| 1. |
- Einarsdottir, Berglind Osk, 1979, et al.
(författare)
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A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma
- 2018
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Ingår i: Cell Death & Disease. - : Springer Science and Business Media LLC. - 2041-4889. ; 9:8
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Tidskriftsartikel (refereegranskat)abstract
- Karonudib (TH1579) is a novel compound that exerts anti-tumor activities and has recently entered phase I clinical testing. The aim of this study was to conduct a pre-clinical trial in patient-derived xenografts to identify the possible biomarkers of response or resistance that could guide inclusion of patients suffering from metastatic melanoma in phase II clinical trials. Patient-derived xenografts from 31 melanoma patients with metastatic disease were treated with karonudib or a vehicle for 18 days. Treatment responses were followed by measuring tumor sizes, and the models were categorized in the response groups. Tumors were harvested and processed for RNA sequencing and protein analysis. To investigate the effect of karonudib on T-cell-mediated anti-tumor activities, tumor-infiltrating T cells were injected in mice carrying autologous tumors and the mice treated with karonudib. We show that karonudib has heterogeneous anti-tumor effect on metastatic melanoma. Thus, based on the treatment responses, we could divide the 31 patient-derived xenografts in three treatment groups: progression group (32%), suppression group (42%), and regression group (26%). Furthermore, we show that karonudib has anti-tumor effect, irrespective of major melanoma driver mutations. Also, we identify high expression of ABCB1, which codes for p-gp pumps as a resistance biomarker. Finally, we show that karonudib treatment does not hamper T-cell-mediated anti-tumor responses. These findings can be used to guide future use of karonudib in clinical use with a potential approach as precision medicine.
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| 2. |
- Abarenkov, Kessy, et al.
(författare)
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Protax-fungi: A web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences
- 2018
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 220:2, s. 517-525
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Tidskriftsartikel (refereegranskat)abstract
- © 2018 New Phytologist Trust. Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax-fungi, a general tool for taxonomic placement of fungal internal transcribed spacer (ITS) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. With empirical data on root- and wood-associated fungi, Protax-fungi reliably identified (with at least 90% identification probability) the majority of sequences to the order level but only around one-fifth of them to the species level, reflecting the current limited coverage of the databases. Protax-fungi outperformed the Sintax and Rdb classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. We applied Protax-fungi to examine the internal consistencies of the Index Fungorum and UNITE databases. This revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. Protax-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships.
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| 3. |
- Alveteg, Mattias, et al.
(författare)
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Vad räknas som belägg för studenters måluppfyllelse?
- 2018
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Ingår i: 10:e Pedagogiska Inspirationskonferensen 2018. - 2003-3761 .- 2003-377X. ; 10
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Konferensbidrag (refereegranskat)abstract
- Universitetskanslerämbetet (UKÄ) ställer numera krav på svenska lärosäten att vi ska utvärdera oss själva. Vi på LTH bör då gemensamt försöka hitta sätt att uppfylla UKÄs krav som även ger de verktyg vi själva behöver för att förbättra våra utbildningars kvalitét.Hur tar vi reda på våra utbildningars styrkor och svagheter och vad vi kan göra för att förbättra dem ytterligare? Ett sätt är att undersöka hur väl studenterna uppfyller examensmålen. Vad som ska räknas som belägg för studenters måluppfyllelse är dock svårt, av flera olika skäl. Vår rekommendation blir att triangulera olika typer av belägg samt att tydligt involvera institutionerna i arbetet.
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| 4. |
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| 5. |
- Andersson, Henrik, et al.
(författare)
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Economic Analysis and Investment Priorities in Sweden's Transport Sector
- 2018
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Ingår i: Journal of Benefit-Cost Analysis. - : Cambridge University Press. - 2194-5888 .- 2152-2812. ; 9:1, s. 120-146
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Tidskriftsartikel (refereegranskat)abstract
- Beginning as a planning tool within Sweden's national road administration some 50 years ago, benefit-cost analysis (BCA) has come to be a pillar of the national transport policy because of subsequent strategic choices made by the national parliament. These choices made it necessary to widen the analysis of costs to include also externalities and a foregone conclusion was that efficient investment priorities should be made based on BCA. But no one asked whether the political decision makers or the BCA models were up to that task. This paper reviews the institutional framework and practice of BCA in Sweden for transport infrastructure investment, and considers design issues that have been and still are debated, such as whether the discount rate should include a risk term and how to account for the marginal cost of public funds. A main concern with BCA results is the underestimation of construction costs, making transport sector projects look better than they are. Several ex post analyses have established that a higher NPV ratio increases the probability of being included in the investment program proposal prepared by the agency. The requirement to let projects undergo BCA seems to make planners trim project proposals by trying to reduce investment costs without significantly reducing benefits. This relationship is weaker among profitable projects. Moreover, there is no correlation between rate of return and the probability of being included in the final program, which is established on political grounds.
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| 6. |
- Anslan, Sten, et al.
(författare)
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Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
- 2018
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 39, s. 29-40
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Tidskriftsartikel (refereegranskat)abstract
- Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.
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| 7. |
- Ardö, Hakan, et al.
(författare)
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Convolutional neural network-based cow interaction watchdog
- 2018
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Ingår i: IET Computer Vision. - : Institution of Engineering and Technology (IET). - 1751-9632 .- 1751-9640. ; 12:2, s. 171-177
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Tidskriftsartikel (refereegranskat)abstract
- In the field of applied animal behaviour, video recordings of a scene of interest are often made and then evaluated by experts. This evaluation is based on different criteria (number of animals present, an occurrence of certain interactions, the proximity between animals and so forth) and aims to filter out video sequences that contain irrelevant information. However, such task requires a tremendous amount of time and resources, making manual approach ineffective. To reduce the amount of time the experts spend on watching the uninteresting video, this study introduces an automated watchdog system that can discard some of the recorded video material based on user-defined criteria. A pilot study on cows was made where a convolutional neural network detector was used to detect and count the number of cows in the scene as well as include distances and interactions between cows as filtering criteria. This approach removed 38% (50% for additional filter parameters) of the recordings while only losing 1% (4%) of the potentially interesting video frames.
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| 8. |
- Augustinsson, Sören, et al.
(författare)
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Making sense of assignment : on the complexity of being a school leader
- 2018
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Ingår i: Nordic Journal of Comparative and International Education. - Oslo : OsloMet University Library. - 2535-4051. ; 2:2-3, s. 149-164
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Tidskriftsartikel (refereegranskat)abstract
- The primary aim of this paper is to narrow down the description of how school leaders interpret the assignment (the task) and identify the markers for how they look upon the conditions of doing a good job in Sweden. The aim is in the context of practice-based and process-oriented research. We use complexity and complexity theories to frame the emerging practice of leading and organizing. This is in contrast to technocratic homogenization—that is, law texts, steering documents, documentation, standardized methods, planning, and ceremonies. A questionnaire was conducted with three open questions (n=363 out of a possible 548 participants) and four focus groups (n=21). Complexity, dilemmas, and inconsistency emerge in the respondents’ answers the closer they are to everyday action. The results show that complexity theories put focus on a conflict between the image of schools as complicated and complex. Complicated is accompanied by generalizing and weak contextualizing of control systems, standardized methods, planning, law texts, and evidence-based education—that is, the concept of technocratic homogenization. Complexity theories emphasize the life in organizations, everyday practice as leaders, and a conflict between weak and robust contextualizing from the perspective as practice-based and process-oriented research.
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| 9. |
- Balliu, Enkeleda, et al.
(författare)
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Selective laser sintering of inkjet-printed silver nanoparticle inks on paper substrates to achieve highly conductive patterns
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Development of cost-effective and environmentally friendly manufacturing methods will enable important advances for the production of large-scale flexible electronics. Laser processing has shown to be a promising candidate that offers a fast and non-destructive way to produce highly conductive patterns on flexible substrates such as plastics. However, an emerging option with a lower environmental impact is instead the use of cellulose-based flexible substrates, such as paper. In this work we investigate the use of laser sintering of silver nanoparticle inks, which were inkjet-printed on three different types of paper. Patterns with a high conductivity could be manufactured where a special care was taken to prevent the substrates from damage by the intense laser light. We found that the best results was obtained for a photopaper, with a conductivity of 1.63 107 S/m corresponding to nearly 26% of the bulk silver conductivity. In addition, we demonstrate laser sintering to fabricate a fully functional near field communication tag printed on a photopaper. Our results can have an important bearing for the development of cost-effective and environmentally friendly production methods for flexible electronics on a large scale.
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| 10. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
- 2018
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Ingår i: Bioinformatics (Oxford, England). - : Oxford University Press (OUP). - 1367-4811 .- 1367-4803. ; 34:23, s. 4027-4033
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Tidskriftsartikel (refereegranskat)abstract
- Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.We evaluated the Metaxa2 Database Builder on eleven commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.Supplementary data are available at Bioinformatics online.
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