| 1. |
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| 2. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 4. |
- Glasbey, JC, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 5. |
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| 6. |
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| 7. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 8. |
- Singh, B., et al.
(författare)
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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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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 95:3
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Tidskriftsartikel (refereegranskat)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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| 9. |
- Collaboration, The PANDA, et al.
(författare)
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Feasibility studies of time-like proton electromagnetic form factors at PANDA at FAIR
- 2016
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Ingår i: European Physical Journal A. - : Springer Publishing Company. - 1434-6001 .- 1434-601X. ; 52:10
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Tidskriftsartikel (refereegranskat)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.
(författare)
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Study of doubly strange systems using stored antiprotons
- 2016
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Ingår i: Nuclear Physics A. - : Elsevier. - 0375-9474 .- 1873-1554. ; 954, s. 323-340
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Tidskriftsartikel (refereegranskat)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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| 11. |
- Barucca, G., et al.
(författare)
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Study of excited Ξ baryons with the P¯ ANDA detector
- 2021
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Ingår i: European Physical Journal A. - : Springer Nature. - 1434-6001 .- 1434-601X. ; 57:4
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Tidskriftsartikel (refereegranskat)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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| 12. |
- Barucca, G., et al.
(författare)
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The potential of Λ and Ξ- studies with PANDA at FAIR
- 2021
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Ingår i: European Physical Journal A. - : Springer Nature. - 1434-6001 .- 1434-601X. ; 57:4
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Tidskriftsartikel (refereegranskat)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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| 13. |
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| 14. |
- Beral, V, et al.
(författare)
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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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Ingår i: British Journal of Cancer. - : Springer Science and Business Media LLC. - 1532-1827 .- 0007-0920. ; 87, s. 1234-45
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Tidskriftsartikel (refereegranskat)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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| 15. |
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| 16. |
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| 17. |
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| 18. |
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| 19. |
- Marcaide, J. M., et al.
(författare)
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Discovery of shell-like radio-structure in SN1993J
- 1995
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Ingår i: Nature. - London : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 373:6509, s. 44-45
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Tidskriftsartikel (refereegranskat)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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| 20. |
- Persson, Martin, 1971-, et al.
(författare)
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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
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Ingår i: Orthod Craniofac Res. - 1601-6343 (Electronic) 1601-6335 (Linking) ; 18 Suppl 2, s. 1-13
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Tidskriftsartikel (refereegranskat)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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| 21. |
- Antonarakis, S. E., et al.
(författare)
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Factor VIII gene inversions in severe hemophilia A : Results of an international consortium study
- 1995
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 86:6, s. 2206-2212
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Tidskriftsartikel (refereegranskat)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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| 22. |
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| 23. |
- Ness, A. R., et al.
(författare)
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Centralization of cleft care in the UK. Part 6 : a tale of two studies
- 2015
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Ingår i: Orthod Craniofac Res. - 1601-6343 (Electronic) 1601-6335 (Linking) ; 18 Suppl 2, s. 56-62
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Tidskriftsartikel (refereegranskat)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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| 24. |
- Sztuk-Dambietz, J., et al.
(författare)
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Operational experience with Adaptive Gain Integrating Pixel Detectors at European XFEL
- 2024
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Ingår i: Frontiers in Physics. - : Frontiers Media SA. - 2296-424X. ; 11
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Forskningsöversikt (refereegranskat)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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| 25. |
- Marcaide, J. M., et al.
(författare)
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The quasars 1038+528 A and B
- 1985
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Ingår i: Astronomy and Astrophysics. - Les Ulis : EDP Sciences. - 0004-6361 .- 1432-0746. ; 142:1, s. 71-84
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Tidskriftsartikel (refereegranskat)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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| 26. |
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| 27. |
- Dornheim, T., et al.
(författare)
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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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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 14:1
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Tidskriftsartikel (refereegranskat)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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| 28. |
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| 29. |
- Klačková, I., et al.
(författare)
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Five years operation experience with the AGIPD detectors at the European XFEL
- 2023
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Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE - International Society for Optical Engineering. - 9781510662827
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Konferensbidrag (refereegranskat)abstract
- The European X-ray Free Electron Laser (EuXFEL) began its user operation five years ago, opening and offering new research possibilities. The facility delivers high brilliance, ultra-short, spatially coherent X-ray pulses with a high repetition rate to six instruments (FXE, SPB/SFX, MID, HED, SCS and SQS) by means of three different beamlines (SASE 1, SASE 2 and SASE 3). One of the first detectors used for early-stage experiments was the Adaptive Gain Integrating Pixel Detector (AGIPD), custom designed to meet the challenging needs of scientific instruments. The AGIPD is a megahertz-rate integrating hybrid megapixel camera with a per-pixel adaptive gain amplification, allowing the integration of up to 104 of 12 keV photons per pixel in its low gain stage. Currently, three scientific instruments, namely SPB/SFX, MID and HED employ the AGIPD systems, the latter mentioned using a prototype, half-megapixel camera with an upgraded version of readout ASICs. The AGIPDs at EuXFEL are successfully used for experimental techniques like serial femtosecond crystallography, MHz single particle imaging, MHz X-ray photon correlation spectroscopy or MHz diffraction of materials under high pressures in a diamond anvil cell. Since September 2017, the AGIPD is continuously used and has become an established detector technology, with further advancements and developments planned. Delivering quality experimental data requires reliable and reproducible detector characterisation and calibration that have to be performed regularly with a continuous improvement of correction methods in close collaboration with scientific instruments. This work summarises five years of experience operating the AGIPD detectors at the EuXFEL scientific instruments. It gives an overview of scientific capabilities and examples of successful studies performed with AGIPD detectors. Moreover, challenges concerning detector calibration and characterisation are presented.
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| 30. |
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| 31. |
- Vinko, S. M., et al.
(författare)
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Time-Resolved XUV Opacity Measurements of Warm Dense Aluminum
- 2020
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Ingår i: Physical Review Letters. - : American Physical Society. - 1079-7114 .- 0031-9007. ; 124:22
-
Tidskriftsartikel (refereegranskat)abstract
- The free-free opacity in plasmas is fundamental to our understanding of energy transport in stellar interiors and for inertial confinement fusion research. However, theoretical predictions in the challenging dense plasma regime are conflicting and there is a dearth of accurate experimental data to allow for direct model validation. Here we present time-resolved transmission measurements in solid-density Al heated by an XUV free-electron laser. We use a novel functional optimization approach to extract the temperature-dependent absorption coefficient directly from an oversampled pool of single-shot measurements, and find a pronounced enhancement of the opacity as the plasma is heated to temperatures of order of the Fermi energy. Plasma heating and opacity enhancement are observed on ultrafast timescales, within the duration of the femtosecond XUV pulse. We attribute further rises in the opacity on ps timescales to melt and the formation of warm dense matter.
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| 32. |
- Duarte, N., et al.
(författare)
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Calibration procedures and data correction of ePix100 detectors at the European XFEL
- 2023
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 18:11
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Tidskriftsartikel (refereegranskat)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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| 33. |
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| 34. |
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| 35. |
- Itzhaki, Ruth F., et al.
(författare)
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Microbes and Alzheimer's Disease
- 2016
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Ingår i: Journal of Alzheimer's Disease. - 1387-2877 .- 1875-8908. ; 51:4, s. 979-984
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We are researchers and clinicians working on Alzheimer’s disease (AD) or related topics, and we write to express our concern that one particular aspect of the disease has been neglected, even though treatment based on it might slow or arrest AD progression. We refer to the many studies, mainly on humans, implicating specific microbes in the elderly brain, notably herpes simplex virus type 1 (HSV1), Chlamydia pneumoniae, and several types of spirochaete, in the etiology of AD [1–4]. Fungal infection of AD brain [5, 6] has also been described, as well as abnormal microbiota in AD patient blood [7]. The first observations of HSV1 in AD brain were reported almost three decades ago [8]. The ever-increasing number of these studies (now about 100 on HSV1 alone) warrants re-evaluation of the infection and AD concept.AD is associated with neuronal loss and progressive synaptic dysfunction, accompanied by the deposition of amyloid-β (Aβ) peptide, a cleavage product of the amyloid-β protein precursor (AβPP), and abnormal forms of tau protein, markers that have been used as diagnostic criteria for the disease [9, 10]. These constitute the hallmarks of AD, but whether they are causes of AD or consequences is unknown. We suggest that these are indicators of an infectious etiology. In the case of AD, it is often not realized that microbes can cause chronic as well as acute diseases; that some microbes can remain latent in the body with the potential for reactivation, the effects of which might occur years after initial infection; and that people can be infected but not necessarily affected, such that ‘controls’, even if infected, are asymptomatic
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| 36. |
- Itzhaki, Ruth F., et al.
(författare)
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Microbes and Alzheimer's disease
- 2017
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Ingår i: Handbook of infection and Alzheimer's disease. - : IOS Press. - 9781614997054 - 9781614997061 ; , s. 3-8
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Bokkapitel (refereegranskat)
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| 37. |
- Machiela, Mitchell J, et al.
(författare)
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Genetic Variants Related to Longer Telomere Length are Associated with Increased Risk of Renal Cell Carcinoma.
- 2017
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Ingår i: European Urology. - : Elsevier BV. - 0302-2838 .- 1873-7560. ; 72:5, s. 747-754
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Relative telomere length in peripheral blood leukocytes has been evaluated as a potential biomarker for renal cell carcinoma (RCC) risk in several studies, with conflicting findings.OBJECTIVE: We performed an analysis of genetic variants associated with leukocyte telomere length to assess the relationship between telomere length and RCC risk using Mendelian randomization, an approach unaffected by biases from temporal variability and reverse causation that might have affected earlier investigations.DESIGN, SETTING, AND PARTICIPANTS: Genotypes from nine telomere length-associated variants for 10 784 cases and 20 406 cancer-free controls from six genome-wide association studies (GWAS) of RCC were aggregated into a weighted genetic risk score (GRS) predictive of leukocyte telomere length.OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Odds ratios (ORs) relating the GRS and RCC risk were computed in individual GWAS datasets and combined by meta-analysis.RESULTS AND LIMITATIONS: Longer genetically inferred telomere length was associated with an increased risk of RCC (OR=2.07 per predicted kilobase increase, 95% confidence interval [CI]:=1.70-2.53, p<0.0001). As a sensitivity analysis, we excluded two telomere length variants in linkage disequilibrium (R2>0.5) with GWAS-identified RCC risk variants (rs10936599 and rs9420907) from the telomere length GRS; despite this exclusion, a statistically significant association between the GRS and RCC risk persisted (OR=1.73, 95% CI=1.36-2.21, p<0.0001). Exploratory analyses for individual histologic subtypes suggested comparable associations with the telomere length GRS for clear cell (N=5573, OR=1.93, 95% CI=1.50-2.49, p<0.0001), papillary (N=573, OR=1.96, 95% CI=1.01-3.81, p=0.046), and chromophobe RCC (N=203, OR=2.37, 95% CI=0.78-7.17, p=0.13).CONCLUSIONS: Our investigation adds to the growing body of evidence indicating some aspect of longer telomere length is important for RCC risk.PATIENT SUMMARY: Telomeres are segments of DNA at chromosome ends that maintain chromosomal stability. Our study investigated the relationship between genetic variants associated with telomere length and renal cell carcinoma risk. We found evidence suggesting individuals with inherited predisposition to longer telomere length are at increased risk of developing renal cell carcinoma.
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- Scelo, Ghislaine, et al.
(författare)
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Genome-wide association study identifies multiple risk loci for renal cell carcinoma.
- 2017
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Previous genome-wide association studies (GWAS) have identified six risk loci for renal cell carcinoma (RCC). We conducted a meta-analysis of two new scans of 5,198 cases and 7,331 controls together with four existing scans, totalling 10,784 cases and 20,406 controls of European ancestry. Twenty-four loci were tested in an additional 3,182 cases and 6,301 controls. We confirm the six known RCC risk loci and identify seven new loci at 1p32.3 (rs4381241, P=3.1 × 10-10), 3p22.1 (rs67311347, P=2.5 × 10-8), 3q26.2 (rs10936602, P=8.8 × 10-9), 8p21.3 (rs2241261, P=5.8 × 10-9), 10q24.33-q25.1 (rs11813268, P=3.9 × 10-8), 11q22.3 (rs74911261, P=2.1 × 10-10) and 14q24.2 (rs4903064, P=2.2 × 10-24). Expression quantitative trait analyses suggest plausible candidate genes at these regions that may contribute to RCC susceptibility.
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- Schwartz, David A., et al.
(författare)
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Placental Tissue Destruction and Insufficiency From COVID-19 Causes Stillbirth and Neonatal Death From Hypoxic-Ischemic Injury
- 2022
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Ingår i: Archives of Pathology & Laboratory Medicine. - : COLL AMER PATHOLOGISTS. - 0003-9985 .- 1543-2165. ; 146:6, s. 660-676
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Tidskriftsartikel (refereegranskat)abstract
- Context.-Perinatal death is an increasingly important problem as the coronavirus disease 2019 (COVID-19) pandemic continues, but the mechanism of death has been unclear. Objective.-To evaluate the role of the placenta in causing stillbirth and neonatal death following maternal infection with COVID-19 and confirmed placental positivity for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Design.-Case-based retrospective clinicopathologic analysis by a multinational group of 44 perinatal specialists from 12 countries of placental and autopsy pathology findings from 64 stillborns and 4 neonatal deaths having placentas testing positive for SARS-CoV-2 following delivery to mothers with COVID-19. Results.-Of the 3 findings constituting SARS-CoV-2 placentitis, all 68 placentas had increased fibrin deposition and villous trophoblast necrosis and 66 had chronic histiocytic intervillositis. Sixty-three placentas had massive perivillous fibrin deposition. Severe destructive placental disease from SARS-CoV-2 placentitis averaged 77.7% tissue involvement. Other findings included multiple intervillous thrombi (37%; 25 of 68) and chronic villitis (32%; 22 of 68). The majority (19; 63%) of the 30 autopsies revealed no significant fetal abnormalities except for intrauterine hypoxia and asphyxia. Among all 68 cases, SARS-CoV-2 was detected from a body specimen in 16 of 28 cases tested, most frequently from nasopharyngeal swabs. Four autopsied stillborns had SARS-CoV-2 identified in internal organs. Conclusions.-The pathology abnormalities composing SARS-CoV-2 placentitis cause widespread and severe placental destruction resulting in placental malperfusion and insufficiency. In these cases, intrauterine and perinatal death likely results directly from placental insufficiency and fetal hypoxic-ischemic injury. There was no evidence that SARS-CoV-2 involvement of the fetus had a role in causing these deaths.
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- Schwartz, David A., et al.
(författare)
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Placental Tissue Destruction and Insufficiency From COVID-19 Causes Stillbirth and Neonatal Death From Hypoxic-Ischemic Injury : A Study of 68 Cases With SARS-CoV-2 Placentitis From 12 Countries
- 2022
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Ingår i: Archives of Pathology & Laboratory Medicine. - : Archives of Pathology and Laboratory Medicine. - 0003-9985 .- 1543-2165. ; 146:6, s. 660-676
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Tidskriftsartikel (refereegranskat)abstract
- Context: Perinatal death is an increasingly important problem as the coronavirus disease 2019 (COVID-19) pandemic continues, but the mechanism of death has been unclear.Objective: To evaluate the role of the placenta in causing stillbirth and neonatal death following maternal infection with COVID-19 and confirmed placental positivity for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).Design: Case-based retrospective clinicopathologic analysis by a multinational group of 44 perinatal specialists from 12 countries of placental and autopsy pathology findings from 64 stillborns and 4 neonatal deaths having placentas testing positive for SARS-CoV-2 following delivery to mothers with COVID-19.Results: Of the 3 findings constituting SARS-CoV-2 placentitis, all 68 placentas had increased fibrin deposition and villous trophoblast necrosis and 66 had chronic histiocytic intervillositis. Sixty-three placentas had massive perivillous fibrin deposition. Severe destructive placental disease from SARS-CoV-2 placentitis averaged 77.7% tissue involvement. Other findings included multiple intervillous thrombi (37%; 25 of 68) and chronic villitis (32%; 22 of 68). The majority (19; 63%) of the 30 autopsies revealed no significant fetal abnormalities except for intrauterine hypoxia and asphyxia. Among all 68 cases, SARS-CoV-2 was detected from a body specimen in 16 of 28 cases tested, most frequently from nasopharyngeal swabs. Four autopsied stillborns had SARS-CoV-2 identified in internal organs.Conclusions: The pathology abnormalities composing SARS-CoV-2 placentitis cause widespread and severe placental destruction resulting in placental malperfusion and insufficiency. In these cases, intrauterine and perinatal death likely results directly from placental insufficiency and fetal hypoxic-ischemic injury. There was no evidence that SARS-CoV-2 involvement of the fetus had a role in causing these deaths.
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