| 1. |
- Attar, Rubina, et al.
(författare)
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The effect of schizophrenia on major adverse cardiac events, length of hospital stay, and prevalence of somatic comorbidities following acute coronary syndrome
- 2019
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Ingår i: European heart journal. Quality of care & clinical outcomes. - : Oxford University Press (OUP). - 2058-1742 .- 2058-5225. ; 5:2, s. 121-126
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Tidskriftsartikel (refereegranskat)abstract
- AIMS: We aimed to investigate major adverse cardiac events (MACE: defined as all-cause mortality, re-infarction, and stroke), length of hospital stays (LOS), and comorbidities following acute coronary syndrome (ACS) in a population with schizophrenia.METHODS AND RESULTS: This Danish register study included patients diagnosed with ACS in the period between 1995 and 2013 with a preceding diagnosis of schizophrenia (n = 726). Each patient was matched to a psychiatric healthy control 1:2 on sex, age, year of ACS diagnosis, and number of comorbidities (total n = 2178). After performing Cox regression and Kaplan-Meier analyses, we found that patients with schizophrenia had an increased risk of MACE [hazard ratio (HR) 1.62, 95% confidence interval (CI) 1.45-1.81], all-cause mortality (HR 2.54, 95% CI 2.22-2.90), and stroke (HR 1.51, 95% CI 1.15-1.99). No differences were found in the re-infarction rates and LOS between the populations. Patients with schizophrenia had higher prevalence's diabetes, anaemia, heart failure, cardiomyopathy, chronic obstructive lung disease, and stroke. Nonetheless, we found lower prevalence's of hypertension and hyperlipidaemia.CONCLUSION: Schizophrenia is associated with an increased risk of MACE despite a lower prevalence of some diagnosed traditional cardiac risk factors which may indicate underdiagnosing of these. Awareness of treatment bias may improve this increased risk.
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| 2. |
- Bracht Jørgensen, Helene, et al.
(författare)
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Life-history traits of soil collembolans in relation to food quality
- 2008
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Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393. ; 38:2, s. 146-151
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Tidskriftsartikel (refereegranskat)abstract
- Preference studies of many different collembolan species have categorised collembolans being selective in their food choice. To clarify whether collembolan food selectivity is related to fitness parameters, three species, Folsomia fimetaria, Protaphorura armata and Heteromurus nitidus, were fed three fungal species, Alternaria infectoria, Mucor hiemalis and Penicillium hordei, representing fungi of high, medium and low preference. The fungal diets were grown on soil and collembolan growth, survival and fecundity were measured. The fungus A. infectoria supported growth, survival and reproduction best in all three species of collembolans, while the fungus P. hordei was of low food quality. M. hiemalis was of medium quality and F. fimetaria was the only collembolan reproducing on M. hiemalis. F. fimetaria favoured reproduction over growth when confined to M. hiemalis. When P. armata was fed M. hiemalis it reached a size where reproduction normally starts, but no young were produced. This suggests that M. hiemalis lacks nutrients necessary for reproduction. H. nitidus did not perform well on any of the fungi offered, which were generally of low food quality for this species. In this study, where the fungal growth substrate is soil, there is a clear relationship between collembolan fitness and their food choice in contrast to some other studies where substrates optimised for fungal growth had been used. We show that specific fungal species are important for resource allocation to growth or reproduction and closely connected with food choice. Further, we argue that natural fungal growth substrates, such as soil, should be used in experiments of this kind.
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| 3. |
- Hedegård, Erik Donovan, et al.
(författare)
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Multiconfigurational short-range density-functional theory for open-shell systems
- 2018
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 148:21
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Tidskriftsartikel (refereegranskat)abstract
- Many chemical systems cannot be described by quantum chemistry methods based on a single-reference wave function. Accurate predictions of energetic and spectroscopic properties require a delicate balance between describing the most important configurations (static correlation) and obtaining dynamical correlation efficiently. The former is most naturally done through a multiconfigurational (MC) wave function, whereas the latter can be done by, e.g., perturbation theory. We have employed a different strategy, namely, a hybrid between multiconfigurational wave functions and density-functional theory (DFT) based on range separation. The method is denoted by MC short-range DFT (MC-srDFT) and is more efficient than perturbative approaches as it capitalizes on the efficient treatment of the (short-range) dynamical correlation by DFT approximations. In turn, the method also improves DFT with standard approximations through the ability of multiconfigurational wave functions to recover large parts of the static correlation. Until now, our implementation was restricted to closed-shell systems, and to lift this restriction, we present here the generalization of MC-srDFT to open-shell cases. The additional terms required to treat open-shell systems are derived and implemented in the DALTON program. This new method for open-shell systems is illustrated on dioxygen and [Fe(H2O)6]3+.
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| 4. |
- Hedegård, Erik Donovan, et al.
(författare)
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Relativistic Polarizable Embedding
- 2017
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 13:6, s. 2870-2880
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Tidskriftsartikel (refereegranskat)abstract
- Most chemistry, including chemistry where relativistic effects are important, occurs in an environment, and in many cases, this environment has a significant effect on the chemistry. In nonrelativistic quantum chemistry, a lot of progress has been achieved with respect to including environments such as a solvent or protein in the calculations, and now is the time to extend the possibilities for also doing this in relativistic quantum chemistry. The polarizable embedding (PE) model efficiently incorporates electrostatic effects of the environment by describing it as a collection of localized electric multipoles and polarizabilities obtained through quantum chemical calculations. In this article, we present the theory and implementation of four-and exact two-component Hamiltonians within a PE framework. We denote the methods the PE-4c-DFT and PE-X2C-DFT models. The models include a linear response formalism to calculate time-dependent (TD) properties: PE-TD-4c-DFT and PE-TD-X2C-DFT. With this first implementation, we calculate the PE-TD-4c-PBE0 excitation energies of the TcO4 - and ReO4 - ions in an explicit water solvent. This initial investigation focuses on the relative size of relativistic and solvent contributions to the excitation energies. The solvent effect is divided into an indirect solvent effect due to the structural perturbation of the XO4 - ion and a direct electrostatic effect. The relativistic effects as well as both types of solvent effects are found to contribute to a shift in the excitation energies, but they do so to different extents depending on the ion and the electronic transition in question.
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| 5. |
- Kjellgren, Erik Rosendahl, et al.
(författare)
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Triplet excitation energies from multiconfigurational short-range density-functional theory response calculations
- 2019
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 151:12
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Tidskriftsartikel (refereegranskat)abstract
- Linear response theory for the multiconfigurational short-range density functional theory (MC-srDFT) model is extended to triplet response with a singlet reference wave function. The triplet linear response equations for MC-srDFT are derived for a general hybrid srGGA functional and implemented in the Dalton program. Triplet excitation energies are benchmarked against the CC3 model of coupled cluster theory and the complete-active-space second-order perturbation theory using three different short-range functionals (srLDA, srPBE, and srPBE0), both with full linear response and employing the generalized Tamm-Dancoff approximation (gTDA). We find that using gTDA is required for obtaining reliable triplet excitations; for the CAS-srPBE model, the mean absolute deviation decreases from 0.40 eV to 0.26 eV, and for the CAS-srLDA model, it decreases from 0.29 eV to 0.21 eV. As expected, the CAS-srDFT model is found to be superior to the HF-srDFT model when analyzing the calculated triplet excitations for molecules in the benchmark set where increased static correlation is expected.
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| 6. |
- List, Nanna Holmgaard, 1985-
(författare)
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Theoretical Description of Electronic Transitions in Large Molecular Systems in the Optical and X-Ray Regions
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The size and conformational complexity of proteins and other large systems represent major challenges for today's methods of quantum chemistry.This thesis is centered around the development of new computational tools to gain molecular-level insight into electronic transitions in such systems. To meet this challenge, we focus on the polarizable embedding (PE) model, which takes advantage of the fact that many electronic transitions are localized to a smaller part of the entire system.This motivates a partitioning of the large system into two regions that are treated at different levels of theory:The smaller part directly involved in the electronic process is described using accurate quantum-chemical methods, while the effects of the rest of the system, the environment, are incorporated into the Hamiltonian of the quantum region in an effective manner.This thesis presents extensions of the PE model with theaim of expanding its range of applicability to describe electronic transitions in large molecular systemsin the optical and X-ray regions. The developments cover both improvements with regardto the quantum region as well as the embedding potential representing the environment.Regarding the former, a damped linear response formulation has been implemented to allow for calculations of absorption spectra of large molecular systems acrossthe entire frequency range. A special feature of this development is its abilityto address core excitations that are otherwise not easily accessible.Another important development presented in this thesis is the coupling of the PE model to a multi-configuration self-consistent-field description of the quantum region and its further combination with response theory. In essence, this extends the PE model to the study of electronic transitions in large systems that are prone to static correlation --- a situation that is frequently encountered in biological systems. In addition to the direct environmental effects on the electronic structure of the quantum region, another important component of the description of electronic transitions in large molecular systems is an accurate account of the indirect effects of the environment, i.e., the geometrical distortions in the quantum region imposed by the environment. In thisthesis we have taken the first step toward the inclusion of geometry distortions in the PE frameworkby formulating and implementing molecular gradients for the quantum region.To identify critical points related to the environment description, we perform a theoretical analysis of the PE model starting from a full quantum-mechanicaltreatment of a composite system. Based on this, we present strategies for an accurate yet efficient construction of the embedding potentialcovering both the calculation of ground state and transition properties. The accurate representation of the environment makes it possible to reduce the size of the quantum region without compromising the overall accuracy of the final results. This further enables use of highly accurate quantum-chemical methods despite their unfavorable scaling with the size of the system.Finally, some examples of applications will be presented to demonstrate how the PE model may be applied as a tool to gain insight into and rationalize the factors influencing electronic transitions in large molecular systems of increasing complexity.
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| 7. |
- Nørby, Morten Steen
(författare)
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Extending the capabilities of polarizable embedding through damped linear response theory
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- One of the greater challenges of modern quantum chemistry is to meet the growing demands of a detailed description of macro molecules, such as proteins and RNA/DNA. The size of such systems make it an almost impossible task to, from first principle calculations, obtain any detailed information regarding electronic structure. This thesis is focused on development of new computational tools for investigation of electronic transitions within large molecular systems. Central to this is the polarizable embedding (PE) model. For many of these systems electronic transitions are localized to one or a few active sites which in turn will be described by accurate quantum chemical methods. The remaining part of the system, defining the environment, is then treated at a lower level using a classical electrostatic approach. The environment is further incorporated into the Hamiltonian describing the quantum region in an effective manner.The work presented in this thesis covers extensions to the PE model both in the quantum region and in the environmental description. The former, starts by combining the PE model with a damped linear response formalism. This coupling enables the study of electronic processes near resonance and in any frequency range desirable thus covering all from core hole transitions to valence transitions. Another important aspect of this work is the coupling of PE to a polarizable continuum model which allows for inclusion of bulk solvent effects in an effective manner. In addition to these extensions we have further considered alternative ways of acquiring parameters used in the construction of the embedding potential. This is essential for accurate embedding calculations as the embedding potential enters directly in the wave function optimization.
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| 8. |
- Rosal Sandberg, Jaime Axel, 1983-
(författare)
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New efficient integral algorithms for quantum chemistry
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The contents of this thesis are centered in the developement of new efficient algorithms for molecular integral evaluation in quantum chemistry, as well as new design and implementation strategies for such algorithms aimed at maximizing their performance and the utilization of modern hardware.This thesis introduces the K4+MIRROR algorithm for 2-electron repulsion integrals, a new ERI integral scheme effective for both segmented and general contraction, which surpasses the performance of all previous ERI analytic algorithms published in the literature. The performance of the K4 kernel contraction schemeis further boosted by the use of some new recurrence relations, CDR/AERR family of recurrences, and the algorithms is further refined for spherical GTOs with the also new SKS method.New prescreening methods for two-electron integrals are also derived, allowing a more consistent methodology for discarding negligible ERI batches. This thesis introduces new techniques useful to pack integrals efficiently and better exploit the underlying modern SIMD or stream processing hardware. These algorithms and methods are implemented in a new library, the Echidna Fock Solver, a hybrid parallelized module for computing Coulomb and Exchange matrices which has been interfaced to the Dalton suite of quantum chemistry programs. Self-Consistent Field and Response Theory calculations in Dalton using the new EFS library are substantially accelerated, also enabling for the first time the use of general contraction basis sets as default basis for extended calculations.The thesis further describes the derivation and implementation of an integral algorithm for evaluating the matrix elements needed for the recently introduced QM/CMM method, for which many of the techniques previously derived are also used, along with a suitable prescreening method for the matrix elements. The implementation is also interfaced to the Dalton quantum chemistry program, and used in production calculations.The last chapter of the thesis is devoted to the derivation of a general analytic solution for type-II Effective Core Potential integrals, arguably one of the most troublesome molecular integrals in quantum chemistry. A new recurrence is introduced for the integrals, and a screening method is presented. Based on these results, a new efficient algorithm for computing type-II ECPs is also described.
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