| 1. |
- Abelev, Betty, et al.
(författare)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 2. |
- Abelev, Betty, et al.
(författare)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 3. |
- Amare, Azmeraw, et al.
(författare)
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Association of Polygenic Score and the involvement of Cholinergic and Glutamatergic Pathways with Lithium Treatment Response in Patients with Bipolar Disorder.
- 2023
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Ingår i: Research square. - : Research Square Platform LLC.
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Tidskriftsartikel (refereegranskat)abstract
- Lithium is regarded as the first-line treatment for bipolar disorder (BD), a severe and disabling mental disorder that affects about 1% of the population worldwide. Nevertheless, lithium is not consistently effective, with only 30% of patients showing a favorable response to treatment. To provide personalized treatment options for bipolar patients, it is essential to identify prediction biomarkers such as polygenic scores. In this study, we developed a polygenic score for lithium treatment response (Li+PGS) in patients with BD. To gain further insights into lithium's possible molecular mechanism of action, we performed a genome-wide gene-based analysis. Using polygenic score modeling, via methods incorporating Bayesian regression and continuous shrinkage priors, Li+PGS was developed in the International Consortium of Lithium Genetics cohort (ConLi+Gen: N=2,367) and replicated in the combined PsyCourse (N=89) and BipoLife (N=102) studies. The associations of Li+PGS and lithium treatment response - defined in a continuous ALDA scale and a categorical outcome (good response vs. poor response) were tested using regression models, each adjusted for the covariates: age, sex, and the first four genetic principal components. Statistical significance was determined at P<����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������.
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| 4. |
- Amare, Azmeraw T, et al.
(författare)
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Association of polygenic score and the involvement of cholinergic and glutamatergic pathways with lithium treatment response in patients with bipolar disorder.
- 2023
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Ingår i: Molecular psychiatry. - 1476-5578. ; 28, s. 5251-5261
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Tidskriftsartikel (refereegranskat)abstract
- Lithium is regarded as the first-line treatment for bipolar disorder (BD), a severe and disabling mental healthdisorder that affects about 1% of the population worldwide. Nevertheless, lithium is not consistently effective, with only 30% of patients showing a favorable response to treatment. To provide personalized treatment options for bipolar patients, it is essential to identify prediction biomarkers such as polygenic scores. In this study, we developed a polygenic score for lithium treatment response (Li+PGS) in patients with BD. To gain further insights into lithium's possible molecular mechanism of action, we performed a genome-wide gene-based analysis. Using polygenic score modeling, via methods incorporating Bayesian regression and continuous shrinkage priors, Li+PGS was developed in the International Consortium of Lithium Genetics cohort (ConLi+Gen: N=2367) and replicated in the combined PsyCourse (N=89) and BipoLife (N=102) studies. The associations of Li+PGS and lithium treatment response - defined in a continuous ALDA scale and a categorical outcome (good response vs. poor response) were tested using regression models, each adjusted for the covariates: age, sex, and the first four genetic principal components. Statistical significance was determined at P<0.05. Li+PGS was positively associated with lithium treatment response in the ConLi+Gen cohort, in both the categorical (P=9.8×10-12, R2=1.9%) and continuous (P=6.4×10-9, R2=2.6%) outcomes. Compared to bipolar patients in the 1st decile of the risk distribution, individuals in the 10th decile had 3.47-fold (95%CI: 2.22-5.47) higher odds of responding favorably to lithium. The results were replicated in the independent cohorts for the categorical treatment outcome (P=3.9×10-4, R2=0.9%), but not for the continuous outcome (P=0.13). Gene-based analyses revealed 36 candidate genes that are enriched in biological pathways controlled by glutamate and acetylcholine. Li+PGS may be useful in the development of pharmacogenomic testing strategies by enabling a classification of bipolar patients according to their response to treatment.
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| 5. |
- Bishop, Lev S., et al.
(författare)
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Proposal for generating and detecting multi-qubit GHZ states in circuit QED
- 2009
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 11, s. 073040-
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Tidskriftsartikel (refereegranskat)abstract
- We propose methods for the preparation and entanglement detectionof multi-qubit Greenberger–Horne–Zeilinger (GHZ) states in circuit quantumelectrodynamics. Using quantum trajectory simulations appropriate for thesituation of a weak continuous measurement, we show that the joint dispersivereadout of several qubits can be utilized for the probabilistic production ofhigh-fidelity GHZ states. When employing a nonlinear filter on the recordedhomodyne signal, the selected states are found to exhibit values of theBell–Mermin operator exceeding 2 under realistic conditions. We discuss thepotential of the dispersive readout to demonstrate a violation of the Merminbound, and present a measurement scheme avoiding the necessity for fulldetector tomography.
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| 6. |
- Chow, J.M., et al.
(författare)
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Randomized benchmarking and process tomography for gate errors in a solid-state qubit
- 2009
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 102:9
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of single-qubit gate errors for a superconducting qubit. Results from quantum process tomography and randomized benchmarking are compared with gate errors obtained from a double pulse experiment. Randomized benchmarking reveals a minimum average gate error of 1.1±0.3% and a simple exponential dependence of fidelity on the number of gates. It shows that the limits on gate fidelity are primarily imposed by qubit decoherence, in agreement with theory.
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| 7. |
- Forsberg, Simon, et al.
(författare)
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The Shepherds' Tale : A Genome-Wide Study across 9 Dog Breeds Implicates Two Loci in the Regulation of Fructosamine Serum Concentration in Belgian Shepherds
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Diabetes mellitus is a serious health problem in both dogs and humans. Certain dog breeds show high prevalence of the disease, whereas other breeds are at low risk. Fructosamine and glycated haemoglobin (HbA1c) are two major biomarkers of glycaemia, where serum concentrations reflect glucose turnover over the past few weeks to months. In this study, we searched for genetic factors influencing variation in serum fructosamine concentration in healthy dogs using data from nine dog breeds. Considering all breeds together, we did not find any genome-wide significant associations to fructosamine serum concentration. However, by performing breed-specific analyses we revealed an association on chromosome 3 (rho(corrected) approximate to 1:68 x 10(-6)) in Belgian shepherd dogs of the Malinois subtype. The associated region and its close neighbourhood harbours interesting candidate genes such as LETM1 and GAPDH that are important in glucose metabolism and have previously been implicated in the aetiology of diabetes mellitus. To further explore the genetics of this breed specificity, we screened the genome for reduced heterozygosity stretches private to the Belgian shepherd breed. This revealed a region with reduced heterozygosity that shows a statistically significant interaction (rho = 0.025) with the association region on chromosome 3. This region also harbours some interesting candidate genes and regulatory regions but the exact mechanisms underlying the interaction are still unknown. Nevertheless, this finding provides a plausible explanation for breed-specific genetic effects for complex traits in dogs. Shepherd breeds are at low risk of developing diabetes mellitus. The findings in Belgian shepherds could be connected to a protective mechanism against the disease. Further insight into the regulation of glucose metabolism could improve diagnostic and therapeutic methods for diabetes mellitus.
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| 8. |
- George, Julie, et al.
(författare)
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Comprehensive genomic profiles of small cell lung cancer
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 524:7563, s. 47-U73
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Tidskriftsartikel (refereegranskat)abstract
- We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Dex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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| 9. |
- Huthmann, Jens, et al.
(författare)
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Extending High-Level Synthesis with High-Performance Computing Performance Visualization
- 2020
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Ingår i: Proceedings - IEEE International Conference on Cluster Computing, ICCC. - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 371-380
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Konferensbidrag (refereegranskat)abstract
- The recent maturity in High-Level Synthesis (HLS) has renewed the interest of using Field-Programmable Gate-Arrays (FPGAs) to accelerate High-Performance Computing (HPC) applications. Today, several studies have shown performance-and power-benefits of using FPGAs compared to existing approaches for a number of application kernels with ample room for improvements. Unfortunately, modern HLS tools offer little support to gain clarity and insight regarding why a certain application behaves as it does on the FPGA, and most experts rely on intuition or abstract performance models. In this work, we hypothesize that existing profiling and visualization tools used in the HPC domain are also usable for understanding performance on FPGAs. We extend an existing HLS tool-chain to support Paraver-a state-of-the-art visualization and profiling tool well-known in HPC. We describe how each of the events and states are collected, and empirically quantify its hardware overhead. Finally, we practically apply our contribution to two different applications, demonstrating how the tool can be used to provide unique insights into application execution and how it can be used to guide optimizations. In this work, we hypothesize that existing profiling and visualization tools used in the HPC domain are also usable for understanding performance on FPGAs. We extend an existing HLS tool-chain to support Paraver-a state-of-the-art visualization and profiling tool well-known in HPC. We describe how each of the events and states are collected, and empirically quantify its hardware overhead. Finally, we practically apply our contribution to two different applications, demonstrating how the tool can be used to provide unique insights into application execution and how it can be used to guide optimizations.
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| 10. |
- Huthmann, Jens, et al.
(författare)
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Openmp device offloading to fpgas using the nymble infrastructure
- 2020
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Ingår i: Lect. Notes Comput. Sci.. - Cham : Springer Science and Business Media Deutschland GmbH. ; , s. 265-279
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Konferensbidrag (refereegranskat)abstract
- Next to GPUs, FPGAs are an attractive target for OpenMP device offloading, as they allow to implement highly efficient, applications-specific accelerators. However, prior approaches to support OpenMP device offloading for FPGAs have been limited by the interfaces provided by the FPGA vendors’ HLS tool interfaces or their integration with the OpenMP runtime, e.g., for data mapping. This work presents an approach to OpenMP device offloading for FPGAs based on the LLVM compiler infrastructure and the Nymble HLS compiler. The automatic compilation flow uses LLVM IR for HLS-specific optimizations and transformation and for the interaction with the Nymble HLS compiler. Parallel OpenMP constructs are automatically mapped to hardware threads executing simultaneously in the generated FPGA accelerator and the accelerator is integrated into libomptarget to support data-mapping. In a case study, we demonstrate the use of the compilation flow and evaluate its performance.
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