| 1. |
- Augusto Silva, Iran, et al.
(författare)
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Deep learning for rapid and reproducible histology scoring of lung injury in a porcine model
- 2023
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Acute respiratory distress syndrome (ARDS) is a life-threatening condition with mortality rates between 30-50%. Although in vitro models replicate some aspects of ARDS, small and large animal models remain the primary research tools due to the multifactorial nature of the disease. When using these animal models, histology serves as the gold standard method to confirm lung injury and exclude other diagnoses as high-resolution chest images are often not feasible. Semi-quantitative scoring performed by independent observers is the most common form of histologic analysis in pre-clinical animal models of ARDS. Despite progress in standardizing analysis procedures, objectively comparing histological injuries remains challenging, even for highly-trained pathologists. Standardized scoring simplifies the task and allows better comparisons between research groups and across different injury models, but it is time-consuming, and interobserver variability remains a significant concern. Convolutional neural networks (CNNs), which have emerged as a key tool in image analysis, could automate this process, potentially enabling faster and more reproducible analysis. Here we explored the reproducibility of human standardized scoring for an animal model of ARDS and its suitability for training CNNs for automated scoring at the whole slide level. We found large variations between human scorers, even for pre-clinical experts and board-certified pathologies in evaluating ARDS animal models. We demonstrate that CNNs (VGG16, EfficientNetB4) are suitable for automated scoring and achieve up to 83% F1-score and 78% accuracy. Thus, CNNs for histopathological classification of acute lung injury could help reduce human variability and eliminate a time-consuming manual research task with acceptable performance.
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| 2. |
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| 3. |
- Faber, Zachary J, et al.
(författare)
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The genomic landscape of core-binding factor acute myeloid leukemias
- 2016
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 48, s. 1551-1556
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Tidskriftsartikel (refereegranskat)abstract
- Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML. Outside of signaling alterations, RUNX1-RUNX1T1 and CBFB-MYH11 AMLs demonstrated remarkably different spectra of cooperating mutations, as RUNX1-RUNX1T1 cases harbored recurrent mutations in DHX15 and ZBTB7A, as well as an enrichment of mutations in epigenetic regulators, including ASXL2 and the cohesin complex. This detailed analysis provides insights into the pathogenesis and development of CBF-AML, while highlighting dramatic differences in the landscapes of cooperating mutations for these related AML subtypes.
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| 4. |
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| 5. |
- Gutierrez, Jesus, et al.
(författare)
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Subjective evaluation of visual quality and simulator sickness of short 360 videos : ITU-T Rec. P.919
- 2022
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Ingår i: IEEE transactions on multimedia. - 1520-9210 .- 1941-0077. ; 24, s. 3087-3100
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Tidskriftsartikel (refereegranskat)abstract
- Recently an impressive development in immersive technologies, such as Augmented Reality (AR), Virtual Reality (VR) and 360 video, has been witnessed. However, methods for quality assessment have not been keeping up. This paper studies quality assessment of 360 video from the cross-lab tests (involving ten laboratories and more than 300 participants) carried out by the Immersive Media Group (IMG) of the Video Quality Experts Group (VQEG). These tests were addressed to assess and validate subjective evaluation methodologies for 360 video. Audiovisual quality, simulator sickness symptoms, and exploration behavior were evaluated with short (from 10 seconds to 30 seconds) 360 sequences. The following factors' influences were also analyzed: assessment methodology, sequence duration, Head-Mounted Display (HMD) device, uniform and non-uniform coding degradations, and simulator sickness assessment methods. The obtained results have demonstrated the validity of Absolute Category Rating (ACR) and Degradation Category Rating (DCR) for subjective tests with 360 videos, the possibility of using 10-second videos (with or without audio) when addressing quality evaluation of coding artifacts, as well as any commercial HMD (satisfying minimum requirements). Also, more efficient methods than the long Simulator Sickness Questionnaire (SSQ) have been proposed to evaluate related symptoms with 360 videos. These results have been instrumental for the development of the ITU-T Recommendation P.919. Finally, the annotated dataset from the tests is made publicly available for the research community.
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| 6. |
- Gutierrez, Jesus, et al.
(författare)
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Subjective evaluation of visual quality and simulator sickness of short 360 videos : ITU-T Rec. P.919
- 2022
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Ingår i: IEEE transactions on multimedia. - : Institute of Electrical and Electronics Engineers (IEEE). - 1520-9210 .- 1941-0077. ; 24, s. 3087-3100
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Tidskriftsartikel (refereegranskat)abstract
- Recently an impressive development in immersive technologies, such as Augmented Reality (AR), Virtual Reality (VR) and 360 video, has been witnessed. However, methods for quality assessment have not been keeping up. This paper studies quality assessment of 360 video from the cross-lab tests (involving ten laboratories and more than 300 participants) carried out by the Immersive Media Group (IMG) of the Video Quality Experts Group (VQEG). These tests were addressed to assess and validate subjective evaluation methodologies for 360 video. Audiovisual quality, simulator sickness symptoms, and exploration behavior were evaluated with short (from 10 seconds to 30 seconds) 360 sequences. The following factors' influences were also analyzed: assessment methodology, sequence duration, Head-Mounted Display (HMD) device, uniform and non-uniform coding degradations, and simulator sickness assessment methods. The obtained results have demonstrated the validity of Absolute Category Rating (ACR) and Degradation Category Rating (DCR) for subjective tests with 360 videos, the possibility of using 10-second videos (with or without audio) when addressing quality evaluation of coding artifacts, as well as any commercial HMD (satisfying minimum requirements). Also, more efficient methods than the long Simulator Sickness Questionnaire (SSQ) have been proposed to evaluate related symptoms with 360 videos. These results have been instrumental for the development of the ITU-T Recommendation P.919. Finally, the annotated dataset from the tests is made publicly available for the research communit
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| 7. |
- Hedlund, John, et al.
(författare)
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Agriculture, Pesticide Use, and Economic Development: A Global Examination (1990–2014)
- 2020
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Ingår i: Rural Sociology. - : Wiley. - 0036-0112 .- 1549-0831. ; 85, s. 519-544
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Tidskriftsartikel (refereegranskat)abstract
- Modern agricultural production typically requires large quantities of chemical pesticides, a potential source of both environmental and human harm. Previous social science research has suggested that environmental problems such as those associated with pesticide use may begin to decline at higher levels of economic development. Using fixed effects models, we examine whether this possible relationship holds within nations and over time. This study draws on data from the World Bank as well as pesticide use data from the Food and Agriculture Organization of the United Nations to examine the relationship between pesticide use and economic development within nations from 1990 to 2014. The findings are considered from theoretical perspectives in environmental sociology on the drivers of environmental impacts: the treadmill of production theory, structural human ecology, ecological modernization theory, and the environmental Kuznets curve hypothesis. The results of this study show a positive relationship between economic development and pesticide consumption over time, with no decline in use at higher levels of economic development. Thus, they generally support the claims made by treadmill of production and structural human ecology.
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| 8. |
- Holmfeldt, Linda, et al.
(författare)
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The genomic landscape of hypodiploid acute lymphoblastic leukemia
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:3, s. 242-252
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Tidskriftsartikel (refereegranskat)abstract
- The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.
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| 9. |
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| 10. |
- Jakobsson, Jonas K F, et al.
(författare)
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A new method for measuring lung deposition efficiency of airborne nanoparticles in a single breath
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Assessment of respiratory tract deposition of nanoparticles is a key link to understanding their health impacts. An instrument was developed to measure respiratory tract deposition of nanoparticles in a single breath. Monodisperse nanoparticles are generated, inhaled and sampled from a determined volumetric lung depth after a controlled residence time in the lung. The instrument was characterized for sensitivity to inter-subject variability, particle size (22, 50, 75 and 100 nm) and breath-holding time (3-20 s) in a group of seven healthy subjects. The measured particle recovery had an inter-subject variability 26-50 times larger than the measurement uncertainty and the results for various particle sizes and breath-holding times were in accordance with the theory for Brownian diffusion and values calculated from the Multiple-Path Particle Dosimetry model. The recovery was found to be determined by residence time and particle size, while respiratory flow-rate had minor importance in the studied range 1-10 L/s. The instrument will be used to investigate deposition of nanoparticles in patients with respiratory disease. The fast and precise measurement allows for both diagnostic applications, where the disease may be identified based on particle recovery, and for studies with controlled delivery of aerosol-based nanomedicine to specific regions of the lungs.
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