| 1. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 2. |
- Aidas, Kestutis, et al.
(författare)
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The Dalton quantum chemistry program system
- 2014
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 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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| 3. |
- Pennells, Lisa, et al.
(författare)
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Equalization of four cardiovascular risk algorithms after systematic recalibration : individual-participant meta-analysis of 86 prospective studies
- 2019
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Ingår i: European Heart Journal. - : Oxford University Press (OUP). - 0195-668X .- 1522-9645. ; 40:7, s. 621-
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Tidskriftsartikel (refereegranskat)abstract
- Aims: There is debate about the optimum algorithm for cardiovascular disease (CVD) risk estimation. We conducted head-to-head comparisons of four algorithms recommended by primary prevention guidelines, before and after ‘recalibration’, a method that adapts risk algorithms to take account of differences in the risk characteristics of the populations being studied.Methods and results: Using individual-participant data on 360 737 participants without CVD at baseline in 86 prospective studies from 22 countries, we compared the Framingham risk score (FRS), Systematic COronary Risk Evaluation (SCORE), pooled cohort equations (PCE), and Reynolds risk score (RRS). We calculated measures of risk discrimination and calibration, and modelled clinical implications of initiating statin therapy in people judged to be at ‘high’ 10 year CVD risk. Original risk algorithms were recalibrated using the risk factor profile and CVD incidence of target populations. The four algorithms had similar risk discrimination. Before recalibration, FRS, SCORE, and PCE over-predicted CVD risk on average by 10%, 52%, and 41%, respectively, whereas RRS under-predicted by 10%. Original versions of algorithms classified 29–39% of individuals aged ≥40 years as high risk. By contrast, recalibration reduced this proportion to 22–24% for every algorithm. We estimated that to prevent one CVD event, it would be necessary to initiate statin therapy in 44–51 such individuals using original algorithms, in contrast to 37–39 individuals with recalibrated algorithms.Conclusion: Before recalibration, the clinical performance of four widely used CVD risk algorithms varied substantially. By contrast, simple recalibration nearly equalized their performance and improved modelled targeting of preventive action to clinical need.
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| 4. |
- Cerny, Radovan, et al.
(författare)
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Structure and Characterization of KSc(BH4)(4)
- 2010
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Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:45, s. 19540-19549
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Tidskriftsartikel (refereegranskat)abstract
- A new potassium scandium borohydride, KSc(BH4)(4), is presented and characterized by a combination of in situ synchrotron radiation powder X-ray diffraction, thermal analysis, and vibrational and NMR spectroscopy. The title compound, KSc(BH4)(4), forms at ambient conditions in ball milled mixtures of potassium borohydride and ScCl3 together with a new ternary chloride K3ScCl6, which is also structurally characterized. This indicates that the formation of KSc(BH4)(4) differs from a simple metathesis reaction, and the highest scandium borohydride yield (similar to 31 mol %) can be obtained with a reactant ratio KBH4:ScCl3 of 2:1. KSc(BH4)(4) crystallizes in the orthorhombic crystal system, a = 11.856(5), b = 7.800(3), c = 10.126(6) angstrom, v = 936.4(8) angstrom(3) at RT, with the space group symmetry Prima. KSc(BH4)(4) has a BaSO4 type structure where the BH4 tetrahedra take the oxygen positions. Regarding the packing of cations, K+, and complex anions, [Sc(BH4)(4)](-), the structure of KSc(BH4)(4) can be seen as a distorted variant of orthorhombic neptunium, Np, metal. Thermal expansion of KSc(BH4)(4) in the temperature range RT to 405 K is anisotropic, and the lattice parameter b shows strong nonlinearity upon approaching the melting temperature. The vibrational and NMR spectra are consistent with the structural model, and previous investigations of the related compounds ASc(BH4)(4) with A = Li, Na. KSc(BH4)(4) is stable from RT up to similar to 405 K, where the compound melts and then releases hydrogen in two rapid steps approximately at 460-500 K and 510-590 K. The hydrogen release involves the formation of KBH4, which reacts with K3ScCl6 and forms a solid solution, K(BH4)(1-x)Cl-x. The ternary potassium scandium chloride K3ScCl6 observed in all samples has a monoclinic structure at room temperature, P2(1)/a, a = 12.729(3), b = 7.367(2), c = 12.825(3) angstrom, beta = 109.22(2)degrees, V = 1135.6(4) angstrom(3), which is isostructural to K3MoCl6. The monoclinic polymorph transforms to cubic at 635 K, a = 10.694 angstrom (based on diffraction data measured at 769 K), which is isostructural to the high temperature phase of K3YCl6.
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| 5. |
- Ravnsbaek, Dorthe B., et al.
(författare)
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Thermal Polymorphism and Decomposition of Y(BH4)(3)
- 2010
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 49:8, s. 3801-3809
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Tidskriftsartikel (refereegranskat)abstract
- The structure and thermal decomposition of Y(BH4)(3) is studied by in situ synchrotron radiation powder X-ray diffraction (SR-PXD), B-11 MAS NMR spectroscopy, and thermal analysis (thermogravimetric analysis/differential scanning calorimetry). The samples were prepared via a metathesis reaction between LiBH4 and YCl3 in different molar ratios mediated by ball milling. A new high temperature polymorph of Y(BH4)(3), denoted beta-Y(BH4)(3), is discovered besides the Y(BH4)(3) polymorph previously reported, denoted alpha-Y(BH4)(3). beta-Y(BH4)(3) has a cubic crystal structure and crystallizes with the space group symmetry Pm (3) over barm and a bisected a-axis, a = 5.4547(8) angstrom, as compared to alpha-Y(BH4)(3), a = 10.7445(4) angstrom (Pa (3) over bar). beta-Y(BH4)(3) crystallizes with a regular ReO3-type structure, hence the Y3+ cations form cubes with BH4 anions located on the edges. This arrangement is a regular variant of (he distorted Y3+ cube observed in alpha-Y(BH4)(3), which is similar to the high pressure phase of ReO3. The new phase, beta-Y(BH4)(3) is formed in small amounts during ball milling; however, larger amounts are formed under moderate hydrogen pressure via a phase transition from alpha- to beta-Y(BH4)(3), at similar to 180 degrees C. Upon further heating, beta-Y(BH4)(3) decomposes at similar to 190 degrees C to YH3, which transforms to YH2 at 270 degrees C. An unidentified compound is observed in the temperature range 215-280 degrees C, which may be a new Y B H containing decomposition product. The final decomposition product is YB4. These results show that boron remains in the solid phase when Y(BH4)(3) decomposes in a hydrogen atmosphere and that Y(BH4)(3) may store hydrogen reversibly.
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| 6. |
- Willerslev, Eske, et al.
(författare)
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Ancient biomolecules from deep ice cores reveal a forested Southern Greenland
- 2007
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 317:5834, s. 111-114
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Tidskriftsartikel (refereegranskat)abstract
- It is difficult to obtain fossil data from the 10% of Earth's terrestrial surface that is covered by thick glaciers and ice sheets, and hence, knowledge of the paleoenvironments of these regions has remained limited. We show that DNA and amino acids from buried organisms can be recovered from the basal sections of deep ice cores, enabling reconstructions of past flora and fauna. We show that high-altitude southern Greenland, currently lying below more than 2 kilometers of ice, was inhabited by a diverse array of conifer trees and insects within the past million years. The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections.
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| 7. |
- Arnbjerg, Lene M., et al.
(författare)
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Structure and Dynamics for LiBH4-LiCl Solid Solutions
- 2009
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Ingår i: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 21:24, s. 5772-5782
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Tidskriftsartikel (refereegranskat)abstract
- A Surprisingly high degree of structural and compositional dynamics is observed in the system LiBH4-LiCl as a function of temperature and time. Rietveld refinement of synchrotron radiation powder X-ray diffraction (SR-PXD) data reveals that Cl- readily substitutes for BH4- in the Structure of LiBH4. Prolonged heating a sample of LiBH4-LiCl (1:1 molar ratio) above the phase transition temperature and below the melting point (108 < T < 275 degrees C) can produce highly chloride substituted hexagonal lithium borohydride, h-Li(BH4)(l-x)Cl-x, e.g., x similar to 0.42, after heating from room temperature (RT) to 224 degrees C at 2.5 degrees C/min. LiCl has a higher solubility in h-LiBH4 its compared to orthorhombic lithium borohydride, o-LiBH4, which is illustrated by a LiBH4-LiCl (1:1) sample equilibrated at 245 degrees C for 24 days and left at RT for another 13 months. Rietveld refinement reveals that this sample contains o-Li(BH4)(0.91)Cl-0.09 and LiCl. This illustrates a significantly faster dissolution of LiCl in h-LiBH4 its compared to a slower segregation of LiCl from o-LiBH4, which is also demonstrated by in situ SR-PXD from three cycles of heating and cooling of the same Li(BH4)(0.91)Cl-0.09 sample. The substitution of the smaller Cl- for the larger BH4- ion is clearly observed as a reduction in the unit cell volume as a function of time and temperature. A significant stabilization of h-LiBH4 is found to depend on the degree of anion substitution. Variable temperature solid-state magic-angle spinning (MAS) Li-7 and B-13 NMR experiments oil pure LiBH4 show an increase in full width at half maximum (fwhm) when approaching the phase transition from o- to h-LiBH4, which indicates an increase of the relaxation rate (i.e. T-2 decreases). A less pronounced effect is observed for ion-substituted Li(BH4)(1-x)Cl-x, 0.09 < x < 0.42. The MAS NMR experiments also demonstrate a higher degree of motion in the hexagonal phase, i.e., fwhm is reduced by more than a Factor of 10 at the o- to h-LiBH4 phase transition.
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| 8. |
- Beukers, Willemien, et al.
(författare)
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FGFR3, TERT and OTX1 as a Urinary Biomarker Combination for Surveillance of Patients with Bladder Cancer in a Large Prospective Multicenter Study
- 2017
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Ingår i: Journal of Urology. - : Ovid Technologies (Wolters Kluwer Health). - 0022-5347 .- 1527-3792. ; 197:6, s. 1410-1418
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Patients with nonmuscle invasive bladder cancer are followed with frequent cystoscopies. In this study FGFR3, TERT and OTX1 were investigated as a diagnostic urinary marker combination during followup of patients with primary nonmuscle invasive bladder cancer.Materials and Methods: In this international, multicenter, prospective study 977 patients with nonmuscle invasive bladder cancer were included. A total of 2,496 urine samples were collected prior to cystoscopy during regular visits. Sensitivity was estimated to detect concomitant recurrences. Kaplan-Meier curves were used to estimate the development of future recurrences after urinalysis and a negative cystoscopy.Results: Sensitivity of the assay combination for recurrence detection was 57% in patients with primary low grade, nonmuscle invasive bladder cancer. However, sensitivity was 83% for recurrences that were pT1 or muscle invasive bladder cancer. Of the cases 2% progressed to muscle invasive bladder cancer. Sensitivity for recurrence detection in patients with primary high grade disease was 72% and 7% of them had progression to muscle invasive bladder cancer. When no concomitant tumor was found by cystoscopy, positive urine samples were more frequently followed by a recurrence over time compared to a negative urine sample (58% vs 36%, p < 0.001). High stage recurrences were identified within 1 year after a positive urine test and a negative cystoscopy.Conclusions: Recurrences in patients with primary nonmuscle invasive bladder cancer can be detected by a combination of urine assays. This study supports the value of urinalysis as an alternative diagnostic tool in patients presenting with low grade tumors and as a means to identify high stage tumors earlier.
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| 9. |
- Dyrskjot, Lars, et al.
(författare)
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Prognostic Impact of a 12-gene Progression Score in Non-muscle-invasive Bladder Cancer : A Prospective Multicentre Validation Study
- 2017
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Ingår i: European Urology. - : Elsevier BV. - 0302-2838 .- 1873-7560. ; 72:3, s. 461-469
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Tidskriftsartikel (refereegranskat)abstract
- Background: Progression of non-muscle-invasive bladder cancer (NMIBC) to muscle-invasive bladder cancer (MIBC) is life-threatening and cannot be accurately predicted using clinical and pathological risk factors. Biomarkers for stratifying patients to treatment and surveillance are greatly needed. Objective: To validate a previously developed 12-gene progression score to predict progression to MIBC in a large, multicentre, prospective study. Design, setting, and participants: We enrolled 1224 patients in ten European centres between 2008 and 2012. A total of 750 patients (851 tumours) fulfilled the inclusion and sample quality criteria for testing. Patients were followed for an average of 28 mo (range 0-76). A 12-gene real-time qualitative polymerase chain reaction assay was performed for all tumours and progression scores were calculated using a predefined formula and cut-off values. Outcome measurements and statistical analysis: We measured progression to MIBC using Cox regression analysis and log-rank tests for comparing survival distributions. Results and limitations: The progression score was significantly (p < 0.001) associated with age, stage, grade, carcinoma in situ, bacillus Calmette-Guerin treatment, European Organisation for Research and Treatment of Cancer risk score, and disease progression. Univariate Cox regression analysis showed that patients molecularly classified as high risk experienced more frequent disease progression (hazard ratio 5.08, 95% confidence interval 2.2-11.6; p < 0.001). Multivariable Cox regression models showed that the progression score added independent prognostic information beyond clinical and histopathological risk factors (p < 0.001), with an increase in concordance statistic from 0.82 to 0.86. The progression score showed high correlation (R-2 = 0.85) between paired fresh-frozen and formalin-fixed paraffin-embedded tumour specimens, supporting translation potential in the standard clinical setting. A limitation was the relatively low progression rate (5%, 37/ 750 patients). Conclusions: The 12-gene progression score had independent prognostic power beyond clinical and histopathological risk factors, and may help in stratifying NMIBC patients to optimise treatment and follow-up regimens. Patient summary: Clinical use of a 12-gene molecular test for disease aggressiveness may help in stratifying patients with non-muscle-invasive bladder cancer to optimal treatment regimens.
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| 10. |
- Furuya, Hideki, et al.
(författare)
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PAI-1 is a potential transcriptional silencer that supports bladder cancer cell activity
- 2022
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- The extracellular activity of Plasminogen activator inhibitor-1 (PAI-1) is well described, acting as an inhibitor of tissue plasminogen activator and urokinase-type plasminogen activator, impacting fibrinolysis. Recent studies have revealed a pro-tumorigenic role of PAI-1 in human cancers, via the regulation of angiogenesis and tumor cell survival. In this study, immunohistochemical staining of 939 human bladder cancer specimens showed that PAI-1 expression levels correlated with tumor grade, tumor stage and overall survival. The typical subcellular localization of PAI-1 is cytoplasmic, but in approximately a quarter of the cases, PAI-1 was observed to be localized to both the tumor cell cytoplasm and the nucleus. To investigate the potential function of nuclear PAI-1 in tumor biology we applied chromatin immunoprecipitation (ChIP)-sequencing, gene expression profiling, and rapid immunoprecipitation mass spectrometry to a pair of bladder cancer cell lines. ChIP-sequencing revealed that PAI-1 can bind DNA at distal intergenic regions, suggesting a role as a transcriptional coregulator. The downregulation of PAI-1 in bladder cancer cell lines caused the upregulation of numerous genes, and the integration of ChIP-sequence and RNA-sequence data identified 57 candidate genes subject to PAI-1 regulation. Taken together, the data suggest that nuclear PAI-1 can influence gene expression programs and support malignancy.
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