| 1. |
- Cossarizza, A., et al.
(författare)
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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
- 2019
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Ingår i: European Journal of Immunology. - : Wiley. - 0014-2980 .- 1521-4141. ; 49:10, s. 1457-1973
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Tidskriftsartikel (refereegranskat)abstract
- These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
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| 2. |
- de Rojas, I., et al.
(författare)
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Common variants in Alzheimer’s disease and risk stratification by polygenic risk scores
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic discoveries of Alzheimer’s disease are the drivers of our understanding, and together with polygenetic risk stratification can contribute towards planning of feasible and efficient preventive and curative clinical trials. We first perform a large genetic association study by merging all available case-control datasets and by-proxy study results (discovery n = 409,435 and validation size n = 58,190). Here, we add six variants associated with Alzheimer’s disease risk (near APP, CHRNE, PRKD3/NDUFAF7, PLCG2 and two exonic variants in the SHARPIN gene). Assessment of the polygenic risk score and stratifying by APOE reveal a 4 to 5.5 years difference in median age at onset of Alzheimer’s disease patients in APOE ɛ4 carriers. Because of this study, the underlying mechanisms of APP can be studied to refine the amyloid cascade and the polygenic risk score provides a tool to select individuals at high risk of Alzheimer’s disease. © 2021, The Author(s).
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| 3. |
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| 4. |
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| 5. |
- Abbafati, Cristiana, et al.
(författare)
-
- 2020
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Tidskriftsartikel (refereegranskat)
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| 6. |
- Abgrall, N., et al.
(författare)
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The large enriched germanium experiment for neutrinoless double beta decay (LEGEND)
- 2017
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Ingår i: AIP Conference Proceedings. - : Author(s). - 1551-7616 .- 0094-243X. ; 1894
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Konferensbidrag (refereegranskat)abstract
- The observation of neutrinoless double-beta decay (0νββ) would show that lepton number is violated, reveal that neu-trinos are Majorana particles, and provide information on neutrino mass. A discovery-capable experiment covering the inverted ordering region, with effective Majorana neutrino masses of 15 - 50 meV, will require a tonne-scale experiment with excellent energy resolution and extremely low backgrounds, at the level of ∼0.1 count /(FWHM·t·yr) in the region of the signal. The current generation 76Ge experiments GERDA and the Majorana Demonstrator, utilizing high purity Germanium detectors with an intrinsic energy resolution of 0.12%, have achieved the lowest backgrounds by over an order of magnitude in the 0νββ signal region of all 0νββ experiments. Building on this success, the LEGEND collaboration has been formed to pursue a tonne-scale 76Ge experiment. The collaboration aims to develop a phased 0νββ experimental program with discovery potential at a half-life approaching or at 1028 years, using existing resources as appropriate to expedite physics results.
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| 7. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 8. |
- Lambert, J-C, et al.
(författare)
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Genome-wide haplotype association study identifies the FRMD4A gene as a risk locus for Alzheimer's disease
- 2013
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Ingår i: Molecular Psychiatry. - : Springer Science and Business Media LLC. - 1359-4184 .- 1476-5578. ; 18:4, s. 461-470
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Tidskriftsartikel (refereegranskat)abstract
- Recently, several genome-wide association studies (GWASs) have led to the discovery of nine new loci of genetic susceptibility in Alzheimer's disease (AD). However, the landscape of the AD genetic susceptibility is far away to be complete and in addition to single-SNP (single-nucleotide polymorphism) analyses as performed in conventional GWAS, complementary strategies need to be applied to overcome limitations inherent to this type of approaches. We performed a genome-wide haplotype association (GWHA) study in the EADI1 study (n = 2025 AD cases and 5328 controls) by applying a sliding-windows approach. After exclusion of loci already known to be involved in AD (APOE, BIN1 and CR1), 91 regions with suggestive haplotype effects were identified. In a second step, we attempted to replicate the best suggestive haplotype associations in the GERAD1 consortium (2820 AD cases and 6356 controls) and observed that 9 of them showed nominal association. In a third step, we tested relevant haplotype associations in a combined analysis of five additional case-control studies (5093 AD cases and 4061 controls). We consistently replicated the association of a haplotype within FRMD4A on Chr.10p13 in all the data set analyzed (OR: 1.68; 95% CI: (1.43-1.96); P=1.1 x 10(-10)). We finally searched for association between SNPs within the FRMD4A locus and A beta plasma concentrations in three independent non-demented populations (n = 2579). We reported that polymorphisms were associated with plasma A beta 42/A beta 40 ratio (best signal, P=5.4 x 10(-7)). In conclusion, combining both GWHA study and a conservative three-stage replication approach, we characterised FRMD4A as a new genetic risk factor of AD.
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| 9. |
- Calabrese, Claudia, et al.
(författare)
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Genomic basis for RNA alterations in cancer
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 129-136
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Tidskriftsartikel (refereegranskat)abstract
- Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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| 10. |
- Escott-Price, Valentina, et al.
(författare)
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Gene-Wide Analysis Detects Two New Susceptibility Genes for Alzheimer's Disease
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:6, s. e94661-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Alzheimer's disease is a common debilitating dementia with known heritability, for which 20 late onset susceptibility loci have been identified, but more remain to be discovered. This study sought to identify new susceptibility genes, using an alternative gene-wide analytical approach which tests for patterns of association within genes, in the powerful genome-wide association dataset of the International Genomics of Alzheimer's Project Consortium, comprising over 7 m genotypes from 25,580 Alzheimer's cases and 48,466 controls. Principal Findings: In addition to earlier reported genes, we detected genome-wide significant loci on chromosomes 8 (TP53INP1, p = 1.4x10(-6)) and 14 (IGHV1-67 p = 7.9x10(-8)) which indexed novel susceptibility loci. Significance: The additional genes identified in this study, have an array of functions previously implicated in Alzheimer's disease, including aspects of energy metabolism, protein degradation and the immune system and add further weight to these pathways as potential therapeutic targets in Alzheimer's disease.
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| 11. |
- Jones, Lesley, et al.
(författare)
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Convergent genetic and expression data implicate immunity in Alzheimer's disease
- 2015
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Ingår i: Alzheimer's & Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 11:6, s. 658-671
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Tidskriftsartikel (refereegranskat)abstract
- Background: Late-onset Alzheimer's disease (AD) is heritable with 20 genes showing genome-wide association in the International Genomics of Alzheimer's Project (IGAP). To identify the biology underlying the disease, we extended these genetic data in a pathway analysis. Methods: The ALIGATOR and GSEA algorithms were used in the IGAP data to identify associated functional pathways and correlated gene expression networks in human brain. Results: ALIGATOR identified an excess of curated biological pathways showing enrichment of association. Enriched areas of biology included the immune response (P = 3.27 X 10(-12) after multiple testing correction for pathways), regulation of endocytosis (P = 1.31 X 10(-11)), cholesterol transport (P = 2.96 X 10(-9)), and proteasome-ubiquitin activity (P = 1.34 X 10(-6)). Correlated gene expression analysis identified four significant network modules, all related to the immune response (corrected P = .002-.05). Conclusions: The immime response, regulation of endocytosis, cholesterol transport, and protein ubiquitination represent prime targets for AD therapeutics.
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| 12. |
- Ponnath, L., et al.
(författare)
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Measurement of nuclear interaction cross sections towards neutron-skin thickness determination
- 2024
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Ingår i: Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 855
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Tidskriftsartikel (refereegranskat)abstract
- The accuracy of reaction theories used to extract properties of exotic nuclei from scattering experiments is often unknown or not quantified, but of utmost importance when, e.g., constraining the equation of state of asymmetric nuclear matter from observables as the neutron-skin thickness. In order to test the Glauber multiple-scattering model, the total interaction cross section of [Formula presented] on carbon targets was measured at initial beam energies of 400, 550, 650, 800, and 1000 MeV/nucleon. The measurements were performed during the first experiment of the newly constructed R3B (Reaction with Relativistic Radioactive Beams) experiment after the start of FAIR Phase-0 at the GSI/FAIR facility with beam energies of 400, 550, 650, 800, and 1000 MeV/nucleon. The combination of the large-acceptance dipole magnet GLAD and a newly designed and highly efficient Time-of-Flight detector enabled a precise transmission measurement with several target thicknesses for each initial beam energy with an experimental uncertainty of ±0.4%. A comparison with the Glauber model revealed a discrepancy of around 3.1% at higher beam energies, which will serve as a crucial baseline for the model-dependent uncertainty in future fragmentation experiments.
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| 13. |
- Thrane, Kim, et al.
(författare)
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Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells
- 2023
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Ingår i: Journal of Investigative Dermatology. - : Elsevier BV. - 0022-202X .- 1523-1747. ; 143:11, s. 13-2177
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Tidskriftsartikel (refereegranskat)abstract
- Epidermal homeostasis is governed by a balance between keratinocyte proliferation and differentiation with contributions from cell–cell interactions, but conserved or divergent mechanisms governing this equilibrium across species and how an imbalance contributes to skin disease are largely undefined. To address these questions, human skin single-cell RNA sequencing and spatial transcriptomics data were integrated and compared with mouse skin data. Human skin cell–type annotation was improved using matched spatial transcriptomics data, highlighting the importance of spatial context in cell-type identity, and spatial transcriptomics refined cellular communication inference. In cross-species analyses, we identified a human spinous keratinocyte subpopulation that exhibited proliferative capacity and a heavy metal processing signature, which was absent in mouse and may account for species differences in epidermal thickness. This human subpopulation was expanded in psoriasis and zinc-deficiency dermatitis, attesting to disease relevance and suggesting a paradigm of subpopulation dysfunction as a hallmark of the disease. To assess additional potential subpopulation drivers of skin diseases, we performed cell-of-origin enrichment analysis within genodermatoses, nominating pathogenic cell subpopulations and their communication pathways, which highlighted multiple potential therapeutic targets. This integrated dataset is encompassed in a publicly available web resource to aid mechanistic and translational studies of normal and diseased skin.
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| 14. |
- Akdis, M, et al.
(författare)
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Immune responses in healthy and allergic individuals are characterized by a fine balance between allergen-specific T regulatory 1 and T helper 2 cells
- 2004
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Ingår i: Journal of Experimental Medicine. - : Rockefeller University Press. - 0022-1007 .- 1540-9538. ; 199:11, s. 1567-1575
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Tidskriftsartikel (refereegranskat)abstract
- The mechanisms by which immune responses to nonpathogenic environmental antigens lead to either allergy or nonharmful immunity are unknown. Single allergen-specific T cells constitute a very small fraction of the whole CD4(+) T cell repertoire and can be isolated from the peripheral blood of humans according to their cytokine profile. Freshly purified interferon-gamma-, interleukin (IL)-4-, and IL-10-producing allergen-specific CD4(+) T cells display characteristics of T helper cell (Th)1-, Th2, and T regulatory (Tr)1-like cells, respectively. Tr1 cells consistently represent the dominant subset specific for common environmental allergens in healthy individuals; in contrast, there is a high frequency of allergen-specific IL-4-secreting T cells in allergic individuals. Tr1 cells use multiple suppressive mechanisms, IL-10 and TGF-beta as secreted cytokines, and cytotoxic T lymphocyte antigen 4 and programmed death 1 as surface molecules. Healthy and allergic individuals exhibit all three allergen-specific subsets in different proportions, indicating that a change in the dominant subset may lead to allergy development or recovery. Accordingly, blocking the suppressor activity of Tr1 cells or increasing Th2 cell frequency enhances allergen-specific Th2 cell activation ex vivo. These results indicate that the balance between allergen-specific Tr1 cells and Th2 cells may be decisive in the development of allergy.
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| 15. |
- Belyazid, Salim, et al.
(författare)
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A Sustainability Assessment of the Urban Rehabilitation Project of the Medina of Fez, Morocco
- 2003
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Ingår i: Proceedings of the 21st International Conference of the System Dynamics Society. - 9780967291482
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Konferensbidrag (refereegranskat)abstract
- The old city of Fez, Morocco, classified as Heritage of Humankind by the UNESCO, is subject to an integrated rehabilitation plan running over 15 years. The plan aims at restoring and preserving the economy, cultural value, and social heritage of the old city. The study follows a system dynamics approach to describe and analyze the rehabilitation plan in order to identify the strengths and defects of the plan. This study shows that while the plan is giving relatively satisfying results over the short and medium terms, it is unlikely to attain long term sustainability.
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| 16. |
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| 17. |
- Bruce, Louise C, et al.
(författare)
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A multi-lake comparative analysis of the General Lake Model (GLM) : Stress-testing across a global observatory network
- 2018
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Ingår i: Environmental Modelling & Software. - : Elsevier BV. - 1364-8152 .- 1873-6726. ; 102, s. 274-291
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Tidskriftsartikel (refereegranskat)abstract
- The modelling community has identified challenges for the integration and assessment of lake models due to the diversity of modelling approaches and lakes. In this study, we develop and assess a one-dimensional lake model and apply it to 32 lakes from a global observatory network. The data set included lakes over broad ranges in latitude, climatic zones, size, residence time, mixing regime and trophic level. Model performance was evaluated using several error assessment metrics, and a sensitivity analysis was conducted for nine parameters that governed the surface heat exchange and mixing efficiency. There was low correlation between input data uncertainty and model performance and predictions of temperature were less sensitive to model parameters than prediction of thermocline depth and Schmidt stability. The study provides guidance to where the general model approach and associated assumptions work, and cases where adjustments to model parameterisations and/or structure are required.
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| 18. |
- Cecchini, Katharine, et al.
(författare)
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The transcription factor TCFL5 responds to A-MYB to elaborate the male meiotic program in mice
- 2023
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Ingår i: Reproduction. - 1470-1626 .- 1476-3990. ; 165:2, s. 183-196
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Tidskriftsartikel (refereegranskat)abstract
- In male mice, the transcription factors STRA8 and MEISON initiate meiosis I. We report that STRA8/MEISON activates the transcription factors A-MYB and TCFL5, which together reprogram gene expression after spermatogonia enter into meiosis. TCFL5 promotes the transcription of genes required for meiosis, mRNA turnover, miR-34/449 production, meiotic exit, and spermiogenesis. This transcriptional architecture is conserved in rhesus macaque, suggesting TCFL5 plays a central role in meiosis and spermiogenesis in placental mammals. Tcfl5(em1/em1) mutants are sterile, and spermatogenesis arrests at the mid- or late-pachytene stage of meiosis. Moreover, Tcfl5(+/em1) mutants produce fewer motile sperm.
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| 19. |
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| 20. |
- Erdogmus, Deniz, et al.
(författare)
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Asymptotic SNR-performance of some image combination techniques for phased-array MRI
- 2004
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Ingår i: Signal Processing. - Amsterdam, The Netherlands : Elsevier. - 0165-1684 .- 1872-7557. ; 84:6, s. 997-1003
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Tidskriftsartikel (refereegranskat)abstract
- Phased-array magnetic resonance imaging technology is currently flourishing with the promise of obtaining a profitable trade-off between image quality and image acquisition speed. The image quality is generally measured in terms of the signal-to-noise ratio (SNR), which is often calculated using samples taken from the reconstructed image. In this paper, we derive analytical expressions for the asymptotic SNR in the final image for three different phased-array image combination methods, namely: (1) sum-of-squares, (2) singular value decomposition, and (3) normalized coil averaging. The SNR expressions are expressed in terms of the statistics of the noise in the measurements, as well as the coil sensitivity coefficients. Our results can facilitate a better understanding for the phased-array image combination problem, as well as provide a tool for the optimal design of coils.
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| 21. |
- Erdogmus, Deniz, et al.
(författare)
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Image construction methods for phased array magnetic resonance imaging
- 2004
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Ingår i: Journal of Magnetic Resonance Imaging. - : Wiley. - 1053-1807 .- 1522-2586. ; 20:2, s. 306-314
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Tidskriftsartikel (refereegranskat)abstract
- Purpose To study image construction in phased array magnetic resonance imaging (MRI) systems from a statistical signal processing point of view. Materials and Methods Three new approaches for image combination with multiple coils are proposed: 1) one based on the singular value decomposition of the measurement matrix, which is asymptotically optimal in the signal-to-noise ratio sense; 2) one based on a maximum-likelihood formulation, incorporating a priori information on the coil sensitivities in a Bayesian manner; and 3) one based on a least-squares formulation, which incorporates a smoothness constraint on the coil sensitivities. Results Numerical examples using synthetic and real data are presented to illustrate the performance of these new approaches. Results on the synthetic data show improvement in signal-to-error ratio, while results on the real data (a 4.7 T four-coil image of a cat spinal cord) show that the proposed methods can improve the SNR in the final image by up to 3 dB in the regions of interest compared to conventional sum-of-squares processing. Conclusion It is demonstrated that phased array MRI reconstruction performance can be improved by the use of more elaborate statistical signal processing algorithms. J. Magn. Reson. Imaging 2004;20:306–314. © 2004 Wiley-Liss, Inc.
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| 22. |
- Erdogmus, Deniz, et al.
(författare)
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Measuring the signal-to-noise ratio in magnetic resonance imaging: a caveat
- 2004
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Ingår i: Signal Processing. - : Elsevier. - 0165-1684 .- 1872-7557. ; 84:6, s. 1035-1040
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Tidskriftsartikel (refereegranskat)abstract
- The validity of the signal-to-noise ratio (SNR) as an objective quality measure for biomedical images has been the subject of a long-standing debate. Nevertheless, the SNR is the most popularly used measure both for assessing the quality of images and for evaluating the effectiveness of image enhancement and signal processing techniques. In this correspondence, we illustrate that under certain conditions the SNR can be changed by a nonlinear transformation, and also that it is often hard to measure objectively. Therefore, the issue is not only how well the SNR correlates with image quality as perceived by a human observer (which has been the primary subject of earlier debate), but also that SNR is questionable from a quantitative measurement point of view.
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| 23. |
- Erdogmus, Deniz, et al.
(författare)
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Mixture of competitive linear models for phased-array magnetic resonance imaging
- 2004
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Ingår i: 2004 IEEE International Conference on Acoustics, Speech, and Signal Processing. - : IEEE. - 0780384849 ; , s. 585-588
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Konferensbidrag (refereegranskat)abstract
- Phased-array magnetic resonance imaging is an important contemporary research field in terms of the expected clinical gains in medical imaging technology. Recent research focused on heuristic coil image recombination methods as well as statistical signal processing approaches. In this paper, we investigate the performance of an adaptive signal processing approach, namely mixture of competitively trained models. The proposed method has the ability to train on a set of images and generalize its performance to previously unseen images. Performance evaluations on real data validate the effectiveness of this method.
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| 24. |
- Frank, Stefan, et al.
(författare)
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yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs.
- 2019
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Ingår i: Cell stem cell. - : Elsevier BV. - 1875-9777 .- 1934-5909. ; 24:2
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Tidskriftsartikel (refereegranskat)abstract
- Human protein-coding genes are often accompanied by divergently transcribed non-coding RNAs whose functions, especially in cell fate decisions, are poorly understood. Using an hESC-based cardiac differentiation model, we define a class of divergent lncRNAs, termed yin yang lncRNAs (yylncRNAs), that mirror the cell-type-specific expression pattern of their protein-coding counterparts. yylncRNAs arepreferentially encoded from the genomic loci ofkey developmental cell fate regulators. Most yylncRNAs are spliced polyadenylated transcripts showing comparable expression patterns invivo inmouse and in human embryos. Signifying theirdevelopmental function, the key mesoderm specifier BRACHYURY (T) is accompanied by yylncT, whichlocalizes to the active T locus during mesoderm commitment. yylncT binds the de novo DNA methyltransferase DNMT3B, and its transcript is required for activation of the T locus, with yylncTdepletion specifically abolishing mesodermal commitment. Collectively, we report a lncRNA-mediated regulatory layer safeguarding embryonic cell fate transitions.
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| 25. |
- Golub, Malgorzata, et al.
(författare)
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A framework for ensemble modelling of climate change impacts on lakes worldwide : the ISIMIP Lake Sector
- 2022
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Ingår i: Geoscientific Model Development. - : Copernicus Publications. - 1991-959X .- 1991-9603. ; 15:11, s. 4597-4623
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Tidskriftsartikel (refereegranskat)abstract
- Empirical evidence demonstrates that lakes and reservoirs are warming across the globe. Consequently, there is an increased need to project future changes in lake thermal structure and resulting changes in lake biogeochemistry in order to plan for the likely impacts. Previous studies of the impacts of climate change on lakes have often relied on a single model forced with limited scenario-driven projections of future climate for a relatively small number of lakes. As a result, our understanding of the effects of climate change on lakes is fragmentary, based on scattered studies using different data sources and modelling protocols, and mainly focused on individual lakes or lake regions. This has precluded identification of the main impacts of climate change on lakes at global and regional scales and has likely contributed to the lack of lake water quality considerations in policy-relevant documents, such as the Assessment Reports of the Intergovernmental Panel on Climate Change (IPCC). Here, we describe a simulation protocol developed by the Lake Sector of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) for simulating climate change impacts on lakes using an ensemble of lake models and climate change scenarios for ISIMIP phases 2 and 3. The protocol prescribes lake simulations driven by climate forcing from gridded observations and different Earth system models under various representative greenhouse gas concentration pathways (RCPs), all consistently bias-corrected on a 0.5 degrees x 0.5 degrees global grid. In ISIMIP phase 2, 11 lake models were forced with these data to project the thermal structure of 62 well-studied lakes where data were available for calibration under historical conditions, and using uncalibrated models for 17 500 lakes defined for all global grid cells containing lakes. In ISIMIP phase 3, this approach was expanded to consider more lakes, more models, and more processes. The ISIMIP Lake Sector is the largest international effort to project future water temperature, thermal structure, and ice phenology of lakes at local and global scales and paves the way for future simulations of the impacts of climate change on water quality and biogeochemistry in lakes.
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| 26. |
- Gsell, Alena Sonia, et al.
(författare)
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Evaluating early-warning indicators of critical transitions in natural aquatic ecosystems
- 2016
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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. - 0027-8424. ; 113:50, s. 8089-8095
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Tidskriftsartikel (refereegranskat)abstract
- Ecosystems can show sudden and persistent changes in state despite only incremental changes in drivers. Such critical transitions are difficult to predict, because the state of the system often shows little change before the transition. Early-warning indicators (EWIs) are hypothesized to signal the loss of system resilience and have been shown to precede critical transitions in theoretical models, paleo-climate time series, and in laboratory as well as whole lake experiments. The generalizability of EWIs for detecting critical transitions in empirical time series of natural aquatic ecosystems remains largely untested, however. Here we assessed four commonly used EWIs on long-term datasets of five freshwater ecosystems that have experienced sudden, persistent transitions and for which the relevant ecological mechanisms and drivers are well understood. These case studies were categorized by three mechanisms that can generate critical transitions between alternative states: competition, trophic cascade, and intraguild predation. Although EWIs could be detected in most of the case studies, agreement among the four indicators was low. In some cases, EWIs were detected considerably ahead of the transition. Nonetheless, our results show that at present, EWIs do not provide reliable and consistent signals of impending critical transitions despite using some of the best routinely monitored freshwater ecosystems. Our analysis strongly suggests that a priori knowledge of the underlying mechanisms driving ecosystem transitions is necessary to identify relevant state variables for successfully monitoring EWIs.
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| 27. |
- Gutierrez, Jahir M., et al.
(författare)
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Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster ovary cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology.
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| 28. |
- Hansen, Marita G., et al.
(författare)
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Preserved function of afferent parvalbumin-positive perisomatic inhibitory synapses of dentate granule cells in rapidly kindled mice
- 2018
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Ingår i: Frontiers in Cellular Neuroscience. - : Frontiers Media SA. - 1662-5102. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Parvalbumin- (PV-) containing basket cells constitute perisomatic GABAergic inhibitory interneurons innervating principal cells at perisomatic area, a strategic location that allows them to efficiently control the output and synchronize oscillatory activity at gamma frequency (30–90 Hz) oscillations. This oscillatory activity can convert into higher frequency epileptiform activity, and therefore could play an important role in the generation of seizures. However, the role of endogenous modulators of seizure activity, such as Neuropeptide Y (NPY), has not been fully explored in at PV input and output synapses. Here, using selective optogenetic activation of PV cells in the hippocampus, we show that seizures, induced by rapid kindling (RK) stimulations, enhance gamma-aminobutyric acid (GABA) release from PV cells onto dentate gyrus (DG) granule cells (GC). However, PV-GC synapses did not differ between controls and kindled animals in terms of GABA release probability, short-term plasticity and sensitivity to NPY. Kinetics of gamma-aminobutyric acid A (GABA-A) mediated currents in postsynaptic GC were also unaffected. When challenged by repetitive high-frequency optogenetic stimulations, PV synapses in kindled animals responded with enhanced GABA release onto GC. These results unveil a mechanism that might possibly contribute to the generation of abnormal synchrony and maintenance of epileptic seizures.
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| 29. |
- Heil, M., et al.
(författare)
-
A new Time-of-flight detector for the R 3 B setup
- 2022
-
Ingår i: European Physical Journal A. - : Springer Science and Business Media LLC. - 1434-601X .- 1434-6001. ; 58:12
-
Tidskriftsartikel (refereegranskat)abstract
- We present the design, prototype developments and test results of the new time-of-flight detector (ToFD) which is part of the R3B experimental setup at GSI and FAIR, Darmstadt, Germany. The ToFD detector is able to detect heavy-ion residues of all charges at relativistic energies with a relative energy precision σΔE/ ΔE of up to 1% and a time precision of up to 14 ps (sigma). Together with an elaborate particle-tracking system, the full identification of relativistic ions from hydrogen up to uranium in mass and nuclear charge is possible.
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| 30. |
- Janssen, Annette B. G., et al.
(författare)
-
Exploring, exploiting and evolving diversity of aquatic ecosystem models : a community perspective
- 2015
-
Ingår i: Aquatic Ecology. - : Springer Science and Business Media LLC. - 1386-2588 .- 1573-5125. ; 49:4, s. 513-548
-
Tidskriftsartikel (refereegranskat)abstract
- Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5-10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary.
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| 31. |
- Koca, Deniz, et al.
(författare)
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The Rubber Industry and Extended Producers' Responsibility Framework: Opportunities and Threats for Swedish Rubber Manufacturers
- 2002
-
Ingår i: Proceeding of the 20th International Conference of the System Dynamics Society. ; , s. 88-89
-
Konferensbidrag (refereegranskat)abstract
- An array of sustainable ways either to reduce the amount of waste rubber generated or for the re-utilisation of waste rubber products as different means of resources at the end of their service lives are provided and briefly evaluated from economic, social and environmental perspectives. Potential measures which the Swedish rubber industry and its major stakeholders can implement (within the context of extended producer’s responsibility framework) to increase source reduction, reuse, material recycling, and energy recovery from waste rubber are examined. Based on the concept of system dynamics, the links between different issues, possible problems arising from them and the solutions, and their relation to the sustainable waste rubber management system are analysed by understanding the cause and effect relationship between important parameters. A model is developed using Stella 5.1.1u to help the decision makers to evaluate different scenarios in Swedish waste rubber management.
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| 32. |
- Koenig, Julian, et al.
(författare)
-
Cortical thickness and resting-state cardiac function across the lifespan : A cross-sectional pooled mega-analysis
- 2021
-
Ingår i: Psychophysiology. - : Wiley. - 0048-5772 .- 1469-8986 .- 1540-5958. ; 58:7
-
Tidskriftsartikel (refereegranskat)abstract
- Understanding the association between autonomic nervous system [ANS] function and brain morphology across the lifespan provides important insights into neurovisceral mechanisms underlying health and disease. Resting-state ANS activity, indexed by measures of heart rate [HR] and its variability [HRV] has been associated with brain morphology, particularly cortical thickness [CT]. While findings have been mixed regarding the anatomical distribution and direction of the associations, these inconsistencies may be due to sex and age differences in HR/HRV and CT. Previous studies have been limited by small sample sizes, which impede the assessment of sex differences and aging effects on the association between ANS function and CT. To overcome these limitations, 20 groups worldwide contributed data collected under similar protocols of CT assessment and HR/HRV recording to be pooled in a mega-analysis (N = 1,218 (50.5% female), mean age 36.7 years (range: 12–87)). Findings suggest a decline in HRV as well as CT with increasing age. CT, particularly in the orbitofrontal cortex, explained additional variance in HRV, beyond the effects of aging. This pattern of results may suggest that the decline in HRV with increasing age is related to a decline in orbitofrontal CT. These effects were independent of sex and specific to HRV; with no significant association between CT and HR. Greater CT across the adult lifespan may be vital for the maintenance of healthy cardiac regulation via the ANS—or greater cardiac vagal activity as indirectly reflected in HRV may slow brain atrophy. Findings reveal an important association between CT and cardiac parasympathetic activity with implications for healthy aging and longevity that should be studied further in longitudinal research.
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| 33. |
- Larsson, Erik G., et al.
(författare)
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SNR-optimality of sum-of-squares reconstruction for phased-array magnetic resonance imaging
- 2003
-
Ingår i: Journal of magnetic resonance. - : Elsevier. - 1090-7807 .- 1096-0856. ; 163:1, s. 121-123
-
Tidskriftsartikel (refereegranskat)abstract
- We consider the commonly used “Sum-of-Squares” (SoS) reconstruction method for phased-array magnetic resonance imaging with unknown coil sensitivities. We show that the signal-to-noise ratio (SNR) in the image produced by SoS is asymptotically (as the input SNR→∞) equal to that of maximum-ratio combining, which is the best unbiased reconstruction method when the coil sensitivities are known. Finally, we discuss the implications of this result.
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| 34. |
- Lastres-Becker, Isabel, et al.
(författare)
-
alpha-Synuclein expression and Nrf2 deficiency cooperate to aggravate protein aggregation, neuronal death and inflammation in early-stage Parkinson's disease
- 2012
-
Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 21:14, s. 3173-3192
-
Tidskriftsartikel (refereegranskat)abstract
- Although -synuclein (-SYN) aggregation is a hallmark of sporadic and familial Parkinsons disease (PD), it is not known how it contributes to early events of PD pathogenesis such as oxidative and inflammatory stress. Here, we addressed this question in a new animal model based on stereotaxic delivery of an adeno-associated viral vector (rAAV) for expression of human -SYN in the ventral midbrain of mice lacking the transcription factor Nrf2 (Nrf2(/)). Two months after surgery, Nrf2(/) mice exhibited exacerbated degeneration of nigral dopaminergic neurons and increased dystrophic dendrites, reminiscent of Lewy neurites, which correlated with impaired proteasome gene expression and activity. Dopaminergic neuron loss was associated with an increase in neuroinflammation and gliosis that were intensified in Nrf2(/) mice. In response to exogenously added -SYN, Nrf2(/) microglia failed to activate the expression of two anti-inflammatory genes, heme oxygenase-1 (HO-1) and nicotinamide adenine dinucleotide phosphate quinone oxidorreductase-1 (NQO1). This impaired Nrf2 response correlated with a shift in the microglial activation profile, towards increased production of proinflammatory markers, IL-6, IL-1 and iNOS and reduced phagocytic capacity of fluorescent beads, and lower messenger RNA levels for TAM receptors Axl and Mer. Postmortem brain tissue samples from patients in early- to middle-stage progression of PD showed increased HO-1 expression in astrocytes and microglia, suggesting an attempt of the diseased brain to compensate these hallmarks of PD through activation of the Nrf2 pathway. This study demonstrates that -SYN and Nrf2 deficiency cooperate on protein aggregation, neuroinflammation and neuronal death and provides a bifactorial animal model to study early-stage PD.
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| 35. |
- Lévy, Romain, et al.
(författare)
-
Human CARMIL2 deficiency underlies a broader immunological and clinical phenotype than CD28 deficiency.
- 2023
-
Ingår i: The Journal of experimental medicine. - : Rockefeller University Press. - 1540-9538 .- 0022-1007. ; 220:2
-
Tidskriftsartikel (refereegranskat)abstract
- Patients with inherited CARMIL2 or CD28 deficiency have defective T cell CD28 signaling, but their immunological and clinical phenotypes remain largely unknown. We show that only one of three CARMIL2 isoforms is produced and functional across leukocyte subsets. Tested mutant CARMIL2 alleles from 89 patients and 52 families impair canonical NF-κB but not AP-1 and NFAT activation in T cells stimulated via CD28. Like CD28-deficient patients, CARMIL2-deficient patients display recalcitrant warts and low blood counts of CD4+ and CD8+ memory T cells and CD4+ TREGs. Unlike CD28-deficient patients, they have low counts of NK cells and memory B cells, and their antibody responses are weak. CARMIL2 deficiency is fully penetrant by the age of 10 yr and is characterized by numerous infections, EBV+ smooth muscle tumors, and mucocutaneous inflammation, including inflammatory bowel disease. Patients with somatic reversions of a mutant allele in CD4+ T cells have milder phenotypes. Our study suggests that CARMIL2 governs immunological pathways beyond CD28.
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| 36. |
- Marazioti, Antonia, et al.
(författare)
-
KRAS signaling in malignant pleural mesothelioma
- 2022
-
Ingår i: EMBO Molecular Medicine. - : EMBO. - 1757-4684 .- 1757-4676. ; 14:2
-
Tidskriftsartikel (refereegranskat)abstract
- Malignant pleural mesothelioma (MPM) arises from mesothelial cells lining the pleural cavity of asbestos-exposed individuals and rapidly leads to death. MPM harbors loss-of-function mutations in BAP1, NF2, CDKN2A, and TP53, but isolated deletion of these genes alone in mice does not cause MPM and mouse models of the disease are sparse. Here, we show that a proportion of human MPM harbor point mutations, copy number alterations, and overexpression of KRAS with or without TP53 changes. These are likely pathogenic, since ectopic expression of mutant KRASG12D in the pleural mesothelium of conditional mice causes epithelioid MPM and cooperates with TP53 deletion to drive a more aggressive disease form with biphasic features and pleural effusions. Murine MPM cell lines derived from these tumors carry the initiating KRASG12D lesions, secondary Bap1 alterations, and human MPM-like gene expression profiles. Moreover, they are transplantable and actionable by KRAS inhibition. Our results indicate that KRAS alterations alone or in accomplice with TP53 alterations likely play an important and underestimated role in a proportion of patients with MPM, which warrants further exploration.
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| 37. |
- Nava, Veronica, et al.
(författare)
-
Plastic debris in lakes and reservoirs
- 2023
-
Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 619:7969, s. 317-322
-
Tidskriftsartikel (refereegranskat)abstract
- Plastic debris is thought to be widespread in freshwater ecosystems globally(1). However, a lack of comprehensive and comparable data makes rigorous assessment of its distribution challenging(2,3). Here we present a standardized cross-national survey that assesses the abundance and type of plastic debris (>250 mu m) in freshwater ecosystems. We sample surface waters of 38 lakes and reservoirs, distributed across gradients of geographical position and limnological attributes, with the aim to identify factors associated with an increased observation of plastics. We find plastic debris in all studied lakes and reservoirs, suggesting that these ecosystems play a key role in the plastic-pollution cycle. Our results indicate that two types of lakes are particularly vulnerable to plastic contamination: lakes and reservoirs in densely populated and urbanized areas and large lakes and reservoirs with elevated deposition areas, long water-retention times and high levels of anthropogenic influence. Plastic concentrations vary widely among lakes; in the most polluted, concentrations reach or even exceed those reported in the subtropical oceanic gyres, marine areas collecting large amounts of debris(4). Our findings highlight the importance of including lakes and reservoirs when addressing plastic pollution, in the context of pollution management and for the continued provision of lake ecosystem services.
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| 38. |
- Olson, Nathan D., et al.
(författare)
-
precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
- 2020
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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| 39. |
- Olson, Nathan D., et al.
(författare)
-
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
- 2022
-
Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 2:5, s. 1-12
-
Tidskriftsartikel (refereegranskat)abstract
- The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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| 40. |
- Sguazzin, M., et al.
(författare)
-
Determining neutron-induced reaction cross sections through surrogate reactions at storage rings
- 2023
-
Ingår i: Journal of Physics: Conference Series. - 1742-6588 .- 1742-6596. ; 2586:1
-
Konferensbidrag (refereegranskat)abstract
- Determining the cross sections of neutron-induced reactions on short-lived nuclei is imperative to rate calculations in stellar nucleosynthesis and applications of nuclear physics. It is also an immense experimental challenge due to the radioactivity of the targets involved. Our goal is to circumvent this obstacle by using surrogate reactions in inverse kinematics at the heavy-ion storage rings of GSI/FAIR. We present here preliminary results from the first proof of principle experiment, where a beam of 208Pb impinged on a H2 gas jet target in the Experimental Storage Ring (ESR).
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| 41. |
- Tas, Sinem, et al.
(författare)
-
Chain End-Functionalized Polymer Brushes with Switchable Fluorescence Response
- 2019
-
Ingår i: Macromolecular Chemistry and Physics. - : Wiley. - 1022-1352. ; 220:5
-
Tidskriftsartikel (refereegranskat)abstract
- Herein is described the switchable fluorescence response of poly(methyl methacrylate) (PMMA) brushes. Chain end fluorescein labeled PMMA brushes are prepared by combining surface-initiated atom transfer radical polymerization (SI-ATRP) with a copper-catalyzed alkyne-azide cycloaddition (CuAAC) click reaction. Successful attachment of fluorescein is confirmed by measuring fluorescence of the as-prepared films. Utilizing co-solvency of PMMA in isopropanol-water mixtures, responsive behavior of the end-functionalized brushes is demonstrated by measuring the changes in fluorescence intensity between the swollen and collapsed states.
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| 42. |
- Tran, T. Lan Anh, et al.
(författare)
-
Magnetic Properties of bcc-Fe(001)/C-60 Interfaces for Organic Spintronics
- 2013
-
Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 5:3, s. 837-841
-
Tidskriftsartikel (refereegranskat)abstract
- The magnetic structure of the interfaces between organic semiconductors and ferromagnetic contacts plays a key role in the spin injection and extraction processes in organic spintronic devices. We present a combined computational (density functional theory) and experimental (X-ray magnetic circular dichroism) study on the magnetic properties of interfaces between bcc-Fe(001) and C-60 molecules. C-60 is an interesting candidate for application in organic spintronics due to the absence of hydrogen atoms and the associated hyperfine fields. Adsorption of C-60 on Fe(001) reduces the magnetic moments on the top Fe layers by similar to 6%, while inducing an antiparrallel magnetic moment of similar to-0.2 mu(B) on C-60. Adsorption of C-60 on a model ferromagnetic substrate consisting of three Fe monolayers on W(001) leads to a different structure but to very similar interface magnetic properties.
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| 43. |
- Volpicelli-Daley, Laura A, et al.
(författare)
-
How can rAAV-α-synuclein and the fibril α-synuclein models advance our understanding of Parkinson's disease?
- 2016
-
Ingår i: Journal of Neurochemistry. - : Wiley. - 1471-4159 .- 0022-3042. ; 139:S1, s. 131-155
-
Forskningsöversikt (refereegranskat)abstract
- Abstract: Animal models of Parkinson's disease (PD) are important for understanding the mechanisms of the disease and can contribute to developing and validating novel therapeutics. Ideally, these models should replicate the cardinal features of PD, such as progressive neurodegeneration of catecholaminergic neurons and motor defects. Many current PD models emphasize pathological forms of α-synuclein, based on findings that autosomal dominant mutations in α-synuclein and duplications/triplications of the SNCA gene cause PD. In addition, Lewy bodies and Lewy neurites, primarily composed of α-synuclein, represent the predominant pathological characteristics of PD. These inclusions have defined features, such as insolubility in non-ionic detergent, hyperphosphorylation, proteinase K sensitivity, a filamentous appearance by electron microscopy, and β-sheet structure. Furthermore, it has become clear that Lewy bodies and Lewy neurites are found throughout the peripheral and central nervous system, and could account not only for motor symptoms, but also for non-motor symptoms of the disease. The goal of this review is to describe two new α-synuclein-based models: the recombinant adeno-associated viral vector-α-synuclein model and the α-synuclein fibril model. An advantage of both models is that they do not require extensive crossbreeding of rodents transgenic for α-synuclein with other rodents transgenic for genes of interest to study the impact of such genes on PD-related pathology and phenotypes. In addition, abnormal α-synuclein can be expressed in brain regions relevant for disease. Here, we discuss the features of each model, how each model has contributed thus far to our understanding of PD, and the advantages and potential caveats of each model. (Figure presented.) This review describes two α-synuclein-based rodent models of Parkinson's disease: the rAAV-α-synuclein model and the α-synuclein fibril model. The key features of these models are described, and the extent to which they recapitulate features of PD, such as α-synuclein inclusion formation, loss of dopaminergic synapses in the striatum, motor defects, inflammation, and dopamine neuron death. This article is part of a special issue on Parkinson disease.
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| 44. |
- Wilms, H., et al.
(författare)
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Suppression of Map Kinases Inhibits Microglial Activation and Attenuates Neuronal Cell Death Induced by Alpha-Synuclein Protofibrils
- 2009
-
Ingår i: International Journal of Immunopathology and Pharmacology. - 0394-6320. ; 22:4, s. 897-909
-
Tidskriftsartikel (refereegranskat)abstract
- alpha-Synuclein (alpha-Syn) accounts, as a major component of Lewy bodies (LB), for the filamentous deposits in many cases of neurodegenerative diseases. Yet, little is known about the molecular mechanisms of neuronal loss in these diseases. The correlation between alpha-Syn oligomerization/aggregation and pathologies raises the key question of which molecular form of alpha-Syn (i.e. monomeric alpha-Syn, protofibrils or mature fibrils) represents the damage-inducing culprit in the scenario of synucleinopathies. We show that human alpha-Syn protofibrils (PFs) are potent activators of parallel proinflammatory signalling pathways (p38 and ERK1/2 MAP kinases and NF-kappa B) in microglial cells in vitro. Furthermore, stereotactic injection of alpha-Syn PFs into the substantia nigra of adult rats leads to a profound activation of microglia and adjacent neuronal cell loss, which can be attenuated by the MAP kinase inhibitor semapimod. We propose that the neurodegenerative process of alpha-synucleinopathies involves microglial activation through alpha-Syn released or extruded from cells with pathogenic alpha-Syn metabolism. Compounds that inhibit the MAPK/NF-kappa B pathways might be a promising pharmacological strategy for the treatment of the inflammatory component of synucleinopathies including PD.
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| 45. |
- Yan, Rui, et al.
(författare)
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Image combination for high-field phased-array MR
- 2003
-
Ingår i: Proc. of IEEE International Conference on Acoustics,Speech and Signal Processing (ICASSP). - 0780376633 ; , s. V-1-V-4
-
Konferensbidrag (refereegranskat)abstract
- We consider signal processing methods for phased-array magnetic resonance imaging (MRI). A theoretical description of a phased-array MRI data model is presented and three image reconstruction algorithms are proposed to estimate the effective image pixels. An analysis is provided to show how the new algorithms compare to conventional reconstruction methods.
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| 46. |
- Yu, Tiangxiong, et al.
(författare)
-
A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals
- 2023
-
Ingår i: RNA. - : Cold Spring Harbor Laboratory. - 1355-8382 .- 1469-9001. ; 29:1, s. 30-43
-
Tidskriftsartikel (refereegranskat)abstract
- In male mice, the transcription factor A-MYB initiates the transcription of pachytene piRNA genes during meiosis. Here, we report that A-MYB activates the transcription factor Tcfl5 produced in pachytene spermatocytes. Subsequently, A-MYB and TCFL5 reciprocally reinforce their own transcription to establish a positive feedback circuit that triggers pachytene piRNA production. TCFL5 regulates the expression of genes required for piRNA maturation and promotes transcription of evolutionarily young pachytene piRNA genes, whereas A-MYB activates the transcription of older pachytene piRNA genes. Intriguingly, pachytene piRNAs from TCFL5-dependent young loci initiate the production of piRNAs from A-MYB-dependent older loci, ensuring the self-propagation of pachytene piRNAs. A-MYB and TCFL5 act via a set of incoherent feedforward loops that drive regulation of gene expression by pachytene piRNAs during spermatogenesis. This regulatory architecture is conserved in rhesus macaque, suggesting that it was present in the last common ancestor of placental mammals.
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