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| 2. |
- Glasbey, JC, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
- Tabiri, S, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 4. |
- Bravo, L, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 9. |
- 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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| 10. |
- Marconi, A., et al.
(författare)
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ANDES, the high resolution spectrograph for the ELT : science case, baseline design and path to construction
- 2022
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Ingår i: GROUND-BASED AND AIRBORNE INSTRUMENTATION FOR ASTRONOMY IX. - : SPIE - International Society for Optical Engineering. - 9781510653504 - 9781510653498
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Konferensbidrag (refereegranskat)abstract
- The first generation of ELT instruments includes an optical-infrared high resolution spectrograph, indicated as ELT-HIRES and recently christened ANDES (ArmazoNes high Dispersion Echelle Spectrograph). ANDES consists of three fibre-fed spectrographs (UBV, RIZ, YJH) providing a spectral resolution of similar to 100,000 with a minimum simultaneous wavelength coverage of 0.4-1.8 mu m with the goal of extending it to 0.35-2.4 mu m with the addition of a K band spectrograph. It operates both in seeing- and diffraction-limited conditions and the fibre-feeding allows several, interchangeable observing modes including a single conjugated adaptive optics module and a small diffraction-limited integral field unit in the NIR. Its modularity will ensure that ANDES can be placed entirely on the ELT Nasmyth platform, if enough mass and volume is available, or partly in the Coude room. ANDES has a wide range of groundbreaking science cases spanning nearly all areas of research in astrophysics and even fundamental physics. Among the top science cases there are the detection of biosignatures from exoplanet atmospheres, finding the fingerprints of the first generation of stars, tests on the stability of Nature's fundamental couplings, and the direct detection of the cosmic acceleration. The ANDES project is carried forward by a large international consortium, composed of 35 Institutes from 13 countries, forming a team of more than 200 scientists and engineers which represent the majority of the scientific and technical expertise in the field among ESO member states.
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| 11. |
- Marconi, Alessandro, et al.
(författare)
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ELT-HIRES, the high resolution spectrograph for the ELT : Phase A study and path to construction
- 2020
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Ingår i: Ground-based and Airborne Instrumentation for Astronomy VIII. - : SPIE - International Society for Optical Engineering. - 9781510636828 - 9781510636811
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Konferensbidrag (refereegranskat)abstract
- HIRES is the high-resolution spectrograph of the European Extremely Large Telescope at optical and near-infrared wavelengths. It consists of three fibre-fed spectrographs providing a wavelength coverage of 0.4-1.8 µm (goal 0.35-2.4 µm) at a spectral resolution of 100,000. The fibre-feeding allows HIRES to have several, interchangeable observing modes including a SCAO module and a small diffraction-limited IFU in the NIR. Therefore, it will be able to operate both in seeing- and diffraction-limited modes. Its modularity will ensure that HIRES can be placed entirely on the Nasmyth platform, if enough mass and volume is available, or part on the Nasmyth and part in the Coud`e room. ELT-HIRES has a wide range of science cases spanning nearly all areas of research in astrophysics and even fundamental physics. Among the top science cases there are the detection of biosignatures from exoplanet atmospheres, finding the fingerprints of the first generation of stars (PopIII), tests on the stability of Nature’s fundamental couplings, and the direct detection of the cosmic acceleration. The HIRES consortium is composed of more than 30 institutes from 14 countries, forming a team of more than 200 scientists and engineers.
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| 12. |
- Marconi, A., et al.
(författare)
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ELT-HIRES, the high resolution spectrograph for the ELT : results from the Phase A study
- 2018
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Ingår i: GROUND-BASED AND AIRBORNE INSTRUMENTATION FOR ASTRONOMY VII. - : SPIE-INT SOC OPTICAL ENGINEERING. - 9781510619586
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Konferensbidrag (refereegranskat)abstract
- We present the results from the phase A study of ELT-HIRES, an optical-infrared High Resolution Spectrograph for ELT, which has just been completed by a consortium of 30 institutes from 12 countries forming a team of about 200 scientists and engineers. The top science cases of ELT-HIRES will be the detection of life signatures from exoplanet atmospheres, tests on the stability of Nature's fundamental couplings, the direct detection of the cosmic acceleration. However, the science requirements of these science cases enable many other groundbreaking science cases. The baseline design, which allows to fulfil the top science cases, consists in a modular fiber fed cross-dispersed echelle spectrograph with two ultra-stable spectral arms providing a simultaneous spectral range of 0.4-1.8 pm at a spectral resolution of 100, 000. The fiber-feeding allows ELT-HIRES to have several, interchangeable observing modes including a SCAO module and a small diffraction-limited IFU.
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| 13. |
- Di Marcantonio, P., et al.
(författare)
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ELT High Resolution Spectrograph : Phase-A software architecture study
- 2018
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Ingår i: SOFTWARE AND CYBERINFRASTRUCTURE FOR ASTRONOMY V. - : SPIE-INT SOC OPTICAL ENGINEERING. - 9781510619685
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Konferensbidrag (refereegranskat)abstract
- High resolution spectroscopy has been considered of a primary importance to exploit the main scientific cases foreseen for ESO ELT, the Extremely Large Telescope, the future largest optical-infrared telescope in the world. In this context ESO commissioned a Phase-A feasibility study for the construction of a high resolution spectrograph for the ELT, tentatively named HIRES. The study, which lasted 1.5 years, started on March 2016 and was completed with a review phase held at Garching ESO headquarters with the aim to assess the scientific and technical feasibility of the proposed instrument. One of the main tasks of the study is the architectural design of the software covering all the aspects relevant to control an astronomical instrument: from observation preparation through instrument hardware and detectors control till data reduction and analysis. In this paper we present the outcome of the Phase-A study for the proposed HIRES software design highlighting its peculiarities, critical areas and performance aspects for the whole data flow. The End-to-End simulator, a tool already capable of simulating HIRES end products and currently being used to drive some design decision, is also shortly described.
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| 16. |
- Genoni, M., et al.
(författare)
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ELT -HIRES the High Resolution Spectrograph for the ELT : End to End simulator. Design approach and results
- 2018
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Ingår i: MODELING, SYSTEMS ENGINEERING, AND PROJECT MANAGEMENT FOR ASTRONOMY VIII. - : SPIE-INT SOC OPTICAL ENGINEERING. - 9781510619647
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Konferensbidrag (refereegranskat)abstract
- We present the updated design and architecture of the End-to-End simulator model of the high resolution spectrograph HIRES for the future Extremely Large Telescope (ELT). The model allows to simulate the propagation of photons starting from the scientific object of interest up to the detector, allowing to evaluate the performance impact of the different parameters in the spectrograph design. The model also includes a calibration light module, suitable to evaluate data reduction requirements. In this paper, we will detail the architecture of the simulator and the computational model which are strongly characterized by modularity and flexibility that will be crucial in the next generation instrumentation for projects such as the ELT due to of the high complexity and long-time design and development. We also highlight the Cloud Computing Architecture adopted for this software based on Amazon Web Services (AWS). We also present synthetic images obtained with the current version of the End-to-End simulator based on the requirements for ELT-HIRES (especially high radial velocity accuracy) that are then ingested in the Data reduction Software (DRS) of CRIRES+ as case study.
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| 17. |
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| 18. |
- Oonk, M. H. M., et al.
(författare)
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European Society of Gynaecological Oncology Guidelines for the Management of Patients With Vulvar Cancer
- 2017
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Ingår i: International Journal of Gynecological Cancer. - : BMJ. - 1048-891X .- 1525-1438. ; 27:4, s. 832-837
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Tidskriftsartikel (refereegranskat)abstract
- Objective The aim of this study was to develop clinically relevant and evidence-based guidelines as part of European Society of Gynaecological Oncology's mission to improve the quality of care for women with gynecologic cancers across Europe. Methods The European Society of Gynaecological Oncology Council nominated an international development group made of practicing clinicians who provide care to patients with vulvar cancer and have demonstrated leadership and interest in the management of patients with vulvar cancer (18 experts across Europe). To ensure that the statements are evidence based, the current literature identified from a systematic search has been reviewed and critically appraised. In the absence of any clear scientific evidence, judgment was based on the professional experience and consensus of the development group (expert agreement). The guidelines are thus based on the best available evidence and expert agreement. Prior to publication, the guidelines were reviewed by 181 international reviewers including patient representatives independent from the development group. Results The guidelines cover diagnosis and referral, preoperative investigations, surgical management (local treatment, groin treatment including sentinel lymph node procedure, reconstructive surgery), radiation therapy, chemoradiation, systemic treatment, treatment of recurrent disease (vulvar recurrence, groin recurrence, distant metastases), and follow-up.
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| 19. |
- Genoni, M., et al.
(författare)
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End to end simulators : a flexible and scalable cloud-based architecture Application to high resolution spectrographs ESPRESSO and ELT-HIRES
- 2020
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Ingår i: Experimental astronomy. - : SPRINGER. - 0922-6435 .- 1572-9508. ; 50:2-3, s. 215-232
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Tidskriftsartikel (refereegranskat)abstract
- Simulations of frames from existing and upcoming high-resolution spectrographs, targeted for high accuracy radial velocity measurements, are computationally demanding (both in time and space). We present in this paper an innovative approach based on both parallelization and distribution of the workload. By using NVIDIA CUDA custom-made kernels and state-of-the-art cloud-computing architectures in a Platform as a Service (PaaS) approach, we implemented a modular and scalable end-to-end simulator that is able to render synthetic frames with an accuracy of the order of few cm/sec, while keeping the computational time low. We applied our approach to two spectrographs. For VLT-ESPRESSO we give a sound comparison between the actual data and the simulations showing the obtained spectral formats and the recovered instrumental profile. We also simulate data for the upcoming HIRES at the ELT and investigate the overall performance in terms of computational time and scalability against the size of the problem. In addition we demonstrate the interface with data-reduction systems and we preliminary show that the data can be reduced successfully by existing methods.
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| 28. |
- Maggino, Laura, et al.
(författare)
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Reappraisal of a 2-Cm Cut-off Size for the Management of Cystic Pancreatic Neuroendocrine Neoplasms : A Multicenter International Study
- 2021
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Ingår i: Annals of Surgery. - : Wolters Kluwer. - 0003-4932 .- 1528-1140. ; 273:5, s. 973-981
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: The aim of this study was to characterize an international cohort of resected cystic pancreatic neuroendocrine neoplasms (cPanNENs) and identify preoperative predictors of aggressive behavior.BACKGROUND: The characteristics of cPanNENs are unknown and their clinical management remains unclear. An observational strategy for asymptomatic cPanNENs ≤2 cm has been proposed by recent guidelines, but evidence is scarce and limited to single-institutional series.METHODS: Resected cPanNENs (1995-2017) from 16 institutions worldwide were included. Solid lesions (>50% solid component), functional tumors, and MEN-1 patients were excluded. Aggressiveness was defined as lymph node (LN) involvement, G3 grading, distant metastases, and/or recurrence.RESULTS: Overall, 263 resected cPanNENs were included, among which 177 (63.5%) were >2 cm preoperatively. A preoperative diagnosis of cPanNEN was established in 162 cases (61.6%) and was more frequent when patients underwent endoscopic ultrasound [EUS, odds ratio (OR) 2.69, 95% confidence interval (CI) 1.52-4.77] and somatostatin-receptor imaging (OR 3.681, 95% CI 1.809-7.490), and for those managed in specialized institutions (OR 3.12, 95% CI 1.57-6.21). Forty-one cPanNENs (15.6%) were considered aggressive. In the whole cohort, LN involvement on imaging, age >65 years, preoperative size >2 cm, and pancreatic duct dilation were independently associated with aggressive behavior. In asymptomatic patients, older age and a preoperative size >2 cm remained independently associated with aggressiveness. Only 1 of 61 asymptomatic cPanNENs ≤2 cm displayed an aggressive behavior.CONCLUSIONS: The diagnostic accuracy of cPanNENs is increased by the use of EUS and somatostatin-receptor imaging and is higher in specialized institutions. Preoperative size >2 cm is independently associated with aggressive behavior. Consequently, a watch-and-wait policy for sporadic asymptomatic cPanNENs ≤2 cm seems justified and safe for most patients.
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| 30. |
- Scheeren, Thomas W. L., et al.
(författare)
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Current use of inotropes in circulatory shock
- 2021
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Ingår i: Annals of Intensive Care. - : Springer. - 2110-5820. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundTreatment decisions on critically ill patients with circulatory shock lack consensus. In an international survey, we aimed to evaluate the indications, current practice, and therapeutic goals of inotrope therapy in the treatment of patients with circulatory shock.MethodsFrom November 2016 to April 2017, an anonymous web-based survey on the use of cardiovascular drugs was accessible to members of the European Society of Intensive Care Medicine (ESICM). A total of 14 questions focused on the profile of respondents, the triggering factors, first-line choice, dosing, timing, targets, additional treatment strategy, and suggested effect of inotropes. In addition, a group of 42 international ESICM experts was asked to formulate recommendations for the use of inotropes based on 11 questions.ResultsA total of 839 physicians from 82 countries responded. Dobutamine was the first-line inotrope in critically ill patients with acute heart failure for 84% of respondents. Two-thirds of respondents (66%) stated to use inotropes when there were persistent clinical signs of hypoperfusion or persistent hyperlactatemia despite a supposed adequate use of fluids and vasopressors, with (44%) or without (22%) the context of low left ventricular ejection fraction. Nearly half (44%) of respondents stated an adequate cardiac output as target for inotropic treatment. The experts agreed on 11 strong recommendations, all of which were based on excellent (> 90%) or good (81–90%) agreement. Recommendations include the indications for inotropes (septic and cardiogenic shock), the choice of drugs (dobutamine, not dopamine), the triggers (low cardiac output and clinical signs of hypoperfusion) and targets (adequate cardiac output) and stopping criteria (adverse effects and clinical improvement).ConclusionInotrope use in critically ill patients is quite heterogeneous as self-reported by individual caregivers. Eleven strong recommendations on the indications, choice, triggers and targets for the use of inotropes are given by international experts. Future studies should focus on consistent indications for inotrope use and implementation into a guideline for circulatory shock that encompasses individualized targets and outcomes.
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