| 1. |
- Galván, Ignacio Fdez., et al.
(författare)
-
OpenMolcas : From Source Code to Insight
- 2019
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
-
Tidskriftsartikel (refereegranskat)abstract
- In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
|
|
| 2. |
- Aquilante, Francesco, et al.
(författare)
-
Modern quantum chemistry with [Open]Molcas
- 2020
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
-
Tidskriftsartikel (refereegranskat)abstract
- MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
|
|
| 3. |
- Bernhardsson, Magnus, et al.
(författare)
-
Shining dead bone-cause for cautious interpretation of [F-18]NaF PET scans
- 2018
-
Ingår i: Acta Orthopaedica. - : Taylor & Francis. - 1745-3674 .- 1745-3682. ; 89:1, s. 124-127
-
Tidskriftsartikel (refereegranskat)abstract
- Background and purpose — [18F]Fluoride ([18F]NaF) PET scan is frequently used for estimation of bone healing rate and extent in cases of bone allografting and fracture healing. Some authors claim that [18F]NaF uptake is a measure of osteoblastic activity, calcium metabolism, or bone turnover. Based on the known affinity of fluoride to hydroxyapatite, we challenged this view.Methods — 10 male rats received crushed, frozen allogeneic cortical bone fragments in a pouch in the abdominal wall on the right side, and hydroxyapatite granules on left side. [18F]NaF was injected intravenously after 7 days. 60 minutes later, the rats were killed and [18F]NaF uptake was visualized in a PET/CT scanner. Specimens were retrieved for micro CT and histology.Results — MicroCT and histology showed no signs of new bone at the implant sites. Still, the implants showed a very high [18F]NaF uptake, on a par with the most actively growing and remodeling sites around the knee joint.Interpretation — [18F]NaF binds with high affinity to dead bone and calcium phosphate materials. Hence, an [18F]NaF PET/CT scan does not allow for sound conclusions about new bone ingrowth into bone allograft, healing activity in long bone shaft fractures with necrotic fragments, or remodeling around calcium phosphate coated prostheses
|
|
| 4. |
- Brink, Rob C., et al.
(författare)
-
Anterior Spinal Overgrowth Is the Result of the Scoliotic Mechanism and Is Located in the Disc
- 2017
-
Ingår i: Spine. - : LIPPINCOTT WILLIAMS & WILKINS. - 0362-2436 .- 1528-1159. ; 42:11, s. 818-822
-
Tidskriftsartikel (refereegranskat)abstract
- Study Design. Cross-sectional study. Objective. To investigate the presence and magnitude of anterior spinal overgrowth in neuromuscular scoliosis and compare this with the same measurements in idiopathic scoliosis and healthy spines. Summary of Background Data. Anterior spinal overgrowth has been described as a potential driver for the onset and progression of adolescent idiopathic scoliosis (AIS). Whether this anterior overgrowth is specific for AIS or also present in nonidiopathic scoliosis has not been reported. Methods. Supine computed tomography (CT) scans of thirty AIS patients (thoracic Cobb 21-81 degrees), thirty neuromuscular (NM) scoliotic patients (thoracic Cobb 19-101 degrees) and 30 nonscoliotic controls were used. The difference in length in per cents between the anterior and posterior side {[(Delta A-P)/P] * 100%, abbreviated to A-P%} of each vertebral body and intervertebral disc, and between the anterior side of the spine and the spinal canal (A-C%) were determined. Results. The A-P% of the thoracic curves did not differ between the AIS (+1.2 perpendicular to 2.2%) and NM patients (+0.9 +/- 4.1%, P = 0.663), both did differ, however, from the same measurements in controls (-3.0 +/- 1.6%; Pamp;lt; 0.001) and correlated linearly with the Cobb angle (AIS r = 0.678, NM r = 0.687). Additional anterior length was caused by anterior elongation of the discs (AIS: A-P% disc +17.5 +/- 12.7% vs. A-P% body - 2.5 +/- 2.6%; Pamp;lt; 0.001, NM: A-P% disc + 19.1 +/- 18.0% vs. A-P% body -3.5 +/- 5.1%; Pamp;lt; 0.001). The A-C% T1-S1 in AIS and NM patients were similar (+ 7.9 +/- 1.8% and + 8.7 +/- 4.0%, P = 0.273), but differed from the controls (+4.2 +/- 3.3%; Pamp;lt; 0.001). Conclusion. So called anterior overgrowth has been postulated as a possible cause for idiopathic scoliosis, but apparently it occurs in scoliosis with a known origin as well. This suggests that it is part of a more generalized scoliotic mechanism, rather than its cause. The fact that the intervertebral discs contribute more to this increased anterior length than the vertebral bodies suggests an adaptation to altered loading, rather than a primary growth disturbance.
|
|
| 5. |
- Hjort, Marcus, et al.
(författare)
-
Increased Inflammatory Activity in Patients 3 Months after Myocardial Infarction with Nonobstructive Coronary Arteries
- 2019
-
Ingår i: Clinical Chemistry. - : AMER ASSOC CLINICAL CHEMISTRY. - 0009-9147 .- 1530-8561. ; 65:8, s. 1023-1030
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Around 5%-10% of patients with myocardial infarction (MI) present with nonobstructive coronary arteries (MINOCA). We aimed to assess pathophysiological mechanisms in MINOCA by extensively evaluating cardiovascular biomarkers in the stable phase after an event, comparing MINOCA patients with cardiovascular healthy controls and MI patients with obstructive coronary artery disease (MI-CAD).METHODS: Ninety-one biomarkers were measured with a proximity extension assay 3 months after MI in 97 MINOCA patients, 97 age-and sex-matched MI-CAD patients, and 98 controls. Lasso analyses (penalized logistic regression models) and adjusted multiple linear regression models were used for statistical analyses.RESULTS: In the Lasso analysis (MINOCA vs MI-CAD), 8 biomarkers provided discriminatory value: P-selectin glycoprotein ligand 1, C-X-C motif chemokine 1, TNF-related activation-induced cytokine, and pappalysin-1 (PAPPA) with increasing probabilities of MINOCA, and tissue-type plasminogen activator, B-type natriuretic peptide, myeloperoxidase, and interleukin-1 receptor antagonist protein with increasing probabilities of MI-CAD. Comparing MINOCA vs controls, 7 biomarkers provided discriminatory value: N-terminal pro-B-type natriuretic peptide, renin, NF-kappa-B essential modulator, PAPPA, interleukin-6, and soluble urokinase plasminogen activator surface receptor with increasing probabilities of MINOCA, and agouti-related protein with increasing probabilities of controls. Adjusted multiple linear regression analyses showed that group affiliation was associated with the concentrations of 7 of the 8 biomarkers in the comparison MINOCA vs MI-CAD and 5 of the 7 biomarkers in MINOCA vs controls.CONCLUSIONS: Three months after the MI, the biomarker concentrations indicated greater inflammatory activity in MINOCA patients than in both MI-CAD patients and healthy controls, and a varying degree of myocardial dysfunction among the 3 cohorts.
|
|
| 6. |
- Malmqvist, Elin, et al.
(författare)
-
CW Laser radar for combustion diagnostics
- 2018
-
Ingår i: EPJ Web of Conferences. - : EDP Sciences. - 2101-6275 .- 2100-014X. ; 176
-
Tidskriftsartikel (refereegranskat)abstract
- A CW-laser radar system developed for combustion diagnostics is described. The system is based on triangulation to attain range information. A portable system has been constructed and here we show some result from measurements in various flames, for example Rayleigh scattering thermometry and monitoring of particle distributions with high temporal and spatial resolution. The concept can equally well be based on pulsed lasers, allowing suppression of background emission through gated detection.
|
|
| 7. |
- Malmqvist, Elin, et al.
(författare)
-
Scheimpflug Lidar for combustion diagnostics
- 2018
-
Ingår i: Optics Express. - 1094-4087. ; 26:12, s. 14842-14858
-
Tidskriftsartikel (refereegranskat)abstract
- A portable Lidar system developed for large-scale (~1-20 m) combustion diagnostics is described and demonstrated. The system is able to perform remote backscattering measurements with range and temporal resolution. The range resolution is obtained by sharply imaging a part of the laser beam onto a CMOS-array or ICCD detector. The large focal depth required to do this is attained by placing the laser beam, the collection optics and the detector in a so-called Scheimpflug configuration. Results from simulations of the range capabilities and range resolution of the system are presented and its temporal resolution is also discussed. Various applications, important for combustion diagnostics, are also demonstrated, including Rayleigh scattering thermometry, aerosol detection and laser-induced fluorescence measurements. These measurements have been carried out using various continuous-wave GaN diode lasers, emitting in the violet-blue (405 – 450 nm) wavelength regime. It is anticipated that Scheimpflug Lidar will provide a useful and versatile diagnostic tool for combustion research, not only for fundamental studies, but in particular for applications at industrial sites.
|
|
| 8. |
- Malmqvist, Elin, et al.
(författare)
-
Two-dimensional OH-thermometry in reacting flows using photofragmentation laser-induced florescence
- 2016
-
Ingår i: Combustion and Flame. - : Elsevier BV. - 0010-2180. ; 169, s. 297-306
-
Tidskriftsartikel (refereegranskat)abstract
- In the present work, the possibility of using photofragmentation laser-induced fluorescence (PFLIF) for thermometry in different reacting flows is investigated. Hydroxyl (OH) fragments are created by UV-laser (266nm) fragmentation of hydrogen peroxides (H2O2 and HO2), whereupon the fluorescence, induced while scanning the wavelength of a second laser across the A2σ+(v = 1)-X2Π(v = 0) absorption band (around 282nm) of the generated OH fragments, is collected and detected. The temperature is determined by fitting simulated OH-excitation spectra of different temperatures to the experimentally recorded spectrum. In combustion, hydrogen peroxides are intermediate species formed during the low-temperature oxidation of the fuel, and hence they are present in a region covering a wide temperature span, ranging from unburnt to burnt gas temperatures. Thus, LIF of OH photofragments stemming from hydrogen peroxides allows for thermometry covering a wider temperature range than LIF of naturally present OH radicals. There is another important advantage of the concept in that the temperature sensitivity of OH excitation spectra is greater at lower temperatures. The method is demonstrated for two-dimensional (2-D) thermometry in three different measurement situations, namely a free flow of vaporized H2O2 at room temperature, a preheated mixture of CH4/N2/O2/O3 at intermediate temperatures (300-600K), where the OH fragments stem from photodissociation of O3 followed by chemical reactions, and in an optical homogeneous charge compression ignition (HCCI) engine prior to ignition, i.e. at elevated pressures and temperatures. It is found that the technique performs well in all three cases, with measured temperatures in good agreement with thermocouple readings, for the two first cases, and with temperatures calculated based on the ideal gas law using measured pressure traces as input for the engine measurements. The quantitative 2-D temperature images acquired in the engine experiments reveal inhomogeneous temperature distributions, clearly illustrating the capacity of the technique to yield crucial experimental input to engine modelers and designers. The accuracy of the technique in the temperature range 300-600K is lower than 23K. For the room temperature case the precision is 4.3%, corresponding to 12K.
|
|
| 9. |
- Malmqvist, Marcus, et al.
(författare)
-
Patients With Idiopathic Scoliosis Run an Increased Risk of Schizophrenia
- 2019
-
Ingår i: Spine deformity. - : Springer. - 2212-1358 .- 2212-134X. ; 7:2, s. 262-266
-
Tidskriftsartikel (refereegranskat)abstract
- STUDY DESIGN: Retrospective cohort study.OBJECTIVES: To investigate a possible linkage between idiopathic scoliosis (IS) and schizophrenia in an adolescent population.SUMMARY OF BACKGROUND DATA: There is an interesting link between schizophrenia and idiopathic scoliosis: schizophrenia is a disturbance of mental equilibrium, and scoliosis of physical equilibrium, both are multifactorial, genetically determined, start at a young age, and brain development is thought to play a role. Furthermore, both may be presenting symptoms of the genetic disorder 22q11 deletion syndrome. This study poses the question whether these two poorly understood disorders are related.METHODS: A retrospective cohort study was conducted and consisted of 3,702 Swedish adolescents, collected from the National Patient Register, that underwent inpatient care for IS during 1997-2015. These were matched by age, sex, and date of diagnosis to 370,200 controls, collected from Swedish population data, and then followed up in the National Patient Register to identify in- and outpatient care for schizophrenia diagnosis. Follow-up time was calculated from first IS diagnosis date until date of schizophrenia diagnosis or end of follow-up. Cox proportional regression analysis was performed to estimate hazard ratios (HRs) with 95% confidence intervals (CIs) for being diagnosed with schizophrenia.RESULTS: Over a median follow-up time of 9.5 years, 0.7% of patients with IS developed schizophrenia versus 0.5% of controls (p = .04). The risk of schizophrenia was significantly higher in patients with IS (HR, 1.52; 95% CI, 1.03-2.23). Using only hospitalized schizophrenia as event, the prevalence for schizophrenia was 0.5% versus 0.3% (p ≤.01; HR, 1.83; 95% CI, 1.17-2.84).CONCLUSION: This study suggests that patients with IS have increased risk of schizophrenia. Dissatisfaction with one's physical appearance might lead to psychological distress and provoke mental illness in predisposed persons. Alternatively, these two disorders may share a common genetic background.LEVEL OF EVIDENCE: Level 2B.
|
|
| 10. |
- Vavruch, Ludvig, et al.
(författare)
-
Surgical Outcomes of Anterior Versus Posterior Fusion in Lenke Type 1 Adolescent Idiopathic Scoliosis
- 2019
-
Ingår i: Spine. - : Lippincott Williams & Wilkins. - 0362-2436 .- 1528-1159. ; 44:14, s. E823-E832
-
Tidskriftsartikel (refereegranskat)abstract
- Mini Patients with Lenke type 1 idiopathic scoliosis can be effectively managed surgically with an anterior or posterior approach. However, each approach has specific advantages and challenges, as described in this study, which must be considered before treating each patient.Study Design. Retrospective study.Objective. To describe surgical results in two and three dimensions and patient-reported outcomes of scoliosis treatment for Lenke type 1 idiopathic curves with an open anterior or posterior approach.Summary of Background Data. Different surgical techniques have been described to prevent curve progression and to restore spinal alignment in idiopathic scoliosis. The spine can be accessed via an anterior or a posterior approach. However, the surgical outcomes, especially in three dimensions, for different surgical approaches remain unclear.Methods. Cohorts of Lenke curve type 1 idiopathic scoliosis patients, after anterior or posterior spinal fusion were recruited, to measure curve characteristics on conventional radiographs, before and after surgery and after 2 years follow-up, whereas the vertebral axial rotation, true mid-sagittal anterior–posterior height ratio of individual structures, and spinal height differences were measured on 3D reconstructions of the pre- and postoperative supine low-dose computed tomography (CT) scans. Additionally, the intraoperative parameters were described and the patients completed the SRS-22 and EQ-5D-3L questionnaire postoperatively.Results. Fifty-three patients with Lenke curve type 1 idiopathic scoliosis (26 in the anterior cohort and 27 in the posterior cohort) were analyzed. Fewer vertebrae were instrumented in the anterior cohort compared with the posterior cohort (P < 0.001), with less surgery time and lower intraoperative blood loss (P < 0.001). The Cobb angle correction of the primary thoracic curve directly after surgery was 57 ± 12% in the anterior cohort and 73 ± 12% in the posterior cohort (P < 0.001) and 55 ± 13% and 66 ± 12% (P = 0.001) at 2 years follow-up. Postoperative 3D alignment restoration and questionnaires showed no significant differences between the cohorts.Conclusion. This study suggests that Lenke type 1 curves can be effectively managed surgically with either an open anterior or posterior approach. Each approach, however, has specific advantages and challenges, as described in this study, which must be considered before treating each patient.Level of evidence: 3
|
|
