| 1. |
- Baumeister, Hannah, et al.
(författare)
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A generalizable data-driven model of atrophy heterogeneity and progression in memory clinic settings
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Ingår i: Brain : a journal of neurology. - 1460-2156. ; 147:7, s. 2400-2413
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Tidskriftsartikel (refereegranskat)abstract
- Memory clinic patients are a heterogeneous population representing various aetiologies of pathological aging. It is unknown if divergent spatiotemporal progression patterns of brain atrophy, as previously described in Alzheimer's disease (AD) patients, are prevalent and clinically meaningful in this group of older adults. To uncover distinct atrophy subtypes, we applied the Subtype and Stage Inference (SuStaIn) algorithm to baseline structural MRI data from 813 participants enrolled in the DELCODE cohort (mean ± SD age = 70.67 ± 6.07 years, 52% females). Participants were cognitively unimpaired (CU; n = 285) or fulfilled diagnostic criteria for subjective cognitive decline (SCD; n = 342), mild cognitive impairment (MCI; n = 118), or dementia of the Alzheimer's type (n = 68). Atrophy subtypes were compared in baseline demographics, fluid AD biomarker levels, the Preclinical Alzheimer Cognitive Composite (PACC-5), as well as episodic memory and executive functioning. PACC-5 trajectories over up to 240 weeks were examined. To test if baseline atrophy subtype and stage predicted clinical trajectories before manifest cognitive impairment, we analysed PACC-5 trajectories and MCI conversion rates of CU and SCD participants. Limbic-predominant and hippocampal-sparing atrophy subtypes were identified. Limbic-predominant atrophy first affected the medial temporal lobes, followed by further temporal and, finally, the remaining cortical regions. At baseline, this subtype was related to older age, more pathological AD biomarker levels, APOE ε4 carriership, and an amnestic cognitive impairment. Hippocampal-sparing atrophy initially occurred outside the temporal lobe with the medial temporal lobe spared up to advanced atrophy stages. This atrophy pattern also affected individuals with positive AD biomarkers and was associated with more generalised cognitive impairment. Limbic-predominant atrophy, in all and in only unimpaired participants, was linked to more negative longitudinal PACC-5 slopes than observed in participants without or with hippocampal-sparing atrophy and increased the risk of MCI conversion. SuStaIn modelling was repeated in a sample from the Swedish BioFINDER-2 cohort. Highly similar atrophy progression patterns and associated cognitive profiles were identified. Cross-cohort model generalizability, both on the subject and group level, were excellent, indicating reliable performance in previously unseen data. The proposed model is a promising tool for capturing heterogeneity among older adults at early at-risk states for AD in applied settings. The implementation of atrophy subtype- and stage-specific end-points may increase the statistical power of pharmacological trials targeting early AD.
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| 2. |
- Andersen, Casper W., et al.
(författare)
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OPTIMADE, an API for exchanging materials data
- 2021
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Ingår i: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.
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| 3. |
- Ghiringhelli, Luca M., et al.
(författare)
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Shared metadata for data-centric materials science
- 2023
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Ingår i: Scientific Data. - : NATURE PORTFOLIO. - 2052-4463. ; 10
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The expansive production of data in materials science, their widespread sharing and repurposing requires educated support and stewardship. In order to ensure that this need helps rather than hinders scientific work, the implementation of the FAIR-data principles (Findable, Accessible, Interoperable, and Reusable) must not be too narrow. Besides, the wider materials-science community ought to agree on the strategies to tackle the challenges that are specific to its data, both from computations and experiments. In this paper, we present the result of the discussions held at the workshop on “Shared Metadata and Data Formats for Big-Data Driven Materials Science”. We start from an operative definition of metadata, and the features that a FAIR-compliant metadata schema should have. We will mainly focus on computational materials-science data and propose a constructive approach for the FAIRification of the (meta)data related to ground-state and excited-states calculations, potential-energy sampling, and generalized workflows. Finally, challenges with the FAIRification of experimental (meta)data and materials-science ontologies are presented together with an outlook of how to meet them.
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| 4. |
- Knoop, Florian, et al.
(författare)
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Ab initio Green-Kubo simulations of heat transport in solids: Method and implementation
- 2023
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 107:22
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Tidskriftsartikel (refereegranskat)abstract
- Ab initio Green-Kubo (aiGK) simulations of heat transport in solids allow for assessing lattice thermalconductivity in anharmonic or complex materials from first principles. In this work, we present a detailed accountof their practical application and evaluation with an emphasis on noise reduction and finite-size corrections insemiconductors and insulators. To account for such corrections, we propose strategies in which all necessarynumerical parameters are chosen based on the dynamical properties displayed during molecular dynamicssimulations in order to minimize manual intervention. This paves the way for applying the aiGK method insemiautomated and high-throughput frameworks. The proposed strategies are presented and demonstrated forcomputing the lattice thermal conductivity at room temperature in the mildly anharmonic periclase MgO, andfor the strongly anharmonic marshite CuI.
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| 5. |
- Knoop, Florian, et al.
(författare)
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Anharmonicity in Thermal Insulators: An Analysis from First Principles
- 2023
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Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 130:23
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Tidskriftsartikel (refereegranskat)abstract
- The anharmonicity of atomic motion limits the thermal conductivity in crystalline solids. However, amicroscopic understanding of the mechanisms active in strong thermal insulators is lacking. In this Letter,we classify 465 experimentally known materials with respect to their anharmonicity and perform fullyanharmonic ab initio Green-Kubo calculations for 58 of them, finding 28 thermal insulators withκ < 10 W=mK including 6 with ultralow κ ≲ 1 W=mK. Our analysis reveals that the underlying stronganharmonic dynamics is driven by the exploration of metastable intrinsic defect geometries. This is atvariance with the frequently applied perturbative approach, in which the dynamics is assumed to evolvearound a single stable geometry.
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| 6. |
- Lejaeghere, Kurt, et al.
(författare)
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Reproducibility in density functional theory calculations of solids.
- 2016
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 351:6280, s. 1415-1422
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Tidskriftsartikel (refereegranskat)abstract
- The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.
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| 7. |
- Ribaldi, Federica, et al.
(författare)
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Brain connectivity and metacognition in persons with subjective cognitive decline (COSCODE) : rationale and study design
- 2021
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Ingår i: Alzheimer's Research & Therapy. - : BioMed Central (BMC). - 1758-9193. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Background: Subjective cognitive decline (SCD) is the subjective perception of a decline in memory and/or other cognitive functions in the absence of objective evidence. Some SCD individuals however may suffer from very early stages of neurodegenerative diseases (such as Alzheimer's disease, AD), minor psychiatric conditions, neurological, and/or somatic comorbidities. Even if a theoretical framework has been established, the etiology of SCD remains far from elucidated. Clinical observations recently lead to the hypothesis that individuals with incipient AD may have overestimated metacognitive judgements of their own cognitive performance, while those with psychiatric disorders typically present underestimated metacognitive judgements. Moreover, brain connectivity changes are known correlates of AD and psychiatric conditions and might be used as biomarkers to discriminate SCD individuals of different etiologies. The aim of the COSCODE study is to identify metacognition, connectivity, behavioral, and biomarker profiles associated with different etiologies of SCD. Here we present its rationale and study design.Methods: COSCODE is an observational, longitudinal (4 years), prospective clinical cohort study involving 120 SCD, and 80 control study participants (40 individuals with no cognitive impairment, and 40 living with mild cognitive impairment - MCI, or dementia due to AD), all of which will undergo diffusion magnetic resonance imaging (MRI) and functional magnetic resonance imaging (fMRI) as well as behavioral and biomarker assessments at baseline and after 1 and 2 years. Both hypothesis-driven and data-driven cluster analysis approaches will be used to identify SCD sub-types based on metacognition, connectivity, behavioral, and biomarker features.Conclusion: COSCODE will allow defining and interpreting the constellation of signs and symptoms associated with different etiologies of SCD, paving the way to the development of cost-effective risk assessment and prevention protocols.
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| 8. |
- Schijven, Dick, et al.
(författare)
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Large-scale analysis of structural brain asymmetries in schizophrenia via the ENIGMA consortium
- 2023
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 120:14
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Tidskriftsartikel (refereegranskat)abstract
- Left-right asymmetry is an important organizing feature of the healthy brain that may be altered in schizophrenia, but most studies have used relatively small samples and heterogeneous approaches, resulting in equivocal findings. We carried out the largest case-control study of structural brain asymmetries in schizophrenia, with MRI data from 5,080 affected individuals and 6,015 controls across 46 datasets, using a single image analysis protocol. Asymmetry indexes were calculated for global and regional cortical thickness, surface area, and subcortical volume measures. Differences of asymmetry were calculated between affected individuals and controls per dataset, and effect sizes were meta-analyzed across datasets. Small average case-control differences were observed for thickness asymmetries of the rostral anterior cingulate and the middle temporal gyrus, both driven by thinner left-hemispheric cortices in schizophrenia. Analyses of these asymmetries with respect to the use of antipsychotic medication and other clinical variables did not show any significant associations. Assessment of age- and sex-specific effects revealed a stronger average leftward asymmetry of pallidum volume between older cases and controls. Case-control differences in a multivariate context were assessed in a subset of the data (N = 2,029), which revealed that 7% of the variance across all structural asymmetries was explained by case-control status. Subtle case-control differences of brain macrostructural asymmetry may reflect differences at the molecular, cytoarchitectonic, or circuit levels that have functional relevance for the disorder. Reduced left middle temporal cortical thickness is consistent with altered left-hemisphere language network organization in schizophrenia.
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| 9. |
- Schnadt, Joachim, et al.
(författare)
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Experimental and theoretical study of oxygen adsorption structures on Ag(111)
- 2009
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121. ; 80:7
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Tidskriftsartikel (refereegranskat)abstract
- The oxidized Ag(111) surface has been studied by a combination of experimental and theoretical methods, scanning tunneling microscopy, x-ray photoelectron spectroscopy, and density functional theory. A large variety of different surface structures is found, depending on the detailed preparation conditions. The observed structures fall into four classes: (a) individually chemisorbed atomic oxygen atoms, (b) three different oxygen overlayer structures, including the well-known p(4x4) phase, formed from the same Ag-6 and Ag-10 building blocks, (c) a c(4x8) structure not previously observed, and (d) at higher oxygen coverages structures characterized by stripes along the high-symmetry directions of the Ag(111) substrate. Our analysis provides a detailed explanation of the atomic-scale geometry of the Ag-6/Ag-10 building block structures and the c(4x8) and stripe structures are discussed in detail. The observation of many different and co-existing structures implies that the O/Ag(111) system is characterized by a significantly larger degree of complexity than previously anticipated, and this will impact our understanding of oxidation catalysis processes on Ag catalysts.
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| 10. |
- Schnadt, Joachim, et al.
(författare)
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Revisiting the structure of the p(4x4) surface oxide on Ag(111)
- 2006
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Ingår i: Physical Review Letters. - 1079-7114. ; 96
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Tidskriftsartikel (refereegranskat)abstract
- Scanning tunneling microscopy (STM) and density-functional theory are used to reexamine the structure of the renowned p(4×4)-O/Ag(111) surface oxide. The accepted structural model [C. I. Carlisle et al., Phys. Rev. Lett. 84, 3899 (2000)] is incompatible with the enhanced resolution of the current STM measurements. An "Ag6 model" is proposed that is more stable than its predecessor and accounts for the coexistence of the p(4×4) and a novel c(3×5sqrt(3))rect phase. This coexistence is an indication of the dynamic complexity of the system that until now has not been appreciated.
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