| 11. |
- Eltoft, Agnethe, et al.
(författare)
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Statistical analysis plan for the randomized controlled trial Tenecteplase in Wake-up Ischaemic Stroke Trial (TWIST)
- 2022
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Ingår i: Trials. - : Springer Nature. - 1745-6215. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Patients with wake-up ischemic stroke are frequently excluded from thrombolytic treatment due to unknown symptom onset time and limited availability of advanced imaging modalities. The Tenecteplase in Wake-up lschaemic Stroke Trial (TWIST) is a randomized controlled trial of intravenous tenecteplase 0.25 mg/kg and standard care versus standard care alone (no thrombolysis) in patients who wake up with acute ischemic stroke and can be treated within 4.5 h of wakening based on non-contrast CT findings. Objective: To publish the detailed statistical analysis plan for TWIST prior to unblinding. Methods: The TWIST statistical analysis plan is consistent with the Consolidating Standard of Reporting Trials (CON-SORT) statement and provides clear and open reporting. Discussion: Publication of the statistical analysis plan serves to reduce potential trial reporting bias and clearly outlines the pre-specified analyses.
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| 12. |
- Hasslöf, Helen, et al.
(författare)
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Science and technological innovations as drivers for educational change : Teachers' perspectives of an inquiry-based project into the unknown
- 2017
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Konferensbidrag (refereegranskat)abstract
- This study started in connection to two similar parallel on-going Teacher Development Programs (TPDs) in Sweden, within the PARRISE-project (2014-2017). It is a project funded by EU, where 18 universities from eleven countries cooperate to explore and develop ways to address political and ethical questions in science education, with starting point from Responsible Research and Innovation (RRI), embracing the SSIBL framework (cf. Levinson 2016). Preliminary results shows how teachers from the TPDs formulated mutual and competing aims concerning the role of science education regarding how to address the knowledge base of science in relation to new relatively uncertain areas. This is done in relation to innovation processes and their products as for example nanotechnology. Critical thinking and awareness of ignorance were formulated as important tools for a scientific literacy discourse of a more humbled view of knowledge production, connected to science research and innovation, and identifying conflicting interest from different actors.
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| 13. |
- Hoefener, Henning, et al.
(författare)
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Deep learning nuclei detection: A simple approach can deliver state-of-the-art results
- 2018
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Ingår i: Computerized Medical Imaging and Graphics. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0895-6111 .- 1879-0771. ; 70, s. 43-52
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Tidskriftsartikel (refereegranskat)abstract
- Background: Deep convolutional neural networks have become a widespread tool for the detection of nuclei in histopathology images. Many implementations share a basic approach that includes generation of an intermediate map indicating the presence of a nucleus center, which we refer to as PMap. Nevertheless, these implementations often still differ in several parameters, resulting in different detection qualities. Methods: We identified several essential parameters and configured the basic PMap approach using combinations of them. We thoroughly evaluated and compared various configurations on multiple datasets with respect to detection quality, efficiency and training effort. Results: Post-processing of the PMap was found to have the largest impact on detection quality. Also, two different network architectures were identified that improve either detection quality or runtime performance. The best-performing configuration yields f1-measures of 0.816 on Hamp;E stained images of colorectal adenocarcinomas and 0.819 on Ki-67 stained images of breast tumor tissue. On average, it was fully trained in less than 15,000 iterations and processed 4.15 megapixels per second at prediction time. Conclusions: The basic PMap approach is greatly affected by certain parameters. Our evaluation provides guidance on their impact and best settings. When configured properly, this simple and efficient approach can yield equal detection quality as more complex and time-consuming state-of-the-art approaches. (C) 2018 The Authors. Published by Elsevier Ltd.
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| 14. |
- Holmstrom, Jesper, et al.
(författare)
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Do we Read what we Share? Analyzing the Click Dynamic of News Articles Shared on Twitter
- 2019
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Ingår i: PROCEEDINGS OF THE 2019 IEEE/ACM INTERNATIONAL CONFERENCE ON ADVANCES IN SOCIAL NETWORKS ANALYSIS AND MINING (ASONAM 2019). - New York, NY, USA : Institute of Electrical and Electronics Engineers (IEEE). - 9781450368681 ; , s. 420-425
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Konferensbidrag (refereegranskat)abstract
- News and information spread over social media can have big impact on thoughts, beliefs, and opinions. It is therefore important to understand the sharing dynamics on these forums. However, most studies trying to capture these dynamics rely only on Twitters open APIs to measure how frequently articles are shared/retweeted, and therefore do not capture how many users actually read the articles linked in these tweets. To address this problem, in this paper, we first develop a novel measurement methodology, which combines the Twitter steaming API, the Bitly API, and careful sample rate selection to simultaneously collect and analyze the timeline of both the number of retweets and clicks generated by news article links. Second, we present a temporal analysis of the news cycle based on five-day-long traces (containing both clicks and retweet over time) for the news article links discovered during a seven-day period. Among other things, our analysis highlights differences in the relative timelines observed for clicks and retweets (e.g., retweet data often lags and underestimates the bias towards reading popular links/articles), and helps answer important questions regarding differences in how age-based biases and churn affect how frequently news articles shared on Twitter are accessed over time.
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| 15. |
- Kost, Henning, et al.
(författare)
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Training nuclei detection algorithms with simple annotations
- 2017
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Ingår i: Journal of Pathology Informatics. - : Elsevier BV. - 2229-5089 .- 2153-3539. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Generating good training datasets is essential for machine learning-based nuclei detection methods. However, creating exhaustive nuclei contour annotations, to derive optimal training data from, is often infeasible. Methods: We compared different approaches for training nuclei detection methods solely based on nucleus center markers. Such markers contain less accurate information, especially with regard to nuclear boundaries, but can be produced much easier and in greater quantities. The approaches use different automated sample extraction methods to derive image positions and class labels from nucleus center markers. In addition, the approaches use different automated sample selection methods to improve the detection quality of the classification algorithm and reduce the run time of the training process. We evaluated the approaches based on a previously published generic nuclei detection algorithm and a set of Ki-67-stained breast cancer images. Results: A Voronoi tessellation-based sample extraction method produced the best performing training sets. However, subsampling of the extracted training samples was crucial. Even simple class balancing improved the detection quality considerably. The incorporation of active learning led to a further increase in detection quality. Conclusions: With appropriate sample extraction and selection methods, nuclei detection algorithms trained on the basis of simple center marker annotations can produce comparable quality to algorithms trained on conventionally created training sets.
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| 16. |
- Krebs, Georgina, et al.
(författare)
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The association between body dysmorphic symptoms and suicidality among adolescents and young adults : a genetically informative study
- 2022
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Ingår i: Psychological Medicine. - : Cambridge University Press. - 0033-2917 .- 1469-8978. ; 52:7, s. 1268-1276
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Previous research indicates that body dysmorphic disorder (BDD) is associated with risk of suicidality. However, studies have relied on small and/or specialist samples and largely focussed on adults, despite these difficulties commonly emerging in youth. Furthermore, the aetiology of the relationship remains unknown.METHODS: Two independent twin samples were identified through the Child and Adolescent Twin Study in Sweden, at ages 18 (N = 6027) and 24 (N = 3454). Participants completed a self-report measure of BDD symptom severity. Young people and parents completed items assessing suicidal ideation/behaviours. Logistic regression models tested the association of suicidality outcomes with: (a) probable BDD, classified using an empirically derived cut-off; and (b) continuous scores of BDD symptoms. Bivariate genetic models examined the aetiology of the association between BDD symptoms and suicidality at both ages.RESULTS: Suicidal ideation and behaviours were common among those with probable BDD at both ages. BDD symptoms, measured continuously, were linked with all aspects of suicidality, and associations generally remained significant after adjusting for depressive and anxiety symptoms. Genetic factors accounted for most of the covariance between BDD symptoms and suicidality (72.9 and 77.7% at ages 18 and 24, respectively), but with significant non-shared environmental influences (27.1 and 22.3% at ages 18 and 24, respectively).CONCLUSIONS: BDD symptoms are associated with a substantial risk of suicidal ideation and behaviours in late adolescence and early adulthood. This relationship is largely explained by common genetic liability, but non-shared environmental effects are also significant and could provide opportunities for prevention among those at high-risk.
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| 17. |
- Krebs, Georgina, et al.
(författare)
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The association between body dysmorphic symptoms and suicidality among adolescents and young adults : a genetically-informative study
- 2020
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Ingår i: Behavior Genetics. - : Springer. - 0001-8244 .- 1573-3297. ; 50:6, s. 462-462
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Previous research indicates that body dysmorphic disorder (BDD) is associated with risk of suicidality. However, studies have relied on small and/or specialist samples and largely focused on adults, despite these difficulties commonly emerging in youth. Furthermore, the aetiology of the relationship remains unknown.Two independent twin samples were identified through the Child and Adolescent Twin Study in Sweden, at ages 18 (N = 6027) and 24 (N = 3454). Participants completed a self-report measure of BDD symptom severity. Young people and parents completed items assessing suicidal ideation and suicide attempts. Logistic regression models tested the association between continuous scores of BDD symptoms and suicidality outcomes. Bivariate genetic models examined the aetiology of the association between BDD symptoms and a suicidality composite at both ages.BDD symptoms were positively associated with suicidal ideation and suicide attempts at age 18 and 24. These associations generally remained significant after adjusting for depressive and anxiety symptoms. Genetic factors accounted for most of the covariance between BDD symptoms and suicidality (74.1% and 79.4% at ages 18 and 24, respectively), but with significant non-shared environmental influences (25.9% and 20.6% at ages 18 and 24, respectively).BDD symptoms are associated with substantial risk of suicidal ideation and behaviours in late adolescence and early adulthood. This relationship is largely explained by common genetic liability, but non-shared environmental effects are also significant and could provide opportunities for prevention among those at high-risk.
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| 18. |
- Källén, Hanna, et al.
(författare)
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Towards Grading Gleason Score using Generically Trained Deep convolutional Neural Networks
- 2016
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Ingår i: 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI). - : Institute of Electrical and Electronics Engineers (IEEE). - 9781479923496 - 9781479923502 ; 2016-June, s. 1163-1167
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Konferensbidrag (refereegranskat)abstract
- We developed an automatic algorithm with the purpose to assist pathologists to report Gleason score on malignant prostatic adenocarcinoma specimen. In order to detect and classify the cancerous tissue, a deep convolutional neural network that had been pre-trained on a large set of photographic images was used. A specific aim was to support intuitive interaction with the result, to let pathologists adjust and correct the output. Therefore, we have designed an algorithm that makes a spatial classification of the whole slide into the same growth patterns as pathologists do. The 22-layer network was cut at an earlier layer and the output from that layer was used to train both a random forest classifier and a support vector machines classifier. At a specific layer a small patch of the image was used to calculate a feature vector and an image is represented by a number of those vectors. We have classified both the individual patches and the entire images. The classification results were compared for different scales of the images and feature vectors from two different layers from the network. Testing was made on a dataset consisting of 213 images, all containing a single class, benign tissue or Gleason score 3-5. Using 10-fold cross validation the accuracy per patch was 81 %. For whole images, the accuracy was increased to 89 %.
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| 19. |
- Lundström, Jesper
(författare)
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Gene networks and modules in atherosclerosis
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis we are using global gene expression profiles to unravel functional gene networks and modules. The focus is atherosclerosis, a disease with manifestations in the artery wall where deposits of lipids accumulate and trigger immune responses causing the development of plaques, which upon rupture can lead to a myocardial infarction or stroke. Atherosclerosis is a complex disease influenced by energy metabolism in multiple organs and by several genetic and environmental risk factors. To meet this complexity, we believe the most appropriate approach is to identify gene networks and modules in patients suffering coronary artery disease as well as a relevant mouse model with human-like dyslipidemia prone to atherosclerosis development. First, we investigate structural properties of the regulatory gene network in yeast, integrating protein protein interactions with the transcription network resulting in an estimate the effective gene network underlying gene expression data. In this effective gene network, we show evidence of in-hubs and provide a method for predicting in-hubs directly from gene expression data. In the second study, we used the Ldlr−/− Apob100/100 Mttpflox/flox Mx1-Cre mouse model to study atherosclerosis development and how this development is effected by plasma cholesterollowering. This mouse model has a lipid profile similar to human hyperlipidemia and develops atherosclerosis on a chow diet. Moreover, it contains a genetic switch (Mttpflox/flox Mx1-Cre) to turn off the VLDL synthesis in the liver and lowering plasma cholesterol by > 80%. Atherosclerotic lesions progressed slowly at first, then expanded rapidly, and plateaued after advanced lesions formed. Analysis of lesion expression profiles indicated lipid-poor macrophages accumulated prior the rapid expansion of the plaques. When macrophage concentration reached a critical point it was followed by a rapid expansion phase with accelerated foam-cell formation and inflammation, an interpretation also supported by lesion histology. A network of 8 cholesterol-responsive atherosclerosis genes was identified as central to the rapid expansion of the plaques. Third, in the Stockholm Atherosclerosis Gene Expression (STAGE) study, including 124 well-characterized patients undergoing coronary artery bypass surgery, we measured and analyzed 278 expression profiles from the liver, skeletal muscle, mediastinal fat, and aortic lesion (atherosclerotic artery expression with unaffected arterial wall expression subtracted). Clustering of these gene expression profiles performed separately in each organ generated a total of 60 clusters. Two clusters, in aortic lesion (n = 49) and fat (n = 59), related to degree of atherosclerosis. Remarkably, in a validation cohort 27 genes were replicated in a cluster (n =55) also related to the degree of atherosclerosis. In all three clusters relating to atherosclerosis (i.e., the atherosclerosis module), genes in the transendothelial migration of leukocyte pathway (TEML) were overrepresented and the transcription co-factor LIM-domain binding 2 (LDB2) expressed in lesion macrophages and endothelial cells was identified as a potential regulator of this module. In the last study, we first identified 2457 cholesterol-responsive genes in the atherosclerotic arterial wall by lowering plasma cholesterol at 10-weeks intervals during atherosclerosis development using the mouse model of Study II. To prioritize the most atherosclerosis-relevant genes among these 2457, we used a list of 1259 genes active during atherogenesis (Study II) together with three global gene networks generated from human atherosclerosis gene expression profiles in study III, public literature mining, and protein-protein interaction data. Using an integrative network approach to identify genes neighboring any of 68 atherosclerosis seed genes, we identified 35 cholesterol-responsive genes that were believed to be highly relevant to atherosclerosis. Taken together, this thesis provides evidence that systems biological analysis of global gene expression profiles isolated from a wide range of biological specimens can be used to infer functional interactions of genes in modules or networks. The content and architecture of these modules and networks can be used to improve our understanding how complex disorders like atherosclerosis develop.
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| 20. |
- Lundström, Mats, et al.
(författare)
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Hälsoval och kritisk hälsolitteracitet
- 2019
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Annan publikation (populärvet., debatt m.m.)abstract
- I denna text diskuteras individuella hälsoval. Utgångspunkten är de två begreppen hälsa och ”hälsolitteracitet” (health literacy). Båda berör kunskaper, värderingar, förhållningssätt och handlingsberedskap kopplat till hälsofrågor. Syftet med texten är dels att presentera en vidgad syn på hälsobegreppet, dels att beskriva vad som menas med hälsolitteracitet. Olika perspektiv på hälsa diskuteras. Vilken utgångspunkt som väljs i olika sammanhang kommer att ha betydelse för behandlingar och olika hälsoval. Detta är något som påverkar skolans undervisning, som bland annat bör syfta till att utveckla elevernas ”kritiska hälsolitteracitet”. Liksom andra litteraciteter syftar begreppet till att beskriva en bred kunskap som inte bara innehåller fakta om hälsa utan även ger en handlingsberedskap för olika situationer i vardagslivet. Dessa situationer är ofta komplexa med motstridig information, där egen kunskap och erfarenhet ställs mot annan tillgänglig information eller rådgivning.
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