| 1. |
- Hillier, Ladeana W, et al.
(författare)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Tidskriftsartikel (refereegranskat)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 2. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 3. |
- Bick, Ulrich, et al.
(författare)
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Image-guided breast biopsy and localisation : recommendations for information to women and referring physicians by the European Society of Breast Imaging
- 2020
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Ingår i: Insights into Imaging. - : Springer Science and Business Media LLC. - 1869-4101. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- We summarise here the information to be provided to women and referring physicians about percutaneous breast biopsy and lesion localisation under imaging guidance. After explaining why a preoperative diagnosis with a percutaneous biopsy is preferred to surgical biopsy, we illustrate the criteria used by radiologists for choosing the most appropriate combination of device type for sampling and imaging technique for guidance. Then, we describe the commonly used devices, from fine-needle sampling to tissue biopsy with larger needles, namely core needle biopsy and vacuum-assisted biopsy, and how mammography, digital breast tomosynthesis, ultrasound, or magnetic resonance imaging work for targeting the lesion for sampling or localisation. The differences among the techniques available for localisation (carbon marking, metallic wire, radiotracer injection, radioactive seed, and magnetic seed localisation) are illustrated. Type and rate of possible complications are described and the issue of concomitant antiplatelet or anticoagulant therapy is also addressed. The importance of pathological-radiological correlation is highlighted: when evaluating the results of any needle sampling, the radiologist must check the concordance between the cytology/pathology report of the sample and the radiological appearance of the biopsied lesion. We recommend that special attention is paid to a proper and tactful approach when communicating to the woman the need for tissue sampling as well as the possibility of cancer diagnosis, repeat tissue sampling, and or even surgery when tissue sampling shows a lesion with uncertain malignant potential (also referred to as “high-risk” or B3 lesions). Finally, seven frequently asked questions are answered.
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| 4. |
- Boita, Joana, et al.
(författare)
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Development and content validity evaluation of a candidate instrument to assess image quality in digital mammography : A mixed-method study
- 2021
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Ingår i: European Journal of Radiology. - : Elsevier BV. - 0720-048X. ; 134
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To develop a candidate instrument to assess image quality in digital mammography, by identifying clinically relevant features in images that are affected by lower image quality. Methods: Interviews with fifteen expert breast radiologists from five countries were conducted and analysed by using adapted directed content analysis. During these interviews, 45 mammographic cases, containing 44 lesions (30 cancers, 14 benign findings), and 5 normal cases, were shown with varying image quality. The interviews were performed to identify the structures from breast tissue and lesions relevant for image interpretation, and to investigate how image quality affected the visibility of those structures. The interview findings were used to develop tentative items, which were evaluated in terms of wording, understandability, and ambiguity with expert breast radiologists. The relevance of the tentative items was evaluated using the content validity index (CVI) and modified kappa index (k*). Results: Twelve content areas, representing the content of image quality in digital mammography, emerged from the interviews and were converted into 29 tentative items. Fourteen of these items demonstrated excellent CVI ≥ 0.78 (k* > 0.74), one showed good CVI < 0.78 (0.60 ≤ k* ≤ 0.74), while fourteen were of fair or poor CVI < 0.78 (k* ≤ 0.59). In total, nine items were deleted and five were revised or combined resulting in 18 items. Conclusions: By following a mixed-method methodology, a candidate instrument was developed that may be used to characterise the clinically-relevant impact that image quality variations can have on digital mammography.
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| 5. |
- Boita, Joana, et al.
(författare)
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How does image quality affect radiologists’ perceived ability for image interpretation and lesion detection in digital mammography?
- 2021
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Ingår i: European Radiology. - : Springer Science and Business Media LLC. - 0938-7994 .- 1432-1084. ; 31:7, s. 5335-5343
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: To study how radiologists’ perceived ability to interpret digital mammography (DM) images is affected by decreases in image quality. Methods: One view from 45 DM cases (including 30 cancers) was degraded to six levels each of two acquisition-related issues (lower spatial resolution and increased quantum noise) and three post-processing-related issues (lower and higher contrast and increased correlated noise) seen during clinical evaluation of DM systems. The images were shown to fifteen breast screening radiologists from five countries. Aware of lesion location, the radiologists selected the most-degraded mammogram (indexed from 1 (reference) to 7 (most degraded)) they still felt was acceptable for interpretation. The median selected index, per degradation type, was calculated separately for calcification and soft tissue (including normal) cases. Using the two-sided, non-parametric Mann-Whitney test, the median indices for each case and degradation type were compared. Results: Radiologists were not tolerant to increases (medians: 1.5 (calcifications) and 2 (soft tissue)) or decreases (median: 2, for both types) in contrast, but were more tolerant to correlated noise (median: 3, for both types). Increases in quantum noise were tolerated more for calcifications than for soft tissue cases (medians: 3 vs. 4, p = 0.02). Spatial resolution losses were considered less acceptable for calcification detection than for soft tissue cases (medians: 3.5 vs. 5, p = 0.001). Conclusions: Perceived ability of radiologists for image interpretation in DM was affected not only by image acquisition-related issues but also by image post-processing issues, and some of those issues affected calcification cases more than soft tissue cases. Key Points: • Lower spatial resolution and increased quantum noise affected the radiologists’ perceived ability to interpret calcification cases more than soft tissue lesion or normal cases. • Post-acquisition image processing-related effects, not only image acquisition-related effects, also impact the perceived ability of radiologists to interpret images and detect lesions. • In addition to current practices, post-acquisition image processing-related effects need to also be considered during the testing and evaluation of digital mammography systems.
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| 6. |
- Boita, Joana, et al.
(författare)
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Validation of a candidate instrument to assess image quality in digital mammography using ROC analysis
- 2021
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Ingår i: European Journal of Radiology. - : Elsevier BV. - 1872-7727 .- 0720-048X. ; 139
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Tidskriftsartikel (refereegranskat)abstract
- PurposeTo validate a candidate instrument, to be used by different professionals to assess image quality in digital mammography (DM), against detection performance results.MethodsA receiver operating characteristics (ROC) study was conducted to assess the detection performance in DM images with four different image quality levels due to different quality issues. Fourteen expert breast radiologists from five countries assessed a set of 80 DM cases, containing 60 lesions (40 cancers, 20 benign findings) and 20 normal cases. A visual grading analysis (VGA) study using a previously-described candidate instrument was conducted to evaluate a subset of 25 of the images used in the ROC study. Eight radiologists that had participated in the ROC study, and seven expert breast-imaging physicists, evaluated this subset. The VGA score (VGAS) and the ROC and visual grading characteristics (VGC) areas under the curve (AUCROC and AUCVGC) were compared.ResultsNo large differences in image quality among the four levels were detected by either ROC or VGA studies. However, the ranking of the four levels was consistent: level 1 (partial AUCROC: 0.070, VGAS: 6.77) performed better than levels 2 (0.066, 6.15), 3 (0.061, 5.82), and 4 (0.062, 5.37). Similarity between radiologists’ and physicists’ assessments was found (average VGAS difference of 10 %).ConclusionsThe results from the candidate instrument were found to correlate with those from ROC analysis, when used by either observer group. Therefore, it may be used by different professionals, such as radiologists, radiographers, and physicists, to assess clinically-relevant image quality variations in DM.
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| 7. |
- Fredenberg, Erik, et al.
(författare)
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Measurement of breast-tissue x-ray attenuation by spectral mammography : solid lesions
- 2016
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Ingår i: Physics in Medicine and Biology. - : Institute of Physics Publishing (IOPP). - 0031-9155 .- 1361-6560. ; 61:7, s. 2595-2612
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of x-ray attenuation is essential for developing and evaluating x-ray imaging technologies. For instance, techniques to distinguish between cysts and solid tumours at mammography screening would be highly desirable to reduce recalls, but the development requires knowledge of the x-ray attenuation for cysts and tumours. We have previously measured the attenuation of cyst fluid using photon-counting spectral mammography. Data on x-ray attenuation for solid breast lesions are available in the literature, but cover a relatively wide range, likely caused by natural spread between samples, random measurement errors, and different experimental conditions. In this study, we have adapted a previously developed spectral method to measure the linear attenuation of solid breast lesions. A total of 56 malignant and 5 benign lesions were included in the study. The samples were placed in a holder that allowed for thickness measurement. Spectral (energy-resolved) images of the samples were acquired and the image signal was mapped to equivalent thicknesses of two known reference materials, which can be used to derive the x-ray attenuation as a function of energy. The spread in equivalent material thicknesses was relatively large between samples, which is likely to be caused mainly by natural variation and only to a minor extent by random measurement errors and sample inhomogeneity. No significant difference in attenuation was found between benign and malignant solid lesions. The separation between cyst-fluid and tumour attenuation was, however, significant, which suggests it may be possible to distinguish cystic from solid breast lesions, and the results lay the groundwork for a clinical trial. In addition, the study adds a relatively large sample set to the published data and may contribute to a reduction in the overall uncertainty in the literature.
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| 8. |
- Rodriguez-Ruiz, Alejandro, et al.
(författare)
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Can we reduce the workload of mammographic screening by automatic identification of normal exams with artificial intelligence? A feasibility study
- 2019
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Ingår i: European Radiology. - : Springer Science and Business Media LLC. - 0938-7994 .- 1432-1084. ; 29:9, s. 4825-4832
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To study the feasibility of automatically identifying normal digital mammography (DM) exams with artificial intelligence (AI) to reduce the breast cancer screening reading workload. Methods and materials: A total of 2652 DM exams (653 cancer) and interpretations by 101 radiologists were gathered from nine previously performed multi-reader multi-case receiver operating characteristic (MRMC ROC) studies. An AI system was used to obtain a score between 1 and 10 for each exam, representing the likelihood of cancer present. Using all AI scores between 1 and 9 as possible thresholds, the exams were divided into groups of low- and high likelihood of cancer present. It was assumed that, under the pre-selection scenario, only the high-likelihood group would be read by radiologists, while all low-likelihood exams would be reported as normal. The area under the reader-averaged ROC curve (AUC) was calculated for the original evaluations and for the pre-selection scenarios and compared using a non-inferiority hypothesis. Results: Setting the low/high-likelihood threshold at an AI score of 5 (high likelihood > 5) results in a trade-off of approximately halving (− 47%) the workload to be read by radiologists while excluding 7% of true-positive exams. Using an AI score of 2 as threshold yields a workload reduction of 17% while only excluding 1% of true-positive exams. Pre-selection did not change the average AUC of radiologists (inferior 95% CI > − 0.05) for any threshold except at the extreme AI score of 9. Conclusion: It is possible to automatically pre-select exams using AI to significantly reduce the breast cancer screening reading workload. Key Points: • There is potential to use artificial intelligence to automatically reduce the breast cancer screening reading workload by excluding exams with a low likelihood of cancer. • The exclusion of exams with the lowest likelihood of cancer in screening might not change radiologists’ breast cancer detection performance. • When excluding exams with the lowest likelihood of cancer, the decrease in true-positive recalls would be balanced by a simultaneous reduction in false-positive recalls.
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| 9. |
- Rodriguez-Ruiz, Alejandro, et al.
(författare)
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Stand-Alone Artificial Intelligence for Breast Cancer Detection in Mammography : Comparison With 101 Radiologists
- 2019
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 111:9, s. 916-922
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Artificial intelligence (AI) systems performing at radiologist-like levels in the evaluation of digital mammography (DM) would improve breast cancer screening accuracy and efficiency. We aimed to compare the stand-alone performance of an AI system to that of radiologists in detecting breast cancer in DM.METHODS: Nine multi-reader, multi-case study datasets previously used for different research purposes in seven countries were collected. Each dataset consisted of DM exams acquired with systems from four different vendors, multiple radiologists' assessments per exam, and ground truth verified by histopathological analysis or follow-up, yielding a total of 2652 exams (653 malignant) and interpretations by 101 radiologists (28 296 independent interpretations). An AI system analyzed these exams yielding a level of suspicion of cancer present between 1 and 10. The detection performance between the radiologists and the AI system was compared using a noninferiority null hypothesis at a margin of 0.05.RESULTS: The performance of the AI system was statistically noninferior to that of the average of the 101 radiologists. The AI system had a 0.840 (95% confidence interval [CI] = 0.820 to 0.860) area under the ROC curve and the average of the radiologists was 0.814 (95% CI = 0.787 to 0.841) (difference 95% CI = -0.003 to 0.055). The AI system had an AUC higher than 61.4% of the radiologists.CONCLUSIONS: The evaluated AI system achieved a cancer detection accuracy comparable to an average breast radiologist in this retrospective setting. Although promising, the performance and impact of such a system in a screening setting needs further investigation.
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| 10. |
- van Schie, Guido, et al.
(författare)
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Mass detection in reconstructed digital breast tomosynthesis volumes with a computer-aided detection system trained on 2D mammograms
- 2013
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Ingår i: Medical physics (Lancaster). - : Wiley. - 0094-2405. ; 40:4, s. 041902-
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To develop a computer-aided detection (CAD) system for masses in digital breast tomosynthesis (DBT) which can make use of an existing CAD system for detection of breast masses in full-field digital mammography (FFDM). This approach has the advantage that large digital screening databases that are becoming available can be used for training. DBT is currently not used for screening which makes it hard to obtain sufficient data for training. Methods: The proposed CAD system is applied to reconstructed DBT volumes and consists of two stages. In the first stage, an existing 2D CAD system is applied to slabs composed of multiple DBT slices, after processing the slabs to a representation similar to that of the FFDM training data. In the second stage, the authors group detections obtained in the slabs that detect the same object and determine the 3D location of the grouped findings using one of three different approaches, including one that uses a set of features extracted from the DBT slabs. Experiments were conducted to determine performance of the CAD system, the optimal slab thickness for this approach and the best method to establish the 3D location. Experiments were performed using a database of 192 patients (752 DBT volumes). In 49 patients, one or more malignancies were present which were described as a mass, architectural distortion, or asymmetry. Free response receiver operating characteristic analysis and bootstrapping were used for statistical evaluation. Results: Best performance was obtained when slab thickness was in the range of 1-2 cm. Using the feature based 3D localization procedure developed in the study, accurate 3D localization could be obtained in most cases. Case sensitivities of 80% and 90% were achieved at 0.35 and 0.99 false positives per volume, respectively. Conclusions: This study indicates that there may be a large benefit in using 2D mammograms for the development of CAD for DBT and that there is no need to exclusively limit development to DBT data.
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