| 1. |
- Botvinik-Nezer, Rotem, et al.
(författare)
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Variability in the analysis of a single neuroimaging dataset by many teams
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 582, s. 84-88
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Tidskriftsartikel (refereegranskat)abstract
- Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses(1). The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset(2-5). Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed. The results obtained by seventy different teams analysing the same functional magnetic resonance imaging dataset show substantial variation, highlighting the influence of analytical choices and the importance of sharing workflows publicly and performing multiple analyses.
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| 2. |
- Pfeiffer, D., et al.
(författare)
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Genetic Imbalance Is Associated With Functional Outcome After Ischemic Stroke
- 2019
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Ingår i: Stroke. - : Ovid Technologies (Wolters Kluwer Health). - 0039-2499 .- 1524-4628. ; 50:2, s. 298-304
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Tidskriftsartikel (refereegranskat)abstract
- Background and Purpose-We sought to explore the effect of genetic imbalance on functional outcome after ischemic stroke (IS). Methods-Copy number variation was identified in high-density single-nucleotide polymorphism microarray data of IS patients from the CADISP (Cervical Artery Dissection and Ischemic Stroke Patients) and SiGN (Stroke Genetics Network)/ GISCOME (Genetics of Ischaemic Stroke Functional Outcome) networks. Genetic imbalance, defined as total number of protein-coding genes affected by copy number variations in an individual, was compared between patients with favorable (modified Rankin Scale score of 0-2) and unfavorable (modified Rankin Scale score of = 3) outcome after 3 months. Subgroup analyses were confined to patients with imbalance affecting ohnologs-a class of dose-sensitive genes, or to those with imbalance not affecting ohnologs. The association of imbalance with outcome was analyzed by logistic regression analysis, adjusted for age, sex, stroke subtype, stroke severity, and ancestry. Results-The study sample comprised 816 CADISP patients (age 44.2 +/- 10.3 years) and 2498 SiGN/GISCOME patients (age 67.7 +/- 14.2 years). Outcome was unfavorable in 122 CADISP and 889 SiGN/GISCOME patients. Multivariate logistic regression analysis revealed that increased genetic imbalance was associated with less favorable outcome in both samples (CADISP: P=0.0007; odds ratio=0.89; 95% CI, 0.82-0.95 and SiGN/GISCOME: P=0.0036; odds ratio=0.94; 95% CI, 0.91-0.98). The association was independent of age, sex, stroke severity on admission, stroke subtype, and ancestry. On subgroup analysis, imbalance affecting ohnologs was associated with outcome (CADISP: odds ratio=0.88; 95% CI, 0.80-0.95 and SiGN/GISCOME: odds ratio=0.93; 95% CI, 0.89-0.98) whereas imbalance without ohnologs lacked such an association. Conclusions-Increased genetic imbalance was associated with poorer functional outcome after IS in both study populations. Subgroup analysis revealed that this association was driven by presence of ohnologs in the respective copy number variations, suggesting a causal role of the deleterious effects of genetic imbalance.
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| 3. |
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| 5. |
- Otto, Thomas D., et al.
(författare)
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A comprehensive evaluation of rodent malaria parasite genomes and gene expression
- 2014
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Ingår i: BMC Biology. - : BioMed Central. - 1741-7007. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function.RESULTS: We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilised it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the 'Plasmodium interspersed repeat genes' (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family.CONCLUSIONS: Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.
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| 7. |
- Ruestes, C. J., et al.
(författare)
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Atomistic simulation of tantalum nanoindentation: Effects of indenter diameter, penetration velocity, and interatomic potentials on defect mechanisms and evolution
- 2014
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Ingår i: Materials Science & Engineering A: Structural Materials: Properties, Microstructure and Processing. - : Elsevier BV. - 0921-5093. ; 613, s. 390-403
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Tidskriftsartikel (refereegranskat)abstract
- Nanoindentation simulations are a helpful complement to experiments. There is a dearth of nanoindentation simulations for bcc metals, partly due to the lack of computationally efficient and reliable interatomic potentials at large strains. We carry out indentation simulations for bcc tantalum using three different interatomic potentials and present the defect mechanisms responsible for the creation and expansion of the plastic deformation zone: twins are initially formed, giving rise to shear loop expansion and the formation of sequential prismatic loops. The calculated elastic constants as function of pressure as well as stacking fault energy surfaces explain the significant differences found in the defect structures generated for the three potentials investigated in this study. The simulations enable the quantification of total dislocation length and twinning fraction. The indenter velocity is varied and, as expected, the penetration depth for the first pop-in (defect emission) event shows a strain rate sensitivity m in the range of 0.037-0.055. The effect of indenter diameter on the first pop-in is discussed. A new intrinsic length-scale model is presented based on the profile of the residual indentation and geometrically necessary dislocation theory.
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| 8. |
- Aurino, Pier Paolo, 1985, et al.
(författare)
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Reversible metal-insulator transition of Ar-irradiated LaAlO3/SrTiO3 interfaces
- 2015
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Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 92:15
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Tidskriftsartikel (refereegranskat)abstract
- The conducting state of a quasi-two-dimensional electron gas (q2DEG), formed at the heterointerface between the two wide-bandgap insulators LaAlO3 (LAO) and SrTiO3, can be made completely insulating by low-energy, 150-eV, Ar+ irradiation. The metallic behavior of the interface can be recovered by high-temperature oxygen annealing. The electrical transport properties of the recovered q2DEG are exactly the same as before the irradiation. Microstructural investigations confirm that the transition is not due to physical etching or crystal lattice distortion of the LAO film below its critical thickness. They also reveal a correlation between electrical state, LAO film surface amorphization, and argon ion implantation. The experimental results are in agreement with density functional theory calculations of Ar implantation and migration in the LAO film. This suggests that the metal-insulator transition may be caused by charge trapping in the defect amorphous layer created during the ion irradiation.
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| 9. |
- Brorsson, Joakim, 1988, et al.
(författare)
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Efficient Calculation of the Lattice Thermal Conductivity by Atomistic Simulations with Ab Initio Accuracy
- 2022
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Ingår i: Advanced Theory and Simulations. - : Wiley. - 2513-0390. ; 5:2
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Tidskriftsartikel (refereegranskat)abstract
- High-order force constant expansions can provide accurate representations of the potential energy surface relevant to vibrational motion. They can be efficiently parametrized using quantum mechanical calculations and subsequently sampled at a fraction of the cost of the underlying reference calculations. Here, force constant expansions are combined via the hiphive package with GPU-accelerated molecular dynamics simulations via the GPUMD package to obtain an accurate, transferable, and efficient approach for sampling the dynamical properties of materials. The performance of this methodology is demonstrated by applying it both to materials with very low thermal conductivity (Ba8Ga16Ge30, SnSe) and a material with a relatively high lattice thermal conductivity (monolayer-MoS2). These cases cover both situations with weak (monolayer-MoS2, SnSe) and strong (Ba8Ga16Ge30) pho renormalization. The simulations also enable to access complementary information such as the spectral thermal conductivity, which allows to discriminate the contribution by different phonon modes while accounting for scattering to all orders. The software packages described here are made available to the scientific community as free and open-source software in order to encourage the more widespread use of these techniques as well as their evolution through continuous and collaborative development.
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| 10. |
- Hashemi, A., et al.
(författare)
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Photoluminescence line shapes for color centers in silicon carbide from density functional theory calculations
- 2021
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Ingår i: Physical Review B. - 2469-9969 .- 2469-9950. ; 103:12
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Tidskriftsartikel (refereegranskat)abstract
- Silicon carbide with optically and magnetically active point defects offers unique opportunities for quantum technology applications. Since interaction with these defects commonly happens through optical excitation and deexcitation, a complete understanding of their light-matter interaction in general and optical signatures in particular is crucial. Here, we employ quantum mechanical density functional theory calculations to investigate the photoluminescence line shapes of selected, experimentally observed color centers (including single vacancies, double vacancies, and vacancy-impurity pairs) in 4H-SiC. The analysis of zero-phonon lines as well as Huang-Rhys and Debye-Waller factors is accompanied by a detailed study of the underlying lattice vibrations. We show that the defect line shapes are governed by strong coupling to bulk phonons at lower energies and localized vibrational modes at higher energies. Generally, good agreement with the available experimental data is obtained, and thus we expect our theoretical work to be beneficial for the identification of defect signatures in the photoluminescence spectra and thereby advance the research in quantum photonics and quantum information processing.
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