photon energy, measurements above the pion threshold may offer a way for an improved determination of the neutron polarizabilities. In this Rapid Communiciation, the first measurement of the cross section for coherent Compton scattering on the deuteron above the pion-production threshold is presented.
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| 42. |
- Strandberg, B., et al.
(author)
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Near-threshold π-photoproduction on the deuteron
- 2020
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In: Physical Review C. - 2469-9985. ; 101:3
-
Journal article (peer-reviewed)abstract
- The first experimental investigation of the near-threshold cross section for incoherent π-photoproduction on the deuteron γd→π-pp is presented. The experimental technique involved detection of the ≈131 MeV γ ray resulting from the radiative capture of photoproduced π-in the target. The total cross section was measured using an unpolarized tagged-photon beam, a liquid-deuterium target, and three very large NaI(Tl) spectrometers. The data are compared to theoretical models that give insight into the elementary reaction γn→π-p and pion-nucleon and nucleon-nucleon final-state interactions.
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| 43. |
- Vera, P. L., et al.
(author)
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Elevated Urine Levels of Macrophage Migration Inhibitory Factor in Inflammatory Bladder Conditions: A Potential Biomarker for a Subgroup of Interstitial Cystitis/Bladder Pain Syndrome Patients
- 2018
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In: Urology. - : Elsevier BV. - 0090-4295. ; 116, s. 55-61
-
Journal article (peer-reviewed)abstract
- OBJECTIVE To investigate whether urinary levels of macrophage migration inhibitory factor (MIF) are elevated in interstitial cystitis/bladder pain syndrome (IC/BPS) patients with Hunner lesions and also whether urine MIF is elevated in other forms of inflammatory cystitis. METHODS Urine samples were assayed for MIF by enzyme-linked immunosorbent assay. Urine samples from 3 female groups were examined: IC/BPS patients without (N = 55) and with Hunner lesions (N = 43), and non-IC/BPS patients (N = 100; control group; no history of IC/BPS; cancer or recent bacterial cystitis). Urine samples from 3 male groups were examined: patients with bacterial cystitis (N = 50), radiation cystitis (N = 18) and noncystitis patients (N = 119; control group; negative for bacterial cystitis). RESULTS Urine MIF (mean MIF pg/mL +/- standard error of the mean) was increased in female IC/BPS patients with Hunner lesions (2159 +/- 435.3) compared with IC/BPS patients without Hunner lesions (460 +/- 114.5) or non-IC/BPS patients (414 +/- 47.6). Receiver operating curve analyses showed that urine MIF levels discriminated between the 2 IC groups (area under the curve = 72%; confidence interval 61%-82%). Male patients with bacterial and radiation cystitis had elevated urine MIF levels (2839 +/- 757.1 and 4404 +/- 1548.1, respectively) compared with noncystitis patients (681 +/- 75.2). CONCLUSION Urine MIF is elevated in IC/BPS patients with Hunner lesions and also in patients with other bladder inflammatory and painful conditions. MIF may also serve as a noninvasive biomarker to select IC/BPS patients more accurately for endoscopic evaluation and possible anti-inflammatory treatment. (c) 2018 Elsevier Inc.
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| 44. |
- Baiocchi, Gian Luca, et al.
(author)
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International consensus on a complications list after gastrectomy for cancer
- 2019
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In: Gastric Cancer. - : Springer Science and Business Media LLC. - 1436-3291 .- 1436-3305. ; 22:1, s. 172-189
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Journal article (peer-reviewed)abstract
- Background: Perioperative complications can affect outcomes after gastrectomy for cancer, with high mortality and morbidity rates ranging between 10 and 40%. The absence of a standardized system for recording complications generates wide variation in evaluating their impacts on outcomes and hinders proposals of quality-improvement projects. The aim of this study was to provide a list of defined gastrectomy complications approved through international consensus. Methods: The Gastrectomy Complications Consensus Group consists of 34 European gastric cancer experts who are members of the International Gastric Cancer Association. A group meeting established the work plan for study implementation through Delphi surveys. A consensus was reached regarding a set of standardized methods to define gastrectomy complications. Results: A standardized list of 27 defined complications (grouped into 3 intraoperative, 14 postoperative general, and 10 postoperative surgical complications) was created to provide a simple but accurate template for recording individual gastrectomy complications. A consensus was reached for both the list of complications that should be considered major adverse events after gastrectomy for cancer and their specific definitions. The study group also agreed that an assessment of each surgical case should be completed at patient discharge and 90 days postoperatively using a Complication Recording Sheet. Conclusion: The list of defined complications (soon to be validated in an international multicenter study) and the ongoing development of an electronic datasheet app to record them provide the basic infrastructure to reach the ultimate goals of standardized international data collection, establishment of benchmark results, and fostering of quality-improvement projects.
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| 45. |
- Biggs, Reinette, et al.
(author)
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Preparing for the future : teaching scenario planning at the graduate level
- 2010
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In: Frontiers in Ecology and the Environment. - : Wiley. - 1540-9295. ; 8:5, s. 267-273
-
Journal article (peer-reviewed)abstract
- Are environmental science students developing the mindsets and obtaining the tools needed to help address the considerable challenges posed by the 21st century? Today's major environmental issues are characterized by high-stakes decisions and high levels of uncertainty. Although traditional scientific approaches are valuable, contemporary environmental issues also require new tools and new ways of thinking. We provide an example of how such new, or “post-normal”, approaches have been taught at the graduate level, through practical application of scenario planning. Surveyed students reported that they found the scenario planning course highly stimulating, thought-provoking, and inspiring. Key learning points included recognizing the need for multiple points of view when considering complex environmental issues, and better appreciating the pervasiveness of uncertainty. Collaborating with non-academic stakeholders was also particularly helpful. Most students left the course feeling more positive about the potential contribution they can make in addressing the environmental challenges that society faces. Read More: http://www.esajournals.org/doi/abs/10.1890/080075
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| 46. |
- Dornheim, Tobias, et al.
(author)
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Electronic density response of warm dense matter
- 2023
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In: Physics of Plasmas. - : AIP Publishing. - 1070-664X .- 1089-7674. ; 30:3, s. 032705-
-
Journal article (peer-reviewed)abstract
- Matter at extreme temperatures and pressures-commonly known as warm dense matter (WDM)-is ubiquitous throughout our Universe and occurs in astrophysical objects such as giant planet interiors and brown dwarfs. Moreover, WDM is very important for technological applications such as inertial confinement fusion and is realized in the laboratory using different techniques. A particularly important property for the understanding of WDM is given by its electronic density response to an external perturbation. Such response properties are probed in x-ray Thomson scattering (XRTS) experiments and are central for the theoretical description of WDM. In this work, we give an overview of a number of recent developments in this field. To this end, we summarize the relevant theoretical background, covering the regime of linear response theory and nonlinear effects, the fully dynamic response and its static, time-independent limit, and the connection between density response properties and imaginary-time correlation functions (ITCF). In addition, we introduce the most important numerical simulation techniques, including path-integral Monte Carlo simulations and different thermal density functional theory (DFT) approaches. From a practical perspective, we present a variety of simulation results for different density response properties, covering the archetypal model of the uniform electron gas and realistic WDM systems such as hydrogen. Moreover, we show how the concept of ITCFs can be used to infer the temperature from XRTS measurements of arbitrary complex systems without the need for any models or approximations. Finally, we outline a strategy for future developments based on the close interplay between simulations and experiments.
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| 47. |
- Dornheim, T., et al.
(author)
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X-ray Thomson scattering absolute intensity from the f-sum rule in the imaginary-time domain
- 2024
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 14:1
-
Journal article (peer-reviewed)abstract
- We present a formally exact and simulation-free approach for the normalization of X-ray Thomson scattering (XRTS) spectra based on the f-sum rule of the imaginary-time correlation function (ITCF). Our method works for any degree of collectivity, over a broad range of temperatures, and is applicable even in nonequilibrium situations. In addition to giving us model-free access to electronic correlations, this new approach opens up the intriguing possibility to extract a plethora of physical properties from the ITCF based on XRTS experiments.
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| 48. |
- Duarte, N., et al.
(author)
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Calibration procedures and data correction of ePix100 detectors at the European XFEL
- 2023
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In: Journal of Instrumentation. - 1748-0221. ; 18:11
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Journal article (peer-reviewed)abstract
- The European XFEL is a research facility that delivers extremely bright and short coherent X-ray pulses of tunable energy at MHz repetition rate, providing unprecedented capabilities to conduct scientific research across multiple domains. Among the suite of deployed detectors, several ePix100 modules, belonging to the family of ePix detectors developed at SLAC, are used. These charge-integrating hybrid pixel detectors offer single-photon resolution for energies above 2 keV and a dynamic range of 100 photons at 8 keV. Their low noise, small pixel size, compact dimensions, maneuverability and vacuum compatibility make them an attractive choice for some of the hard X-ray instruments at the European XFEL for imaging, spectroscopy, and scattering experiments. The European XFEL is committed to providing users with completely corrected detector data. To achieve this goal, periodic calibration procedures are conducted to generate calibration constants that allow the conversion of raw detector output into physically meaningful information through a series of successive data correction steps. In this work, an overview of the ePix100 calibration procedures and correction algorithms will be provided, with a focus on particularly relevant processes for this detector, such as common mode noise and charge sharing correction.
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| 49. |
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| 50. |
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