| 1. |
- Bergström, Anders, et al.
(författare)
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Origins and genetic legacy of prehistoric dogs
- 2020
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 370:6516, s. 557-563
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Tidskriftsartikel (refereegranskat)abstract
- Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.
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| 2. |
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| 3. |
- Bergström, Anders, et al.
(författare)
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Grey wolf genomic history reveals a dual ancestry of dogs
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 607:7918, s. 313-320
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Tidskriftsartikel (refereegranskat)abstract
- The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
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| 4. |
- Frantz, David, et al.
(författare)
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High contrast, isotropic, and uniform 3D-imaging of centimeter-scale scattering samples using structured illumination light-sheet microscopy with axial sweeping
- 2022
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Ingår i: Biomedical Optics Express. - 2156-7085. ; 13:9, s. 4907-4925
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Tidskriftsartikel (refereegranskat)abstract
- Light-sheet fluorescent microscopy (LSFM) has, in recent years, allowed for rapid 3D-imaging of cleared biomedical samples at larger and larger scale. However, even in cleared samples, multiple light scattering often degrades the imaging contrast and widens the optical sectioning. Accumulation of scattering intensifies these negative effects as light propagates inside the tissue, which accentuates the issues when imaging large samples. With axially swept light-sheet microscopy (ASLM), centimeter-scale samples can be scanned with a uniform micrometric optical sectioning. But to fully utilize these benefits for 3D-imaging in biomedical tissue samples, suppression of scattered light is needed. Here, we address this by merging ASLM with light-sheet based structured illumination into Structured Illumination Light-sheet Microscopy with Axial Sweeping (SILMAS). The SILMAS method thus enables high-contrast imaging, isotropic micrometric resolution and uniform optical sectioning in centimeter-scale scattering samples, creating isotropic 3D-volumes of e.g., whole mouse brains without the need for any computation-heavy post-processing. We demonstrate the effectiveness of the approach in agarose gel phantoms with fluorescent beads, and in an PFF injected alpha-synuclein transgenic mouse model tagged with a green fluorescent protein (SynGFP). SILMAS imaging is compared to standard ASLM imaging on the same samples and using the same optical setup, and is shown to increase contrast by as much as 370% and reduce widening of optical sectioning by 74%. With these results, we show that SILMAS improves upon the performance of current state-of-the-art light-sheet microscopes for large and imperfectly cleared tissue samples and is a valuable addition to the LSFM family.
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| 5. |
- Frantz, David, et al.
(författare)
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Multi-scattering software part II : Experimental validation for the light intensity distribution
- 2022
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Ingår i: Optics Express. - 1094-4087. ; 30:2, s. 1261-1279
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Tidskriftsartikel (refereegranskat)abstract
- This article, Part II of an article series on GPU-accelerated Monte Carlo simulation of photon transport through turbid media, focuses on the validation of the online software Multi-Scattering. While Part I detailed the implementation of the computational model, simulated and experimental results are now compared for the distribution of the scattered light intensity. The scattering phantoms prepared here are aqueous dispersions of polystyrene microspheres of diameter D= 0.5, 2 and 5 μm and at various concentrations, resulting in optical depth ranging from OD= 1 to 17.5. The Lorenz-Mie scattering phase functions used in the simulations have been verified experimentally at low particle concentrations by analyzing the angular light intensity distribution at the Fourier plane of a collecting lens. The validation approach herein accounts for the specific light collection and image formation by the camera. The front and side surfaces of the medium are imaged and the corresponding light intensity distributions are compared qualitatively and quantitatively. It is concluded that the model enables reliable simulations over the tested parameters, offering predictive simulations of transmitted intensities with a mean relative error ≤∼19% over the full range.
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| 6. |
- Frantz, David, et al.
(författare)
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Structured light sheet microscopy for high contrast 3D imaging of whole mouse brain
- 2021
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Ingår i: Novel Techniques in Microscopy, NTM 2021. - 9781557528209
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Konferensbidrag (refereegranskat)abstract
- Tissue clearing allows 3D-imaging of large biomedical samples, but can be affected by blur effects limiting individual cells detection. Using a structured illumination light sheet we solve this issue, obtaining high-contrast images in turbid samples.
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| 7. |
- Garpered, Sabine, et al.
(författare)
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Evaluation of 18F-FDG uptake in lung parenchyma compensating for tissue fraction : Comparison between non-enhanced low dose CT and intravenous contrast-enhanced diagnostic CT
- 2020
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Ingår i: Nuklearmedizin. - : Georg Thieme Verlag KG. - 0029-5566 .- 2567-6407. ; 59:1, s. 20-25
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Tidskriftsartikel (refereegranskat)abstract
- AIM: To determine how the presence of intravenous (IV) contrast-enhanced CT influences SUV measurements corrected for both attenuation and tissue fraction. MATERIAL AND METHODS: Eighteen patients with different malignancies, free from lung disorders, lung cancer or metastasis, were prospectively recruited when referred for staging with combined 18F-FDG-PET/CT examination. A non-enhanced low-dose CT over the chest was immediately followed by a whole-body IV contrast-enhanced diagnostic CT and finally the PET acquisition. PET data were reconstructed with attenuation correction based on the two CT data sets. The lungs were segmented in the CT images and lung density was measured. Uptake of 18F-FDG in lung parenchyma was recorded using both non-enhanced and IV contrast-enhanced CT as well as with and without compensation for lung aeration. A comparison of SUV values of corrected and uncorrected PET images was performed. RESULTS: There was no significant difference between low dose PET/CT and IV contrast-enhanced PET/CT when removing the impact of air fraction (p = 0.093 for the right lung and p = 0.085 for the left lung). When tissue fraction was not corrected for, there was a significant difference between low dose PET/CT and IV contrast enhanced PET/CT used for attenuation correction (p = 0.006 for the right lung and p = 0.015 for the left lung). CONCLUSION: There was only a marginal effect on the assessement of SUV in the lung tissue when using IV contrast enhanced CT for attenuation correction when the air fraction was accounted for.
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| 8. |
- Gustafsson, Agneta, et al.
(författare)
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A multicentre simulation study of planar whole-body bone scintigraphy in Sweden
- 2022
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Ingår i: EJNMMI Physics. - : Springer Science and Business Media LLC. - 2197-7364. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Whole-body bone scintigraphy is a clinically useful non-invasive and highly sensitive imaging method enabling detection of metabolic changes at an early stage of disease, often earlier than with conventional radiologic procedures. Bone scintigraphy is one of the most common nuclear medicine methods used worldwide. Therefore, it is important that the examination is implemented and performed in an optimal manner giving the patient added value in the subsequent care process. The aim of this national multicentre survey was to investigate Swedish nuclear medicine departments compliance with European practice guidelines for bone scintigraphy. In addition, the effect of image acquisition parameters on the ability to detect metabolic lesions was investigated. Methods: Twenty-five hospital sites participated in the study. The SIMIND Monte Carlo (MC) simulation and the XCAT phantom were used to simulate ten fictive patient cases with increased metabolic activity distributed at ten different locations in the skeleton. The intensity of the metabolic activity was set into six different levels. Individual simulations were performed for each site, corresponding to their specific camera system and acquisition parameters. Simulated image data sets were then sent to each site and were visually evaluated in terms of if there was one or several locations with increased metabolic activity relative to normal activity. Result: There is a high compliance in Sweden with the EANM guidelines regarding image acquisition parameters for whole-body bone scintigraphy. However, up to 40% of the participating sites acquire lower count density in the images than recommended. Despite this, the image quality was adequate to maintain a stable detection level. None of the hospital sites or individual responders deviated according to the statistical analysis. There is a need for at least 2.5 times metabolic activity compared to normal for a lesion to be detected. Conclusion: The imaging process is well harmonized throughout the country and there is a high compliance with the EANM guidelines. There is a need for at least 2.5 times the normal metabolic activity for a lesion to be detected as abnormal.
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| 9. |
- Lin, Audrey T., et al.
(författare)
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The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge
- 2023
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Ingår i: Science. - 0036-8075 .- 1095-9203. ; 382:6676, s. 1303-1308
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Tidskriftsartikel (refereegranskat)abstract
- Ancestral Coast Salish societies in the Pacific Northwest kept long-haired woolly dogs that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton", collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.
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| 10. |
- Lindgren Belal, Sarah, et al.
(författare)
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Applications of Artificial Intelligence in PSMA PET/CT for Prostate Cancer Imaging
- 2024
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Ingår i: Seminars in Nuclear Medicine. - 1558-4623 .- 0001-2998. ; 54:1, s. 141-149
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Forskningsöversikt (refereegranskat)abstract
- Prostate-specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT) has emerged as an important imaging technique for prostate cancer. The use of PSMA PET/CT is rapidly increasing, while the number of nuclear medicine physicians and radiologists to interpret these scans is limited. Additionally, there is variability in interpretation among readers. Artificial intelligence techniques, including traditional machine learning and deep learning algorithms, are being used to address these challenges and provide additional insights from the images. The aim of this scoping review was to summarize the available research on the development and applications of AI in PSMA PET/CT for prostate cancer imaging. A systematic literature search was performed in PubMed, Embase and Cinahl according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A total of 26 publications were included in the synthesis. The included studies focus on different aspects of artificial intelligence in PSMA PET/CT, including detection of primary tumor, local recurrence and metastatic lesions, lesion classification, tumor quantification and prediction/prognostication. Several studies show similar performances of artificial intelligence algorithms compared to human interpretation. Few artificial intelligence tools are approved for use in clinical practice. Major limitations include the lack of external validation and prospective design. Demonstrating the clinical impact and utility of artificial intelligence tools is crucial for their adoption in healthcare settings. To take the next step towards a clinically valuable artificial intelligence tool that provides quantitative data, independent validation studies are needed across institutions and equipment to ensure robustness.
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