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- Hamdi, Yosr, et al.
(författare)
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Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression : identification of a modifier of breast cancer risk at locus 11q22.3
- 2017
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Ingår i: Breast Cancer Research and Treatment. - : Springer Science and Business Media LLC. - 0167-6806 .- 1573-7217. ; 161:1, s. 117-134
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Cis-acting regulatory SNPs resulting in differential allelic expression (DAE) may, in part, explain the underlying phenotypic variation associated with many complex diseases. To investigate whether common variants associated with DAE were involved in breast cancer susceptibility among BRCA1 and BRCA2 mutation carriers, a list of 175 genes was developed based of their involvement in cancer-related pathways. Methods: Using data from a genome-wide map of SNPs associated with allelic expression, we assessed the association of ~320 SNPs located in the vicinity of these genes with breast and ovarian cancer risks in 15,252 BRCA1 and 8211 BRCA2 mutation carriers ascertained from 54 studies participating in the Consortium of Investigators of Modifiers of BRCA1/2. Results: We identified a region on 11q22.3 that is significantly associated with breast cancer risk in BRCA1 mutation carriers (most significant SNP rs228595 p = 7 × 10−6). This association was absent in BRCA2 carriers (p = 0.57). The 11q22.3 region notably encompasses genes such as ACAT1, NPAT, and ATM. Expression quantitative trait loci associations were observed in both normal breast and tumors across this region, namely for ACAT1, ATM, and other genes. In silico analysis revealed some overlap between top risk-associated SNPs and relevant biological features in mammary cell data, which suggests potential functional significance. Conclusion: We identified 11q22.3 as a new modifier locus in BRCA1 carriers. Replication in larger studies using estrogen receptor (ER)-negative or triple-negative (i.e., ER-, progesterone receptor-, and HER2-negative) cases could therefore be helpful to confirm the association of this locus with breast cancer risk.
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- Henrichsen, Peter Juel, et al.
(författare)
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SMALLWorlds: Multilingual Content-Controlled Monologues
- 2012
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Ingår i: Proceedings of the Eight International Conference on Language Resources and Evaluation (LREC'12). - 9782951740877 ; , s. 3362-3368
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Konferensbidrag (refereegranskat)
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- Klang, Marcus, et al.
(författare)
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Hedwig : A named entity linker
- 2020
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Ingår i: LREC 2020 - 12th International Conference on Language Resources and Evaluation, Conference Proceedings. - 9791095546344 ; , s. 4501-4508
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Konferensbidrag (refereegranskat)abstract
- Named entity linking is the task of identifying mentions of named things in text, such as “Barack Obama” or “New York”, and linking these mentions to unique identifiers. In this paper, we describe Hedwig, an end-to-end named entity linker, which uses a combination of word and character BILSTM models for mention detection, a Wikidata and Wikipedia-derived knowledge base with global information aggregated over nine language editions, and a PageRank algorithm for entity linking. We evaluated Hedwig on the TAC2017 dataset, consisting of news texts and discussion forums, and we obtained a final score of 59.9% on CEAFmC+, an improvement over our previous generation linker Ugglan, and a trilingual entity link score of 71.9%.
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- Moloney, Kristen, et al.
(författare)
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Development of a surgical competency assessment tool for sentinel lymph node dissection by minimally invasive surgery for endometrial cancer
- 2021
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Ingår i: International Journal of Gynecological Cancer. - : BMJ. - 1048-891X .- 1525-1438. ; 31:5, s. 647-655
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Tidskriftsartikel (refereegranskat)abstract
- Sentinel lymph node dissection is widely used in the staging of endometrial cancer. Variation in surgical techniques potentially impacts diagnostic accuracy and oncologic outcomes, and poses barriers to the comparison of outcomes across institutions or clinical trial sites. Standardization of surgical technique and surgical quality assessment tools are critical to the conduct of clinical trials. By identifying mandatory and prohibited steps of sentinel lymph node (SLN) dissection in endometrial cancer, the purpose of this study was to develop and validate a competency assessment tool for use in surgical quality assurance. A Delphi methodology was applied, included 35 expert gynecological oncology surgeons from 16 countries. Interviews identified key steps and tasks which were rated mandatory, optional, or prohibited using questionnaires. Using the surgical steps for which consensus was achieved, a competency assessment tool was developed and subjected to assessments of validity and reliability. Seventy percent consensus agreement standardized the specific mandatory, optional, and prohibited steps of SLN dissection for endometrial cancer and informed the development of a competency assessment tool. Consensus agreement identified 21 mandatory and three prohibited steps to complete a SLN dissection. The competency assessment tool was used to rate surgical quality in three preselected videos, demonstrating clear separation in the rating of the skill level displayed with mean skills summary scores differing significantly between the three videos (F score=89.4; P<0.001). Internal consistency of the items was high (Cronbach α=0.88). Specific mandatory and prohibited steps of SLN dissection in endometrial cancer have been identified and validated based on consensus among a large number of international experts. A competency assessment tool is now available and can be used for surgeon selection in clinical trials and for ongoing, prospective quality assurance in routine clinical care.
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- Nugues, Pierre, et al.
(författare)
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Connecting a French Dictionary from the Beginning of the 20th Century to Wikidata
- 2022
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Ingår i: 2022 Language Resources and Evaluation Conference, LREC 2022. - 9791095546726 ; , s. 2548-2555
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Konferensbidrag (refereegranskat)abstract
- The Petit Larousse illustré is a French dictionary first published in 1905. Its division in two main parts on language and on history and geography corresponds to a major milestone in French lexicography as well as a repository of general knowledge from this period. Although the value of many entries from 1905 remains intact, some descriptions now have a dimension that is more historical than contemporary. They are nonetheless significant to analyze and understand cultural representations from this time. A comparison with more recent information or a verification of these entries would require a tedious manual work. In this paper, we describe a new lexical resource, where we connected all the dictionary entries of the history and geography part to current data sources. For this, we linked each of these entries to a wikidata identifier. Using the wikidata links, we can automate more easily the identification, comparison, and verification of historically-situated representations. We give a few examples on how to process wikidata identifiers and we carried out a small analysis of the entities described in the dictionary to outline possible applications. The resource, i.e. the annotation of 20,245 dictionary entries with wikidata links, is available from GitHub (https://github.com/pnugues/petit_larousse_1905/).
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- Rehm, Georg, et al.
(författare)
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The strategic impact of META-NET on the regional, national and international level
- 2016
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Ingår i: Language resources and evaluation. - : Springer Science and Business Media LLC. - 1574-020X .- 1572-8412 .- 1574-0218. ; 50:2, s. 351-374
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Tidskriftsartikel (refereegranskat)abstract
- This article provides an overview of the dissemination work carried out in META-NET from 2010 until 2015; we describe its impact on the regional, national and international level, mainly with regard to politics and the funding situation for LT topics. The article documents the initiative’s work throughout Europe in order to boost progress and innovation in our field.
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