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- 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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| 4. |
- Auer, M., et al.
(författare)
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3-D reconstruction of tissue components for atherosclerotic human arteries using ex vivo high-resolution MRI
- 2006
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Ingår i: IEEE Transactions on Medical Imaging. - : Institute of Electrical and Electronics Engineers (IEEE). - 0278-0062 .- 1558-254X. ; 25:3, s. 345-357
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Tidskriftsartikel (refereegranskat)abstract
- Automatic computer-based methods are well suited for the image analysis of the different components in atherosclerotic plaques. Although several groups work on such analysis some of the methods used are oversimplified and require improvements when used within a computational framework for predicting meaningful stress and strain distributions in the heterogeneous arterial wall under various loading conditions. Based on high-resolution magnetic resonance imaging of excised atherosclerotic human arteries and a series of two-dimensional (2-D) contours we present a segmentation tool that permits a three-dimensional (3-D) reconstruction of the most important tissue components of atherosclerotic arteries. The underlying principle of the proposed approach is a model-based snake algorithm for identifying 2-D contours, which uses information about the plaque composition and geometric data of the tissue layers. Validation of the computer-generated tissue boundaries is performed with 100 MR images, which are compared with the results of a manual segmentation performed by four experts. Based on the Hausdorff distance and the average distance for computer-to-expert differences and the interexpert differences for the outer boundary of the adventitia, the adventitia-media, media-intima, intima-lumen and calcification boundaries are less than 1 pixel (0.234 mm). The percentage statistic shows similar results to the modified Williams index in terms of accuracy. Except for the identification of lipid-rich regions the proposed algorithm is automatic. The nonuniform rational B-spline-based computer-generated 3-D models of the individual tissue components provide a basis for clinical and computational analysis.
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| 5. |
- Auer, M., et al.
(författare)
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A methodology to study the morphologic changes in lesions during in vitro angioplasty using MRI and image processing
- 2008
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Ingår i: Medical Image Analysis. - : Elsevier BV. - 1361-8415 .- 1361-8423. ; 12:2, s. 163-173
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Tidskriftsartikel (refereegranskat)abstract
- The assessment of morphologic changes in atherosclerotic lesions during interventional procedures such as transluminal balloon angioplasty is an issue of highest clinical importance. We propose a methodology that allows realistic 3D morphomechanical modeling of the vessel, the plaque and the lumen at different stages of in vitro angioplasty. We elaborate on a novel device designed to guide angioplasty under controlled experimental conditions. The device allows to reproduce in vivo conditions as good as possible, i.e. axial in situ pre-stretch, 100 mmHg intraluminal pressure, 37 degrees C Tyrode solution, balloon inflation without external constraints using a high-pressure syringe and contrast medium. With a standard 1.5 T MR-system we accomplish multi-spectral images at different stages of the angioplasty experiment. After MR image acquisition the specimen is used for histopathological analysis and biomechanical tests. A segmentation process is used to generate NURBS-based 3D geometric models of the individual vessel and plaque components at different balloon pressures. Tissue components are segmented automatically using generalized gradient vector flow active contours. We investigated 10 human femoral arteries. The effects of balloon compression on the individual artery components is particularly described for two obstructed arteries with an intact collagenous cap, a pronounced lipid pool and with calcification. In both arteries we observe a significant increase in lumen area after angioplasty. Dissection between intima and media and reduction of the lipid pool are primary mechanisms of dilatation. This methodology provides a basis for studying plaque biomechanics under supra-physiological loading conditions. It has the potential to improve and validate finite element models of atherosclerotic plaques which may allow a better prediction of angioplasty procedures.
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| 6. |
- Auer, M., et al.
(författare)
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In Vitro Angioplasty of Atherosclerotic Human Femoral Arteries : Analysis of the Geometrical Changes in the Individual Tissues Using MRI and Image Processing
- 2010
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Ingår i: Annals of Biomedical Engineering. - : Springer Science and Business Media LLC. - 0090-6964 .- 1573-9686. ; 38:4, s. 1276-1287
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Tidskriftsartikel (refereegranskat)abstract
- Existing atherosclerotic plaque imaging techniques such as intravascular ultrasound, multidetector computed tomography, optical coherence tomography, and high-resolution magnetic resonance imaging (hrMRI) require computerized methods to separate and analyze the plaque morphology. In this work, we perform in vitro balloon angioplasty experiments with 10 human femoral arteries using hrMRI and image processing. The vessel segments contain low-grade to high-grade lesions with very different plaque compositions. The experiments are designed to mimic the in vivo situation. We use a semi-automatic image processing tool to extract the three-dimensional (3D) geometries of the tissue components at four characteristic stages of the angioplasty procedure. The obtained geometries are then used to determine geometrical and mechanical indices in order to characterize, classify, and analyze the atherosclerotic plaques by their specific geometrical changes. During inflation, three vessels ruptured via helical crack propagation. The adventitia, media, and intima did not preserve their area/volume during inflation; the area changes of the lipid pool during inflation were significant. The characterization of changes in individual 3D tissue geometries, together with tissue-specific mechanical properties, may serve as a basis for refined finite element (FE) modeling, which is key to better understand stress evolution in various atherosclerotic plaque configurations.
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| 11. |
- Robba, Chiara, et al.
(författare)
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Oxygen targets and 6-month outcome after out of hospital cardiac arrest : a pre-planned sub-analysis of the targeted hypothermia versus targeted normothermia after Out-of-Hospital Cardiac Arrest (TTM2) trial
- 2022
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Ingår i: Critical Care. - : Springer Science and Business Media LLC. - 1364-8535 .- 1466-609X. ; 26, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- Background: Optimal oxygen targets in patients resuscitated after cardiac arrest are uncertain. The primary aim of this study was to describe the values of partial pressure of oxygen values (PaO2) and the episodes of hypoxemia and hyperoxemia occurring within the first 72 h of mechanical ventilation in out of hospital cardiac arrest (OHCA) patients. The secondary aim was to evaluate the association of PaO2 with patients’ outcome. Methods: Preplanned secondary analysis of the targeted hypothermia versus targeted normothermia after OHCA (TTM2) trial. Arterial blood gases values were collected from randomization every 4 h for the first 32 h, and then, every 8 h until day 3. Hypoxemia was defined as PaO2 < 60 mmHg and severe hyperoxemia as PaO2 > 300 mmHg. Mortality and poor neurological outcome (defined according to modified Rankin scale) were collected at 6 months. Results: 1418 patients were included in the analysis. The mean age was 64 ± 14 years, and 292 patients (20.6%) were female. 24.9% of patients had at least one episode of hypoxemia, and 7.6% of patients had at least one episode of severe hyperoxemia. Both hypoxemia and hyperoxemia were independently associated with 6-month mortality, but not with poor neurological outcome. The best cutoff point associated with 6-month mortality for hypoxemia was 69 mmHg (Risk Ratio, RR = 1.009, 95% CI 0.93–1.09), and for hyperoxemia was 195 mmHg (RR = 1.006, 95% CI 0.95–1.06). The time exposure, i.e., the area under the curve (PaO2-AUC), for hyperoxemia was significantly associated with mortality (p = 0.003). Conclusions: In OHCA patients, both hypoxemia and hyperoxemia are associated with 6-months mortality, with an effect mediated by the timing exposure to high values of oxygen. Precise titration of oxygen levels should be considered in this group of patients. Trial registration: clinicaltrials.gov NCT02908308, Registered September 20, 2016.
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| 13. |
- Schmied, C., et al.
(författare)
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Community-developed checklists for publishing images and image analyses
- 2024
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Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 21:2
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Tidskriftsartikel (refereegranskat)abstract
- Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data. Community-developed checklists offer best-practice guidance for biologists preparing light microscopy images and describing image analyses for publications.
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| 14. |
- Sicilia, Miguel-Angel, et al.
(författare)
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Navigating learning resources through linked data : A preliminary report on the re-design of organic.edunet
- 2011
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Ingår i: Linked Learning 2011 eLearning Approaches for the Linked Data Age. - : Rheinisch-Westfaelische Technische Hochschule Aachen. ; , s. 1-8
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Konferensbidrag (refereegranskat)abstract
- Learning objects repositories have grown and matured in the last years, being currently a cornerstone for open education. Several current systems are offering metadata openly through mainstream harvesting protocols or providing standardized query interfaces. Also, the use of standardized vocabularies or ontologies is becoming more common to provide a degree of semantic interoperability. However, learning object metadata is typically not linked across repositories, and it is not providing a way to navigate by using other sources of data available on the Web. The linked open data (LOD) approach provides the framework for the evolution of learning object repositories into a more flexible system of sharing learning resource metadata. This paper describes how linked data has been integrated in the design and redesign of the export mechanisms of Organic.Edunet, a federation of learning repositories in the domain of organic agriculture that uses an RDF store and several ontologies to browse and search resources. The paper focuses on how the existing search and semantic browsing mechanisms can benefit from the use of LOD across repositories.
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