{"entity": "journal", "iuid": "2f2edb30cab840939501bcf1bae26e11", "timestamp": "2026-07-20T22:49:11.998Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Virchows%20Arch..json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Virchows%20Arch."}}, "title": "Virchows Arch.", "issn": "1432-2307", "issn-l": "0945-6317", "publications_count": 4, "publications": [{"entity": "publication", "iuid": "a9d473ca72164e18a3db61d78fef3d7a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a9d473ca72164e18a3db61d78fef3d7a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a9d473ca72164e18a3db61d78fef3d7a"}}, "title": "Detection of perineural invasion in prostate needle biopsies with deep neural networks.", "authors": [{"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Str\u00f6m", "given": "Peter", "initials": "P", "orcid": "0000-0002-1631-806X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2798ea6ef2ed4ae88b78dd04d2f14437.json"}}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Delahunt", "given": "Brett", "initials": "B", "orcid": "0000-0002-5398-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/433a3f884f95451383cc746925d9a08c.json"}}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T", "orcid": "0000-0002-4855-4366", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42c993c2c0ab4b50afa03134f70118d9.json"}}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06721510ebc8462386e0e6fc6c84315b.json"}}, {"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Virchows Arch.", "issn": "1432-2307", "issn-l": "0945-6317", "volume": "481", "issue": "1", "pages": "73-82"}, "abstract": "The presence of perineural invasion (PNI) by carcinoma in prostate biopsies has been shown to be associated with poor prognosis. The assessment and quantification of PNI are, however, labor intensive. To aid pathologists in this task, we developed an artificial intelligence (AI) algorithm based on deep neural networks. We collected, digitized, and pixel-wise annotated the PNI findings in each of the approximately 80,000 biopsy cores from the 7406 men who underwent biopsy in a screening trial between 2012 and 2014. In total, 485 biopsy cores showed PNI. We also digitized more than 10% (n = 8318) of the PNI negative biopsy cores. Digitized biopsies from a random selection of 80% of the men were used to build the AI algorithm, while 20% were used to evaluate its performance. For detecting PNI in prostate biopsy cores, the AI had an estimated area under the receiver operating characteristics curve of 0.98 (95% CI 0.97-0.99) based on 106 PNI positive cores and 1652 PNI negative cores in the independent test set. For a pre-specified operating point, this translates to sensitivity of 0.87 and specificity of 0.97. The corresponding positive and negative predictive values were 0.67 and 0.99, respectively. The concordance of the AI with pathologists, measured by mean pairwise Cohen's kappa (0.74), was comparable to inter-pathologist concordance (0.68 to 0.75). The proposed algorithm detects PNI in prostate biopsies with acceptable performance. This could aid pathologists by reducing the number of biopsies that need to be assessed for PNI and by highlighting regions of diagnostic interest.", "doi": "10.1007/s00428-022-03326-3", "pmid": "35449363", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9226086"}, {"db": "pii", "key": "10.1007/s00428-022-03326-3"}], "notes": [], "created": "2024-11-05T16:09:36.259Z", "modified": "2024-11-29T09:29:14.824Z"}, {"entity": "publication", "iuid": "09a071792cf64b67ab7ab31033715e90", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09a071792cf64b67ab7ab31033715e90.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09a071792cf64b67ab7ab31033715e90"}}, "title": "Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies.", "authors": [{"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Delahunt", "given": "Brett", "initials": "B", "orcid": "0000-0002-5398-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/433a3f884f95451383cc746925d9a08c.json"}}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Str\u00f6m", "given": "Peter", "initials": "P", "orcid": "0000-0002-1631-806X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2798ea6ef2ed4ae88b78dd04d2f14437.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "H\u00e4kkinen", "given": "Tomi", "initials": "T"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P"}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Virchows Arch.", "issn": "1432-2307", "issn-l": "0945-6317", "volume": "478", "issue": "6", "pages": "1109-1116"}, "abstract": "Numerous studies have shown a correlation between perineural invasion (PNI) in prostate biopsies and outcome. The reporting of PNI varies widely in the literature. While the interobserver variability of prostate cancer grading has been studied extensively, less is known regarding the reproducibility of PNI. A total of 212 biopsy cores from a population-based screening trial were included in this study (106 with and 106 without PNI according to the original pathology reports). The glass slides were scanned and circulated among four pathologists with a special interest in urological pathology for assessment of PNI. Discordant cases were stained by immunohistochemistry for S-100 protein. PNI was diagnosed by all four observers in 34.0% of cases, while 41.5% were considered to be negative for PNI. In 24.5% of cases, there was a disagreement between the observers. The kappa for interobserver variability was 0.67-0.75 (mean 0.73). The observations from one participant were compared with data from the original reports, and a kappa for intraobserver variability of 0.87 was achieved. Based on immunohistochemical findings among discordant cases, 88.6% had PNI while 11.4% did not. The most common diagnostic pitfall was the presence of bundles of stroma or smooth muscle. It was noted in a few cases that collagenous micronodules could be mistaken for a nerve. The distance between cancer and nerve was another cause of disagreement. Although the results suggest that the reproducibility of PNI may be greater than that of prostate cancer grading, there is still a need for improvement and standardization.", "doi": "10.1007/s00428-021-03039-z", "pmid": "33534005", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8203540"}, {"db": "pii", "key": "10.1007/s00428-021-03039-z"}], "notes": [], "created": "2024-11-05T16:08:21.035Z", "modified": "2024-11-29T10:45:08.430Z"}, {"entity": "publication", "iuid": "29745e524468452d8313b0884f8360b8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/29745e524468452d8313b0884f8360b8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/29745e524468452d8313b0884f8360b8"}}, "title": "Identification of areas of grading difficulties in prostate cancer and comparison with artificial intelligence assisted grading.", "authors": [{"family": "Egevad", "given": "Lars", "initials": "L", "orcid": "0000-0001-8531-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d46f1f5fc047dc8edb910eb4f0645c.json"}}, {"family": "Swanberg", "given": "Daniela", "initials": "D"}, {"family": "Delahunt", "given": "Brett", "initials": "B"}, {"family": "Str\u00f6m", "given": "Peter", "initials": "P"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K"}, {"family": "Olsson", "given": "Henrik", "initials": "H"}, {"family": "Berney", "given": "Dan M", "initials": "DM"}, {"family": "Bostwick", "given": "David G", "initials": "DG"}, {"family": "Evans", "given": "Andrew J", "initials": "AJ"}, {"family": "Humphrey", "given": "Peter A", "initials": "PA"}, {"family": "Iczkowski", "given": "Kenneth A", "initials": "KA"}, {"family": "Kench", "given": "James G", "initials": "JG"}, {"family": "Kristiansen", "given": "Glen", "initials": "G"}, {"family": "Leite", "given": "Katia R M", "initials": "KRM"}, {"family": "McKenney", "given": "Jesse K", "initials": "JK"}, {"family": "Oxley", "given": "Jon", "initials": "J"}, {"family": "Pan", "given": "Chin-Chen", "initials": "C"}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Srigley", "given": "John R", "initials": "JR"}, {"family": "Takahashi", "given": "Hiroyuki", "initials": "H"}, {"family": "Tsuzuki", "given": "Toyonori", "initials": "T"}, {"family": "van der Kwast", "given": "Theo", "initials": "T"}, {"family": "Varma", "given": "Murali", "initials": "M"}, {"family": "Zhou", "given": "Ming", "initials": "M"}, {"family": "Clements", "given": "Mark", "initials": "M"}, {"family": "Eklund", "given": "Martin", "initials": "M"}], "type": "comparative study", "published": "2020-12-00", "journal": {"title": "Virchows Arch.", "issn": "1432-2307", "issn-l": "0945-6317", "volume": "477", "issue": "6", "pages": "777-786"}, "abstract": "The International Society of Urological Pathology (ISUP) hosts a reference image database supervised by experts with the purpose of establishing an international standard in prostate cancer grading. Here, we aimed to identify areas of grading difficulties and compare the results with those obtained from an artificial intelligence system trained in grading. In a series of 87 needle biopsies of cancers selected to include problematic cases, experts failed to reach a 2/3 consensus in 41.4% (36/87). Among consensus and non-consensus cases, the weighted kappa was 0.77 (range 0.68-0.84) and 0.50 (range 0.40-0.57), respectively. Among the non-consensus cases, four main causes of disagreement were identified: the distinction between Gleason score 3 + 3 with tangential cutting artifacts vs. Gleason score 3 + 4 with poorly formed or fused glands (13 cases), Gleason score 3 + 4 vs. 4 + 3 (7 cases), Gleason score 4 + 3 vs. 4 + 4 (8 cases) and the identification of a small component of Gleason pattern 5 (6 cases). The AI system obtained a weighted kappa value of 0.53 among the non-consensus cases, placing it as the observer with the sixth best reproducibility out of a total of 24. AI may serve as a decision support and decrease inter-observer variability by its ability to make consistent decisions. The grading of these cancer patterns that best predicts outcome and guides treatment warrants further clinical and genetic studies. Results of such investigations should be used to improve calibration of AI systems.", "doi": "10.1007/s00428-020-02858-w", "pmid": "32542445", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7683442"}, {"db": "pii", "key": "10.1007/s00428-020-02858-w"}], "notes": [], "created": "2024-11-05T16:08:18.753Z", "modified": "2024-11-29T10:45:14.878Z"}, {"entity": "publication", "iuid": "4844261615474c06a1eb677018d0bbec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4844261615474c06a1eb677018d0bbec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4844261615474c06a1eb677018d0bbec"}}, "title": "SATB1 is an independent prognostic factor in radically resected upper gastrointestinal tract adenocarcinoma.", "authors": [{"family": "Hedner", "given": "Charlotta", "initials": "C"}, {"family": "Gaber", "given": "Alexander", "initials": "A"}, {"family": "Korkocic", "given": "Dejan", "initials": "D"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Kuteeva", "given": "Eugenia", "initials": "E"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}], "type": "journal article", "published": "2014-12-00", "journal": {"title": "Virchows Arch.", "issn": "1432-2307", "volume": "465", "issue": "6", "pages": "649-659", "issn-l": "0945-6317"}, "abstract": "Gastric cancer is the second most common cause of cancer-related death worldwide, and the incidence of esophageal adenocarcinoma is rising. While some progress has been made in treatment strategies, overall survival remains very poor for patients with adenocarcinoma in the upper gastrointestinal tract. Special AT-rich sequence binding protein 1 (SATB1) is a global genome organizer that has been demonstrated to promote aggressive tumor behavior in several different types of cancer, including gastric cancer. The prognostic value of SATB1 expression in esophageal cancer has, however, not yet been described. In this study, expression of SATB1 was examined by immunohistochemistry on tissue microarrays prepared from tissue samples from 175 patients with adenocarcinoma of the esophagus, cardia, or stomach and containing normal tissue, intestinal metaplasia, primary tumors, and metastases. A well-validated antibody was used. We found SATB1 to be an independent prognostic factor in patients with a radically resected tumor, correlating with shorter overall survival as well as with shorter recurrence-free survival. SATB1 expression was also found to be significantly lower in primary tumors associated with intestinal metaplasia than those without intestinal metaplasia. This observation is of potential biological interest as it has been proposed that intestinal metaplasia-associated tumors constitute a less aggressive phenotype. ", "doi": "10.1007/s00428-014-1667-6", "pmid": "25326863", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pmc", "key": "PMC4245492"}], "notes": [], "created": "2018-12-05T09:54:54.916Z", "modified": "2018-12-05T09:54:54.949Z"}], "created": "2018-12-05T09:54:54.929Z", "modified": "2020-11-27T13:12:53.723Z"}