| 1. |
- Hyde, K. D., et al.
(författare)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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Ingår i: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Tidskriftsartikel (refereegranskat)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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| 2. |
- Landén, Mikael, 1966, et al.
(författare)
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Brain aging in major depressive disorder: results from the ENIGMA major depressive disorder working group
- 2021
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Ingår i: Molecular Psychiatry. - : Springer Science and Business Media LLC. - 1359-4184 .- 1476-5578. ; 26, s. 5124-5139
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Tidskriftsartikel (refereegranskat)abstract
- Major depressive disorder (MDD) is associated with an increased risk of brain atrophy, aging-related diseases, and mortality. We examined potential advanced brain aging in adult MDD patients, and whether this process is associated with clinical characteristics in a large multicenter international dataset. We performed a mega-analysis by pooling brain measures derived from T1-weighted MRI scans from 19 samples worldwide. Healthy brain aging was estimated by predicting chronological age (18–75 years) from 7 subcortical volumes, 34 cortical thickness and 34 surface area, lateral ventricles and total intracranial volume measures separately in 952 male and 1236 female controls from the ENIGMA MDD working group. The learned model coefficients were applied to 927 male controls and 986 depressed males, and 1199 female controls and 1689 depressed females to obtain independent unbiased brain-based age predictions. The difference between predicted “brain age” and chronological age was calculated to indicate brain-predicted age difference (brain-PAD). On average, MDD patients showed a higher brain-PAD of +1.08 (SE 0.22) years (Cohen’s d = 0.14, 95% CI: 0.08–0.20) compared with controls. However, this difference did not seem to be driven by specific clinical characteristics (recurrent status, remission status, antidepressant medication use, age of onset, or symptom severity). This highly powered collaborative effort showed subtle patterns of age-related structural brain abnormalities in MDD. Substantial within-group variance and overlap between groups were observed. Longitudinal studies of MDD and somatic health outcomes are needed to further assess the clinical value of these brain-PAD estimates. © 2020, The Author(s).
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| 3. |
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| 4. |
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| 5. |
- Peripato, Vinicius, et al.
(författare)
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More than 10,000 pre-Columbian earthworks are still hidden throughout Amazonia
- 2023
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Ingår i: Science (New York, N.Y.). - 1095-9203. ; 382:6666, s. 103-109
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Tidskriftsartikel (refereegranskat)abstract
- Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.
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| 6. |
- Garcia-Lopez, R., et al.
(författare)
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A measure of the size of the magnetospheric accretion region in TW Hydrae
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 584:7822, s. 547-550
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Tidskriftsartikel (refereegranskat)abstract
- Stars form by accreting material from their surrounding disks. There is a consensus that matter flowing through the disk is channelled onto the stellar surface by the stellar magnetic field. This is thought to be strong enough to truncate the disk close to the corotation radius, at which the disk rotates at the same rate as the star. Spectro-interferometric studies in young stellar objects show that hydrogen emission (a well known tracer of accretion activity) mostly comes from a region a few milliarcseconds across, usually located within the dust sublimation radius1–3. The origin of the hydrogen emission could be the stellar magnetosphere, a rotating wind or a disk. In the case of intermediate-mass Herbig AeBe stars, the fact that Brackett γ (Brγ) emission is spatially resolved rules out the possibility that most of the emission comes from the magnetosphere4–6 because the weak magnetic fields (some tenths of a gauss) detected in these sources7,8 result in very compact magnetospheres. In the case of T Tauri sources, their larger magnetospheres should make them easier to resolve. The small angular size of the magnetosphere (a few tenths of a milliarcsecond), however, along with the presence of winds9,10 make the interpretation of the observations challenging. Here we report optical long-baseline interferometric observations that spatially resolve the inner disk of the T Tauri star TW Hydrae. We find that the near-infrared hydrogen emission comes from a region approximately 3.5 stellar radii across. This region is within the continuum dusty disk emitting region (7 stellar radii across) and also within the corotation radius, which is twice as big. This indicates that the hydrogen emission originates in the accretion columns (funnel flows of matter accreting onto the star), as expected in magnetospheric accretion models, rather than in a wind emitted at much larger distance (more than one astronomical unit).
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| 7. |
- Koutoulaki, M., et al.
(författare)
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The GRAVITY young stellar object survey: IV. The CO overtone emission in 51 Oph at sub-au scales
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 645
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Tidskriftsartikel (refereegranskat)abstract
- Context. 51 Oph is a Herbig Ae/Be star that exhibits strong near-infrared CO ro-vibrational emission at 2.3 μm, most likely originating in the innermost regions of a circumstellar disc. Aims. We aim to obtain the physical and geometrical properties of the system by spatially resolving the circumstellar environment of the inner gaseous disc. Methods. We used the second-generation Very Large Telescope Interferometer instrument GRAVITY to spatially resolve the continuum and the CO overtone emission. We obtained data over 12 baselines with the auxiliary telescopes and derive visibilities, and the differential and closure phases as a function of wavelength. We used a simple local thermal equilibrium ring model of the CO emission to reproduce the spectrum and CO line displacements. Results. Our interferometric data show that the star is marginally resolved at our spatial resolution, with a radius of ∼10.58 ± 2.65R·. The K-band continuum emission from the disc is inclined by 63° ± 1°, with a position angle of 116° ± 1°, and 4 ± 0.8 mas (0.5 ± 0.1 au) across. The visibilities increase within the CO line emission, indicating that the CO is emitted within the dust-sublimation radius. By modelling the CO bandhead spectrum, we derive that the CO is emitted from a hot (T = 1900-2800 K) and dense (NCO = (0.9-9) × 1021 cm-2) gas. The analysis of the CO line displacement with respect to the continuum allows us to infer that the CO is emitted from a region 0.10 ± 0.02 au across, well within the dust-sublimation radius. The inclination and position angle of the CO line emitting region is consistent with that of the dusty disc. Conclusions. Our spatially resolved interferometric observations confirm the CO ro-vibrational emission within the dust-free region of the inner disc. Conventional disc models exclude the presence of CO in the dust-depleted regions of Herbig AeBe stars. Ad hoc models of the innermost disc regions, that can compute the properties of the dust-free inner disc, are therefore required.
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| 8. |
- Potapov, Anton M., et al.
(författare)
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Global fine-resolution data on springtail abundance and community structure
- 2024
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.
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| 9. |
- Potapov, Anton M., et al.
(författare)
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Globally invariant metabolism but density-diversity mismatch in springtails
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Soil life supports the functioning and biodiversity of terrestrial ecosystems. Springtails (Collembola) are among the most abundant soil arthropods regulating soil fertility and flow of energy through above- and belowground food webs. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset representing 2470 sites, we estimate the total soil springtail biomass at 27.5 megatons carbon, which is threefold higher than wild terrestrial vertebrates, and record peak densities up to 2 million individuals per square meter in the tundra. Despite a 20-fold biomass difference between the tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the changes in temperature with latitude. Neither springtail density nor community metabolism is predicted by local species richness, which is high in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation and resource limitation in soil communities. Contrasting relationships of biomass, diversity and activity of springtail communities with temperature suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting soil functioning.
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| 10. |
- Araujo, M. V., et al.
(författare)
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Lorenzetti Showers- A general-purpose framework for supporting signal reconstruction and triggering with calorimeters
- 2023
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Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 286
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Tidskriftsartikel (refereegranskat)abstract
- Calorimeters play an important role in high-energy physics experiments. Their design includes electronic instrumentation, signal processing chain, computing infrastructure, and also a good understanding of their response to particle showers produced by the interaction of incoming particles. This is usually supported by full simulation frameworks developed for specific experiments so that their access is restricted to the collaboration members only. Such restrictions limit the general-purpose developments that aim to propose innovative approaches to signal processing, which may include machine learning and advanced stochastic signal processing models. This work presents the Lorenzetti Showers, a general-purpose framework that mainly targets supporting novel signal reconstruction and triggering strategies using segmented calorimeter information. This framework fully incorporates developments down to the signal processing chain level (signal shaping, energy estimation, and noise mitigation techniques) to allow advanced signal processing approaches in modern calorimetry and triggering systems. The developed framework is flexible enough to be extended in different directions. For instance, it can become a tool for the phenomenology community to go beyond the usual detector design and physics process generation approaches. Program summary Program Title: Lorenzetti Showers CPC Library link to program files: https://doi .org /10 .17632 /sy64367452 .1 Developer's repository link: https://github .com /lorenzetti -hep /lorenzetti Licensing provisions: GPLv3 Programming language: Python, C++. Nature of problem: In experimental high-energy physics, simulation is essential for experiment preparation, design and interpretations of ongoing acquisitions. Especially for calorimeters, an accurate simulation that can describe detector geometry, behavior to different physics processes and signal generation close to the readout electronics and data acquisition levels is required to properly develop signal processing and computational methods. Such detectors may face very challenging demands arising from the new designs, such as pileup mitigation and noise reduction tasks under unprecedented levels. In this sense, simulation requirements continuously increase in complexity and performance, because new physics searches require large datasets and accurate modeling to experimental effects. Solution method: The Lorenzetti Showers is an integrated software framework that provides complete calorimeter information close enough to the electronic readout chain. Thus, the proposed framework allows users to access cell readout values, configurable sensor pulse-shapes, crosstalk modeling, and different energy estimation methods. It aims at supporting designs that target low or high pileup operation conditions in an easy-to-use modular structure. The developed framework is based on Pythia 8 (particle generation) and Geant4 (interactions with the calorimeter technique under analysis). An efficient data recording structure was used to allow full access to the Lorenzetti Showers outputs. In summary, the Lorenzetti Showers tool provides to the scientific community a user-friendly, flexible, user-oriented, and low-level calorimeter simulation framework. Additional comments including restrictions and unusual features: The framework current version provides the implementation of a generic segmented calorimeter (electromagnetic and hadronic sections), which may be modified by the user, if desired. It allows the generation of particles interactions using Pythia 8 (native) or any generator compatible with the HepMC format (which may be integrated using an external input file) and propagation through a user-configurable calorimeter using Geant4.
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| 11. |
- He, Mao Qiang, et al.
(författare)
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Phylogenomics, divergence times and notes of orders in Basidiomycota
- 2024
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Ingår i: Fungal Diversity. - 1560-2745 .- 1878-9129. ; 126, s. 127-406
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Tidskriftsartikel (refereegranskat)abstract
- Basidiomycota is one of the major phyla in the fungal tree of life. The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology. In this study, we present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families, 47 orders, 14 classes and four subphyla; we update the outline of Basidiomycota based on the phylogenomic relationships and the taxonomic studies since 2019; and we provide notes for each order and discuss the history, defining characteristics, evolution, justification of orders, problems, significance, and plates. Our phylogenomic analysis suggests that the subphyla diverged in a time range of 443–490 Myr (million years), classes in a time range of 312–412 Myr, and orders in a time range of 102–361 Myr. Families diverged in a time range of 50–289 Myr, 76–224 Myr, and 62–156 Myr in Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina, respectively. Based on the phylogenomic relationships and divergence times, we propose a new suborder Mycenineae in Agaricales to accommodate Mycenaceae. In the current outline of Basidiomycota, there are four subphyla, 20 classes, 77 orders, 297 families, and 2134 genera accepted. When building a robust taxonomy of Basidiomycota in the genomic era, the generation of molecular phylogenetic data has become relatively easier. Finding phenotypical characters, especially those that can be applied for identification and classification, however, has become increasingly challenging.
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| 12. |
- Brant, Luisa C. C., et al.
(författare)
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Association Between Electrocardiographic Age and Cardiovascular Events in Community Settings : The Framingham Heart Study
- 2023
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Ingår i: Circulation. Cardiovascular Quality and Outcomes. - : Ovid Technologies (Wolters Kluwer Health). - 1941-7713 .- 1941-7705. ; 16:7
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Deep neural networks have been used to estimate age from ECGs, the electrocardiographic age (ECG-age), which predicts adverse outcomes. However, this prediction ability has been restricted to clinical settings or relatively short periods. We hypothesized that ECG-age is associated with death and cardiovascular outcomes in the long-standing community-based FHS (Framingham Heart Study).METHODS: We tested the association of ECG-age with chronological age in the FHS cohorts in ECGs from 1986 to 2021. We calculated the gap between chronological and ECG-age (& UDelta;age) and classified individuals as having normal, accelerated, or decelerated aging, if & UDelta;age was within, higher, or lower than the mean absolute error of the model, respectively. We assessed the associations of & UDelta;age, accelerated and decelerated aging with death or cardiovascular outcomes (atrial fibrillation, myocardial infarction, and heart failure) using Cox proportional hazards models adjusted for age, sex, and clinical factors.RESULTS:The study population included 9877 FHS participants (mean age, 55 & PLUSMN;13 years; 54.9% women) with 34 948 ECGs. ECG-age was correlated to chronological age (r=0.81; mean absolute error, 9 & PLUSMN;7 years). After 17 & PLUSMN;8 years of follow-up, every 10-year increase of & UDelta;age was associated with 18% increase in all-cause mortality (hazard ratio [HR], 1.18 [95% CI, 1.12-1.23]), 23% increase in atrial fibrillation risk (HR, 1.23 [95% CI, 1.17-1.29]), 14% increase in myocardial infarction risk (HR, 1.14 [95% CI, 1.05-1.23]), and 40% increase in heart failure risk (HR, 1.40 [95% CI, 1.30-1.52]), in multivariable models. In addition, accelerated aging was associated with a 28% increase in all-cause mortality (HR, 1.28 [95% CI, 1.14-1.45]), whereas decelerated aging was associated with a 16% decrease (HR, 0.84 [95% CI, 0.74-0.95]).CONCLUSIONS:ECG-age was highly correlated with chronological age in FHS. The difference between ECG-age and chronological age was associated with death, myocardial infarction, atrial fibrillation, and heart failure. Given the wide availability and low cost of ECG, ECG-age could be a scalable biomarker of cardiovascular risk.
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| 13. |
- Chen, B., et al.
(författare)
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Effect of Continuous Positive Airway Pressure on Lipid Profiles in Obstructive Sleep Apnea: A Meta-Analysis
- 2022
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Ingår i: Journal of Clinical Medicine. - : MDPI AG. - 2077-0383. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Obstructive sleep apnea (OSA) is associated with dyslipidemia. However, the effects of continuous positive airway pressure (CPAP) treatment on lipid profiles are unclear. Methods: PubMed/Medline, Embase and Cochrane were searched up to July 2021. Randomized controlled trials (RCTs) of CPAP versus controls with ≥4 weeks treatment and reported pre-and post-intervention lipid profiles were included. Weighted mean difference (WMD) was used to assess the effect size. Meta-regression was used to explore the potential moderators of post-CPAP treatment changes in lipid profiles. Results: A total of 14 RCTs with 1792 subjects were included. CPAP treatment was associated with a significant decrease in total cholesterol compared to controls (WMD = −0.098 mmol/L, 95% CI = −0.169 to −0.027, p = 0.007, I2 = 0.0%). No significant changes in triglyceride, high-density lipoprotein nor low-density lipoprotein were observed after CPAP treatment (all p > 0.2). Furthermore, meta-regression models showed that age, gender, body mass index, daytime sleepiness, OSA severity, follow-up study duration, CPAP compliance nor patients with cardiometabolic disease did not moderate the effects of CPAP treatment on lipid profiles (all p > 0.05). Conclusions: CPAP treatment decreases total cholesterol at a small magnitude but has no effect on other markers of dyslipidemia in OSA patients. Future studies of CPAP therapy should target combined treatment strategies with lifestyle modifications and/or anti-hyperlipidemic medications in the primary as well as secondary cardiovascular prevention models. © 2022 by the authorsLicensee MDPI, Basel, Switzerland.
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| 14. |
- Teixeira, Joao P.V., et al.
(författare)
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Novel Perlin-based phantoms using 3D models of compressed breast shapes and fractal noise
- 2022
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Ingår i: Medical Imaging 2022 : Physics of Medical Imaging - Physics of Medical Imaging. - : SPIE. - 1605-7422. - 9781510649378 ; 12031
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Konferensbidrag (refereegranskat)abstract
- Virtual clinical trials (VCTs) have been used widely to evaluate digital breast tomosynthesis (DBT) systems. VCTs require realistic simulations of the breast anatomy (phantoms) to characterize lesions and to estimate risk of masking cancers. This study introduces the use of Perlin-based phantoms to optimize the acquisition geometry of a novel DBT prototype. These phantoms were developed using a GPU implementation of a novel library called Perlin-CuPy. The breast anatomy is simulated using 3D models under mammography cranio-caudal compression. In total, 240 phantoms were created using compressed breast thickness, chest-wall to nipple distance, and skin thickness that varied in a {[35, 75], [59, 130), [1.0, 2.0]} mm interval, respectively. DBT projections and reconstructions of the phantoms were simulated using two acquisition geometries of our DBT prototype. The performance of both acquisition geometries was compared using breast volume segmentations of the Perlin phantoms. Results show that breast volume estimates are improved with the introduction of posterior-anterior motion of the x-ray source in DBT acquisitions. The breast volume is overestimated in DBT, varying substantially with the acquisition geometry; segmentation errors are more evident for thicker and larger breasts. These results provide additional evidence and suggest that custom acquisition geometries can improve the performance and accuracy in DBT. Perlin phantoms help to identify limitations in acquisition geometries and to optimize the performance of the DBT prototypes.
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