| 1. |
- Aidas, Kestutis, et al.
(författare)
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The Dalton quantum chemistry program system
- 2014
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0876. ; 4:3, s. 269-284
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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| 2. |
- Bernhardsson, Anders, et al.
(författare)
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A direct implementation of the second-order derivatives of multiconfigurational SCF energies and an analysis of the preconditioning in the associated response equation
- 1999
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Ingår i: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 96:4, s. 617-628
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Tidskriftsartikel (refereegranskat)abstract
- A direct implementation of the reduced multiplication scheme of the Rys-Gauss quadrature in the computation of the second-order geometric derivatives for MCSCF wavefunctions is presented. Characteristics unique to this implementation are simultaneous evaluation of first- and second-order two-electron integral derivatives, compact representation of intermediate elements and efficient prescreening. Finally, a novel technique for the preconditioning of the response equations is reported. Applications sizing up to 510 basis functions are included in the presentation.
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| 3. |
- Bombarda, F., et al.
(författare)
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Runaway electron beam control
- 2019
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Ingår i: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 1361-6587 .- 0741-3335. ; 61:1
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Chaitanya, Lakshmi, et al.
(författare)
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Collaborative EDNAP exercise on the IrisPlex system for DNA based prediction of human eye colour
- 2014
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Ingår i: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 11, s. 241-251
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Tidskriftsartikel (refereegranskat)abstract
- The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, >94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organised by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FTA cards by the organising laboratory together with eye colour phenotypes; 99.4% of the genotypes were correctly reported and 99% of the eye colour phenotypes were correctly predicted. Task 2 involved the assessment of 5 DNA samples extracted by the host laboratory from simulated casework samples, artificially degraded, and provided to the participants in varying DNA concentrations. For this task, 98.7% of the genotypes were correctly determined and 96.2% of eye colour phenotypes were correctly inferred. For Tasks 1 and 2 together, 99.2% (1875) of the 1890 genotypes were correctly generated and of the 15 (0.8%) incorrect genotype calls, only 2 (0.1%) resulted in incorrect eye colour phenotypes. The voluntary Task 3 involved participants choosing their own test subjects for IrisPlex genotyping and eye colour phenotype inference, while eye photographs were provided to the organising laboratory and judged; 96% of the eye colour phenotypes were inferred correctly across 100 samples and 19 laboratories. The high success rates in genotyping and eye colour phenotyping clearly demonstrate the reproducibility and the robustness of the IrisPlex assay as well as the accuracy of the IrisPlex model to predict blue and brown eye colour from DNA. Additionally, this study demonstrates the ease with which the IrisPlex system is implementable and applicable across forensic laboratories around the world with varying pre-existing experiences.
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| 5. |
- Citerini, Charlotta, et al.
(författare)
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Inhibition of KCa2 and Kv11.1 Channels in Pigs With Left Ventricular Dysfunction.
- 2020
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Ingår i: Frontiers in pharmacology. - : Frontiers Media SA. - 1663-9812. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Inhibition of KCa2 channels, conducting IKCa, can convert atrial fibrillation (AF) to sinus rhythm and protect against its induction. IKCa inhibition has been shown to possess functional atrial selectivity with minor effects on ventricles. Under pathophysiological conditions with ventricular remodeling, however, inhibiting IKCa can exhibit both proarrhythmic and antiarrhythmic ventricular effects. The aim of this study was to evaluate the effects of the IKCa inhibitor AP14145, when given before or after the IKr blocker dofetilide, on cardiac function and ventricular proarrhythmia markers in pigs with or without left ventricular dysfunction (LVD).Landrace pigs were randomized into an AF group (n = 6) and two control groups: SHAM1 (n = 8) and SHAM2 (n = 4). AF pigs were atrially tachypaced (A-TP) for 43 ± 4 days until sustained AF and LVD developed. A-TP and SHAM1 pigs received 20 mg/kg AP14145 followed by 100 µg/kg dofetilide whereas SHAM2 pigs received the same drugs in the opposite order. Proarrhythmic markers such as short-term variability of QT (STVQT) and RR (STVRR) intervals, and the number of premature ventricular complexes (PVCs) were measured at baseline and after administration of drugs. The influence on cardiac function was assessed by measuring cardiac output, stroke volume, and relevant echocardiographic parameters.IKCa inhibition by AP14145 did not increase STVQT or STVRR in any of the pigs. IKr inhibition by dofetilide markedly increased STVQT in the A-TP pigs, but not in SHAM operated pigs. Upon infusion of AP14145 the number of PVCs decreased or remained unchanged both when AP14145 was infused after baseline and after dofetilide. Conversely, the number of PVCs increased or remained unchanged upon dofetilide infusion. Neither AP14145 nor dofetilide affected relevant echocardiographic parameters, cardiac output, or stroke volume in any of the groups.IKCa inhibition with AP14145 was not proarrhythmic in healthy pigs, or in the presence of LVD resulting from A-TP. In pigs already challenged with 100 µg/kg dofetilide there were no signs of proarrhythmia when 20 mg/kg AP14145 were infused. KCa2 channel inhibition did not affect cardiac function, implying that KCa2 inhibitors can be administered safely also in the presence of LV dysfunction.
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| 6. |
- Citerni, Carlotta, et al.
(författare)
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Characterization of Atrial and Ventricular Structural Remodeling in a Porcine Model of Atrial Fibrillation Induced by Atrial Tachypacing.
- 2020
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Ingår i: Frontiers in veterinary science. - : Frontiers Media SA. - 2297-1769. ; 7:April
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Tidskriftsartikel (refereegranskat)abstract
- Background: Atrial fibrillation (AF) is characterized by electrical and structural remodeling. Irregular and/or fast atrio-ventricular (AV) conduction during AF can result in AV dyssynchrony, tachymyopathy, pressure and volume overload with subsequent dilatation, valve regurgitation, and ventricular dysfunction with progression to heart failure. Objective: To gain further insight into the myocardial pathophysiological changes induced by right atrial tachypacing (A-TP) in a large animal model. Methods: A total of 28 Landrace pigs were randomized as 14 into AF-induced A-TP group and 14 pigs to control group. AF pigs were tachypaced for 43 ± 4 days until in sustained AF. Functional remodeling was investigated by echocardiography (after cardioversion to sinus rhythm). Structural remodeling was quantified by histological preparations with picrosirius red and immunohistochemical stainings. Results: A-TP resulted in decreased left ventricular ejection fraction (LVEF) accompanied by increased end-diastolic and end-systolic left atrium (LA) volume and area. In addition, A-TP was associated with mitral valve (MV) regurgitation, diastolic dysfunction and increased atrial and ventricular fibrotic extracellular matrix (ECM). Conclusions: A-TP induced AF with concomitant LV systolic and diastolic dysfunction, increased LA volume and area, and atrial and ventricular fibrosis.
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| 7. |
- Coriani, Sonia, et al.
(författare)
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Linear-scaling implementation of molecular response theory in self-consistent field electronic-structure theory
- 2007
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 126:15, s. 11930-11935
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Tidskriftsartikel (refereegranskat)abstract
- A linear-scaling implementation of Hartree-Fock and Kohn-Sham self-consistent field theories for the calculation of frequency-dependent molecular response properties and excitation energies is presented, based on a nonredundant exponential parametrization of the one-electron density matrix in the atomic-orbital basis, avoiding the use of canonical orbitals. The response equations are solved iteratively, by an atomic-orbital subspace method equivalent to that of molecular-orbital theory. Important features of the subspace method are the use of paired trial vectors (to preserve the algebraic structure of the response equations), a nondiagonal preconditioner (for rapid convergence), and the generation of good initial guesses (for robust solution). As a result, the performance of the iterative method is the same as in canonical molecular-orbital theory, with five to ten iterations needed for convergence. As in traditional direct Hartree-Fock and Kohn-Sham theories, the calculations are dominated by the construction of the effective Fock/Kohn-Sham matrix, once in each iteration. Linear complexity is achieved by using sparse-matrix algebra, as illustrated in calculations of excitation energies and frequency-dependent polarizabilities of polyalanine peptides containing up to 1400 atoms.
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| 8. |
- Eriksen, Anne Kirstine, et al.
(författare)
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A lifestyle intervention among elderly men on active surveillance for non-aggressive prostate cancer: a randomised feasibility study with whole-grain rye and exercise.
- 2017
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Ingår i: Trials. - : Springer Science and Business Media LLC. - 1745-6215 .- 1745-6215. ; 18:1, s. 20-
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Tidskriftsartikel (refereegranskat)abstract
- The prognosis for men with non-aggressive prostate cancer is good, and several studies have investigated the impact of lifestyle changes including physical activity and diet on the prognosis. Despite positive results in animal studies and a few human interventions with whole-grain rye on markers of prostate cancer progression, the feasibility of trials investigating such dietary changes in combination with physical activity remains largely unstudied. The primary aim was to investigate the feasibility of an intervention with high whole-grain rye intake and vigorous physical activity for 6 months in men diagnosed with prostate cancer.
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| 9. |
- Helgaker, Trygve, et al.
(författare)
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Self-consistent field methods applied to large molecular systems
- 2006
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Ingår i: RECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND 7B. - : VSP BV-C/O BRILL ACAD PUBL. - 9789004155428 ; , s. 1297-1297
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Konferensbidrag (refereegranskat)abstract
- With recent developments in theory and in implementation, Hartree-Fock and density-functional theory (DFT) self-consistent field (SCF) methods can now be applied to large molecular systems, at a cost that scales linearly with system size. In the present talk, such developments are reviewed, with emphasis on the calculation of energy and molecular properties. In particular, it is demonstrated that energies and molecular properties can now be determined entirely in the atomic orbital (AD) basis, with no implicit or explicit introduction of canonical molecular orbitals in the course of the calculation. After a discussion of energy optimization and convergence of the self-consistent field iterations, some applications are presented, with emphasis on polarizabilities and excitation energies and on the comparison of results obtained by Hartree-Fock and DFT theories in extended systems.
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| 10. |
- Jensen, Marie Louise, et al.
(författare)
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Implant migration and functional outcome of Reverse Shoulder Lateralized Glenosphere Line Extension System : a study protocol for a randomized controlled trial
- 2022
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Ingår i: Trials. - : Springer Science and Business Media LLC. - 1745-6215. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Inferior scapular notching is a complication unique to reverse shoulder arthroplasty. The most efficient technique to avoid inferior scapular notching has been reported to be lateralization of the glenoid offset. This study aims to compare radiological and functional outcomes of the DELTA Xtend® Reverse Shoulder System Lateralized Glenosphere Line Extension (intervention group) with the Standard DELTA Xtend® Reverse Shoulder System (control group). We hypothesize that the lateralization improves the patient outcome by decreasing the risk of inferior scapular notching without increasing the risk of migration and loosening of glenoid component. Methods: In this randomized controlled trial, all Danish citizens with rotator cuff arthropathy or degeneration of the glenohumeral joint with severe posterior wear and allocated for a reverse total shoulder arthroplasty at the department of orthopaedic surgery at Herlev and Gentofte Hospital, Copenhagen University Hospital, will be considered for participation. The exclusion criteria are as follows: below 50 years of age, cognitive or linguistic impairment, insufficient glenoid bone stock, previous fracture in the upper extremity and autoimmune-mediated inflammatory arthritis. There will be included a total of 122 patients of which 56 will participate in the radiostereometric analysis. This number of patients allows 20% to drop out. The co-primary outcomes are the pattern and magnitude of the migration of the glenoid component assessed by radiostereometric analysis and the Western Ontario Osteoarthritis of the Shoulder index. The secondary outcomes are inferior scapular notching, patient-reported and functional outcomes (Oxford shoulder score, Constant-Murley score and pain), side effects and complications, changes in bone mineral density and economy. The included patients will be examined before the surgery, within 1 week and 3, 6, 12 and 24 months after. Discussion: No previous studies have compared the conventional reverse shoulder arthroplasty with the lateralized reverse shoulder arthroplasty in a randomized controlled trial regarding migration and functional outcome. Furthermore, radiostereometric analysis has not been used to evaluate the migration of reverse shoulder arthroplasty in a randomized controlled trial. This study intends to determine which treatment has the most optimal outcome for the benefit of future patients with an indication for reverse shoulder arthroplasty. Trial registration: The study has been notified to Pactius and has approval number P-2021-231. Furthermore, the study will be registered on Clinicaltrials.gov before starting the inclusion.
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