| 1. |
- Abat, E., et al.
(författare)
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The ATLAS TRT end-cap detectors
- 2008
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- The ATLAS TRT end-cap is a tracking drift chamber using 245,760 individual tubular drift tubes. It is a part of the TRT tracker which consist of the barrel and two end-caps. The TRT end-caps cover the forward and backward pseudo-rapidity region 1.0 < vertical bar eta vertical bar < 2.0, while the TRT barrel central eta region vertical bar eta vertical bar < 1.0. The TRT system provides a combination of continuous tracking with many measurements in individual drift tubes ( or straws) and of electron identification based on transition radiation from fibers or foils interleaved between the straws themselves. Along with other two sub-systems, namely the Pixel detector and Semi Conductor Tracker (SCT), the TRT constitutes the ATLAS Inner Detector. This paper describes the recently completed and installed TRT end-cap detectors, their design, assembly, integration and the acceptance tests applied during the construction.
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| 2. |
- Abat, E., et al.
(författare)
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The ATLAS Transition Radiation Tracker (TRT) proportional drift tube: design and performance
- 2008
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 3:2
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Tidskriftsartikel (refereegranskat)abstract
- A straw proportional counter is the basic element of the ATLAS Transition Radiation Tracker (TRT). Its detailed properties as well as the main properties of a few TRT operating gas mixtures are described. Particular attention is paid to straw tube performance in high radiation conditions and to its operational stability.
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| 3. |
- Abat, E., et al.
(författare)
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The ATLAS TRT barrel detector
- 2008
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- The ATLAS TRT barrel is a tracking drift chamber using 52,544 individual tubular drift tubes. It is one part of the ATLAS Inner Detector, which consists of three sub-systems: the pixel detector spanning the radius range 4 to 20 cm, the semiconductor tracker (SCT) from 30 to 52 cm, and the transition radiation tracker ( TRT) from 56 to 108 cm. The TRT barrel covers the central pseudo-rapidity region |eta| < 1, while the TRT endcaps cover the forward and backward eta regions. These TRT systems provide a combination of continuous tracking with many measurements in individual drift tubes ( or straws) and of electron identification based on transition radiation from fibers or foils interleaved between the straws themselves. This paper describes the recently-completed construction of the TRT Barrel detector, including the quality control procedures used in the fabrication of the detector.
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| 4. |
- Abat, E., et al.
(författare)
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The ATLAS TRT electronics
- 2008
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 3:6
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Tidskriftsartikel (refereegranskat)abstract
- The ATLAS inner detector consists of three sub-systems: the pixel detector spanning the radius range 4cm-20cm, the semiconductor tracker at radii from 30 to 52 cm, and the transition radiation tracker (TRT), tracking from 56 to 107 cm. The TRT provides a combination of continuous tracking with many projective measurements based on individual drift tubes (or straws) and of electron identification based on transition radiation from fibres or foils interleaved between the straws themselves. This paper describes the on and off detector electronics for the TRT as well as the TRT portion of the data acquisition (DAQ) system.
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| 5. |
- Fresard, Laure, et al.
(författare)
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Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
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Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
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Tidskriftsartikel (refereegranskat)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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| 6. |
- Balázs, C., et al.
(författare)
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A comparison of optimisation algorithms for high-dimensional particle and astrophysics applications
- 2021
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Ingår i: Journal of High Energy Physics (JHEP). - : Springer Nature. - 1126-6708 .- 1029-8479. ; 2021:5
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Tidskriftsartikel (refereegranskat)abstract
- Optimisation problems are ubiquitous in particle and astrophysics, and involve locating the optimum of a complicated function of many parameters that may be computationally expensive to evaluate. We describe a number of global optimisation algorithms that are not yet widely used in particle astrophysics, benchmark them against random sampling and existing techniques, and perform a detailed comparison of their performance on a range of test functions. These include four analytic test functions of varying dimensionality, and a realistic example derived from a recent global fit of weak-scale supersymmetry. Although the best algorithm to use depends on the function being investigated, we are able to present general conclusions about the relative merits of random sampling, Differential Evolution, Particle Swarm Optimisation, the Covariance Matrix Adaptation Evolution Strategy, Bayesian Optimisation, Grey Wolf Optimisation, and the PyGMO Artificial Bee Colony, Gaussian Particle Filter and Adaptive Memory Programming for Global Optimisation algorithms.
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| 7. |
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| 8. |
- Wilson, Catherine A, et al.
(författare)
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Wild sex in zebrafish : loss of the natural sex determinant in domesticated strains.
- 2014
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 198:3
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Tidskriftsartikel (refereegranskat)abstract
- Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this "RAD-sex" method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, "male genotypes" became males and some "female genotypes" also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.
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| 9. |
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| 10. |
- Bennike, Ole, et al.
(författare)
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New interglacial deposits from Copenhagen, Denmark : marine Isotope Stage 7
- 2019
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Ingår i: Boreas. - : Wiley-Blackwell. - 0300-9483 .- 1502-3885. ; 48:1, s. 107-118
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Tidskriftsartikel (refereegranskat)abstract
- During a pre-site survey and construction of a new metro route and station in Copenhagen, fossiliferous organic-rich sediments were encountered. This paper reports on multidisciplinary investigations of these organic sediments, which occurred beneath a sediment succession with a lower till, glacifluvial sand and gravel, an upper till and glacifluvial sand. The organic sediments were underlain by glacifluvial sand and gravel. The organic-rich sediments, which were up to 0.5 m thick, accumulated in a low-energy environment, possibly an oxbow lake. They were rich in plant fossils, which included warmth-demanding trees and other species, such as Najas minor, indicating slightly higher summer temperatures than at present. Freshwater shells were also frequent. Bithynia opercula allowed the sediments to be put into an aminostratigraphical framework. The amino acid racemization (AAR) ratios indicate that the organic sediments formed during Marine Isotope Stage 7 (MIS 7), which is consistent with optically stimulated luminescence dating that gave ages of 206 and 248 ka from the underlying minerogenic deposit. The assemblages from Trianglen are similar to interglacial deposits from the former Free Port (1.4 km away) in Copenhagen, except that Corbicula and Pisidium clessini were not found at Trianglen. The presence of these bivalves at the Free Port and the ostracod Scottia tumida at Trianglen indicates a pre-Eemian age. AAR data from archived Bithynia opercula from the Free Port were almost identical to those from Trianglen, indicating that the two sites are contemporary. We suggest the Trianglen interglacial be used as a local name for the MIS 7 interglacial deposits in Copenhagen. MIS 7 deposits have rarely been documented from the region, but MIS 7 deposits may have been mistaken for other ages. The use of AAR ratios in Bithynia opercula has a great potential for correlation of interglacial non-marine deposits in mainland northern Europe.
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| 11. |
- Boekel, Carolina, 1977-
(författare)
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Integration and topology of membrane proteins
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Membrane proteins comprise around 20-30% of most proteomes. They play important roles in most biochemical pathways. All receptors and ion channels are membrane proteins, which make them attractive targets for drug design. Membrane proteins insert and fold co-translationally into the endoplasmic reticular membrane of eukaryotic cells. The protein-conducting channel that inserts the protein into the membrane is called Sec61 translocon, which is a hetero-oligomeric channel that allows transmembrane segments to insert laterally into the lipid bilayer. The focus of this thesis is how the translocon recognizes the transmembrane helices and integrates them into the membrane.We have investigated the sequence requirements for the translocon-mediated integration of a transmembrane α-helix into the ER by challenging the Sec61 translocon with designed polypeptide segments in an in vitro expression system that allows a quantitative assessment of membrane insertion efficiency. Our studies suggest that helices might interact with each other already during the membrane-insertion step, possibly forming helical hairpins that partition into the membrane as a single unit. Further, the insertion efficiency for Nin-Cout vs. Nout-Cin transmembrane helices and the integration efficiency of Alzheimer’s Aβ-peptide fragments has been investigated.Finally, detailed topology mapping was performed on two biologically interesting proteins with unknown topology, the human seipin protein and Drosophila melanogaster odorant receptor OR83b.
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| 12. |
- Halder, G. E., et al.
(författare)
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Validation of the Surgical Preparedness Assessment in women with pelvic floor disorders
- 2023
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Ingår i: International Urogynecology Journal. - : Springer Science and Business Media LLC. - 0937-3462 .- 1433-3023.
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Tidskriftsartikel (refereegranskat)abstract
- Introduction and hypothesisWe sought to further develop and validate the Surgical Preparedness Assessment (SPA) scale to evaluate patient preparedness for urogynecological surgery. MethodsThis was a planned ancillary analysis of a randomized controlled trial (RCT) evaluating the impact of a preoperative telehealth call on patient preparedness for urogynecological surgery. Patients completed the Preoperative Preparedness Questionnaire (PPQ), the modified Preparedness for Colorectal Cancer Surgery Questionnaire (PCSQ), the Pelvic Floor Distress Inventory (PFDI-20), the Satisfaction Decision Scale (SDS), and the Decision Regret Scale (DRS). Content validity was established through expert opinion and patient cognitive interviews. Factor analysis identified item grouping into domains. Cronbach's alpha reported internal consistency. Known group validity was assessed by comparing intervention arms. External validity was evaluated by comparing intervention arms and correlations with SDS and DRS. ResultsEleven items and 3 domains met the criteria (information needs, satisfaction and pain, and catheterization). Cronbach's alpha values were acceptable for domains and ranged from 0.74 to 0.93. SPA scores did not correlate with other patient-reported outcomes. Mean SPA scores were lower among women who received a telehealth call vs those who did not (1.30 & PLUSMN; 0.31 vs 1.51 & PLUSMN; 0.44; p = 0.002). ConclusionsThe content-valid SPA demonstrates high internal consistency and known group validity.
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| 13. |
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| 14. |
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| 15. |
- Zeiler, Frederick A, et al.
(författare)
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Brain tissue oxygen and cerebrovascular reactivity in traumatic brain injury : a collaborative european neurotrauma effectiveness research in traumatic brain injury exploratory analysis of insult burden
- 2020
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Ingår i: Journal of Neurotrauma. - : Mary Ann Liebert. - 0897-7151 .- 1557-9042. ; 37:17, s. 1854-1863
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Tidskriftsartikel (refereegranskat)abstract
- Pressure reactivity index (PRx) and brain tissue oxygen (PbtO2) are associated with outcome in traumatic brain injury (TBI). This study explores the relationship between PRx and PbtO2 in adult moderate/severe TBI. Using the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) high resolution intensive care unit (ICU) sub-study cohort, we evaluated those patients with archived high-frequency digital intraparenchymal intracranial pressure (ICP) and PbtO2 monitoring data of, a minimum of 6 h in duration, and the presence of a 6 month Glasgow Outcome Scale -Extended (GOSE) score. Digital physiological signals were processed for ICP, PbtO2, and PRx, with the % time above/below defined thresholds determined. The duration of ICP, PbtO2, and PRx derangements was characterized. Associations with dichotomized 6-month GOSE (alive/dead, and favorable/unfavorable outcome; ≤ 4 = unfavorable), were assessed. A total of 43 patients were included. Severely impaired cerebrovascular reactivity was seen during elevated ICP and low PbtO2 episodes. However, most of the acute ICU physiological derangements were impaired cerebrovascular reactivity, not ICP elevations or low PbtO2 episodes. Low PbtO2 without PRx impairment was rarely seen. % time spent above PRx threshold was associated with mortality at 6 months for thresholds of 0 (area under the curve [AUC] 0.734, p = 0.003), > +0.25 (AUC 0.747, p = 0.002) and > +0.35 (AUC 0.745, p = 0.002). Similar relationships were not seen for % time with ICP >20 mm Hg, and PbtO2 < 20 mm Hg in this cohort. Extreme impairment in cerebrovascular reactivity is seen during concurrent episodes of elevated ICP and low PbtO2. However, the majority of the deranged cerebral physiology seen during the acute ICU phase is impairment in cerebrovascular reactivity, with most impairment occurring in the presence of normal PbtO2 levels. Measures of cerebrovascular reactivity appear to display the most consistent associations with global outcome in TBI, compared with ICP and PbtO2.
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