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  • 2020-2024
  • Open Access
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  • Publikationer från KTH

  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Kalpakchi, Dmytro; Boye, Johan;

    This paper describes the creation and evaluation of a synthetic dataset of Swedish multiple-choice questions (MCQs) for reading comprehension using GPT-3. Although GPT-3 is trained mostly on English data, with only 0.11% of Swedish texts in its training material, the model still managed to generate MCQs in Swedish. About 44% of the generated MCQs turned out to be of sufficient quality, i.e.\ they were grammatically correct and relevant, with exactly one answer alternative being correct and the others being plausible but wrong. We provide a detailed analysis of the errors and shortcomings of the rejected MCQs, as well an analysis of the level of difficulty of the accepted MCQs. In addition to giving insights into GPT-3, the synthetic dataset could be used for training and evaluation of special-purpose MCQ-generating models. QC 20230602

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    DSpace at Tartu University Library
    Article . 2023
    License: CC BY NC ND
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      DSpace at Tartu University Library
      Article . 2023
      License: CC BY NC ND
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    Authors: Isabelle Matthiesen; Dimitrios Voulgaris; Polyxeni Nikolakopoulou; Thomas E. Winkler; +1 Authors

    Microphysiological systems mimic the in vivo cellular ensemble and microenvironment with the goal of providing more human-like models for biopharmaceutical research. In this study, the first such model of the blood-brain barrier (BBB-on-chip) featuring both isogenic human induced pluripotent stem cell (hiPSC)-derived cells and continuous barrier integrity monitoring with <2 min temporal resolution is reported. Its capabilities are showcased in the first microphysiological study of nitrosative stress and antioxidant prophylaxis. Relying on off-stoichiometry thiol–ene–epoxy (OSTE+) for fabrication greatly facilitates assembly and sensor integration compared to the prevalent polydimethylsiloxane devices. The integrated cell–substrate endothelial resistance monitoring allows for capturing the formation and breakdown of the BBB model, which consists of cocultured hiPSC-derived endothelial-like and astrocyte-like cells. Clear cellular disruption is observed when exposing the BBB-on-chip to the nitrosative stressor linsidomine, and the barrier permeability and barrier-protective effects of the antioxidant N-acetylcysteine amide are reported. Using metabolomic network analysis reveals further drug-induced changes consistent with prior literature regarding, e.g., cysteine and glutathione involvement. A model like this opens new possibilities for drug screening studies and personalized medicine, relying solely on isogenic human-derived cells and providing high-resolution temporal readouts that can help in pharmacodynamic studies. QC 20220330

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    Other literature type . Article . 2021 . Peer-reviewed
    License: CC BY NC
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Article . 2021
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      Other literature type . Article . 2021 . Peer-reviewed
      License: CC BY NC
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      Article . 2021
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    Authors: Brigita Dalecka; Martins Strods; Talis Juhna; Gunaratna Kuttuva Rajarao;

    Discharge of organic load from treated wastewater may cause environmental eutrophication. Recently, fungi have gained much attention due to their removal of pharmaceutical substances by enzymatic degradation and adsorption. However, the fungal effect in removing nutrients is less investigated. Therefore, two fungal species, the white-rot fungus T. versicolor as a laboratory strain and the mold A. luchuensis as an environmental isolate from the municipal wastewater treatment plant, were studied to determine the fungal potential for phosphorus, nitrogen, and the total organic carbon removal from municipal wastewater, carrying out a batch scale experiment to a fluidized bed pelleted bioreactor. During the batch scale experiment, the total removal (99.9 %) of phosphorus by T. versicolor was attained after a 6 hours-long incubation period while the maximal removal efficiency (99.9 %) for phosphorus from A. luchuensis was gained after an incubation period of 24 hours. Furthermore, both fungi showed that the pH adjustment to 5.5 kept the concentration of nitrogen constant and stabilized the total organic carbon reduction process for the entire incubation period. The results from the fluidized bed bioreactor demonstrated opposite tendencies on a nutrient removal comparing to a batch experiment where no significant effect on phosphorus, nitrogen, and total organics carbon reduction was observed. The obtained results from this study of batch and fluidized bed bioreactor experiments are a promising starting point for a successful fungal treatment optimization and application to wastewater treatment. QC 20210107

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    Microbiological Research
    Article . 2020 . Peer-reviewed
    License: Elsevier Non-Commercial
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Microbiological Rese...arrow_drop_down
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      Microbiological Research
      Article . 2020 . Peer-reviewed
      License: Elsevier Non-Commercial
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sjöbergh, Jonas; Kann, Viggo;

    We present an online API to access a number of Natural Language Processing services developed at KTH. The services work on Swedish text. They include tokenization, part-of-speech tagging, shallow parsing, compound word analysis, word inflection, lemmatization, spelling error detection and correction, grammar checking, and more. The services can be accessed in several ways, including a RESTful interface, direct socket communication, and premade Web forms. The services are open to anyone. The source code is also freely available making it possible to set up another server or run the tools locally. We have also evaluated the performance of several of the services and compared them to other available systems. Both the precision and the recall for the Granska grammar checker are higher than for both Microsoft Word and Google Docs. The evaluation also shows that the recall is greatly improved when combining all the grammar checking services in the API, compared to any one method, and combining services is made easy by the API. QC 20230328

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    https://ecp.ep.liu.se/index.ph...
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    https://doi.org/10.3384/ecp184...
    Conference object . 2021 . Peer-reviewed
    License: CC BY
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      https://doi.org/10.3384/ecp184...
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    Authors: Johansson, Nils;

    QC 20221219

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    Authors: Wang, Teng; Kleiven, Svein; Li, Xiaogai;

    Objective: Cerebral edema characterized as an abnormal accumulation of interstitial fluid has not been treated effectively. We propose a novel edema treatment approach to drive edematous fluid out of the brain by direct current utilizing brain tissue’s electroosmotic property. Methods: A finite element (FE) head model is developed and employed to assess the feasibility of the approach. First, the capacity of the model for electric field prediction is validated against human experiments. Second, two electrode configurations (S and D-montage) are designed to evaluate the distribution of the electric field, electroosmotic flow (EOF), current density, and temperature across the brain under an applied direct current. Results: The S-montage is shown to induce an average EOF velocity of 7e-4 mm/s underneath the anode by a voltage of 15 V, and the D-montage induces a velocity of 9e-4 mm/s by a voltage of 5 V. Meanwhile, the brain temperature in both configurations is below 38 °C, which is within the safety range. Further, the magnitude of EOF is proportional to the electric field, and the EOF direction follows the current flow from anode to cathode. The EOF velocity in the white matter is significantly higher than that in the gray matter under the anode where the fluid is to be drawn out. Conclusion: The proposed electroosmosis based approach allows alleviating brain edema within the critical time window by direct current. Significance: The approach may be further developed as a new treatment solely or as a complement to existing conventional treatments of edema. QC 20210315

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    Authors: Jonatan Abraham; Vania Ceccato;

    This article explores the nature and frequency of crimes and people's safety perceptions in rural areas using a systematic review of the literature. It explores four decades of English-language publications on crime and safety in rural areas from several major databases; mainly Scopus, JSTOR and ScienceDirect. The number of retrieved documents was 840, of which 410 were selected for in-depth analysis and their topics later categorized by theme. We found that rural crime research took off after the mid-1980s and experienced an increase during the 2010s. Despite the domination by North American, British and Australian scholarship, studies from other parts of the world (including the Global South) are increasingly being published as well. Publications on rural crime patterns (e.g., farm crime) compose over one-fifth of the reviewed literature. This together with rural policing/criminal justice and violence constitute the three largest themes in rural criminology research. With ever-increasing links between the local and the global, this review article advocates for tailored multilevel responses to rural crimes that, more than ever, are generated by processes far beyond their localities. QC 20220926

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    Journal of Rural Studies
    Article . 2022 . Peer-reviewed
    License: CC BY
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    Publikationer från KTH
    Article . 2022 . Peer-reviewed
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      Journal of Rural Studies
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      Publikationer från KTH
      Article . 2022 . Peer-reviewed
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    Authors: Van Roy, Peter; Haridi, Seif; Schulte, Christian; Smolka, Gert;

    Oz is a programming language designed to support multiple programming paradigms in a clean factored way that is easy to program despite its broad coverage. It started in 1991 as a collaborative effort by the DFKI (Germany) and SICS (Sweden) and led to an influential system, Mozart, that was released in 1999 and widely used in the 2000s for practical applications and education. We give the history of Oz as it developed from its origins in logic programming, starting with Prolog, followed by concurrent logic programming and constraint logic programming, and leading to its two direct precursors, the concurrent constraint model and the Andorra Kernel Language (AKL). We give the lessons learned from the Oz effort including successes and failures and we explain the principles underlying the Oz design. Oz is defined through a kernel language, which is a formal model similar to a foundational calculus, but that is designed to be directly useful to the programmer. The kernel language is organized in a layered structure, which makes it straightforward to write programs that use different paradigms in different parts. Oz is a key enabler for the book Concepts, Techniques, and Models of Computer Programming (MIT Press, 2004). Based on the book and the implementation, Oz has been used successfully in university-level programming courses starting from 2001 to the present day. QC 20220112

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    Proceedings of the ACM on Programming Languages
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      Proceedings of the ACM on Programming Languages
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    Authors: Giaretta, Lodovico; Savvidis, Ioannis; Marchioro, Thomas; Girdzijauskas, Sarunas; +3 Authors

    We envision PDS2, a decentralized data marketplace in which consumers submit their tasks to be run within the platform, on the data of willing providers. The goal of PDS2is to ensure that users maintain full control on their data and do not compromise their privacy, while being rewarded for the value that their data generates. In order to achieve this, our marketplace architecture employs blockchain technology, privacy-preserving computation and decentralized machine learning. We then compare different potential solutions and identify the Ethereum blockchain, trusted execution environments and gossip learning as the most suitable for the implementation of PDS2. We also discuss the main open challenges that are left to tackle and possible directions for future work QC 20210401

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    https://doi.org/10.1109/icdew5...
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      https://doi.org/10.1109/icdew5...
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    Authors: Poklukar, Petra; Polianskii, Vladislav; Varava, Anastasiia; Pokorny, Florian T.; +1 Authors

    Advanced representation learning techniques require reliable and general evaluation methods. Recently, several algorithms based on the common idea of geometric and topological analysis of a manifold approximated from the learned data representations have been proposed. In this work, we introduce Delaunay Component Analysis (DCA) - an evaluation algorithm which approximates the data manifold using a more suitable neighbourhood graph called Delaunay graph. This provides a reliable manifold estimation even for challenging geometric arrangements of representations such as clusters with varying shape and density as well as outliers, which is where existing methods often fail. Furthermore, we exploit the nature of Delaunay graphs and introduce a framework for assessing the quality of individual novel data representations. We experimentally validate the proposed DCA method on representations obtained from neural networks trained with contrastive objective, supervised and generative models, and demonstrate various use cases of our extended single point evaluation framework. QC 20220614

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    Authors: Kalpakchi, Dmytro; Boye, Johan;

    This paper describes the creation and evaluation of a synthetic dataset of Swedish multiple-choice questions (MCQs) for reading comprehension using GPT-3. Although GPT-3 is trained mostly on English data, with only 0.11% of Swedish texts in its training material, the model still managed to generate MCQs in Swedish. About 44% of the generated MCQs turned out to be of sufficient quality, i.e.\ they were grammatically correct and relevant, with exactly one answer alternative being correct and the others being plausible but wrong. We provide a detailed analysis of the errors and shortcomings of the rejected MCQs, as well an analysis of the level of difficulty of the accepted MCQs. In addition to giving insights into GPT-3, the synthetic dataset could be used for training and evaluation of special-purpose MCQ-generating models. QC 20230602

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    DSpace at Tartu University Library
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    Authors: Isabelle Matthiesen; Dimitrios Voulgaris; Polyxeni Nikolakopoulou; Thomas E. Winkler; +1 Authors

    Microphysiological systems mimic the in vivo cellular ensemble and microenvironment with the goal of providing more human-like models for biopharmaceutical research. In this study, the first such model of the blood-brain barrier (BBB-on-chip) featuring both isogenic human induced pluripotent stem cell (hiPSC)-derived cells and continuous barrier integrity monitoring with <2 min temporal resolution is reported. Its capabilities are showcased in the first microphysiological study of nitrosative stress and antioxidant prophylaxis. Relying on off-stoichiometry thiol–ene–epoxy (OSTE+) for fabrication greatly facilitates assembly and sensor integration compared to the prevalent polydimethylsiloxane devices. The integrated cell–substrate endothelial resistance monitoring allows for capturing the formation and breakdown of the BBB model, which consists of cocultured hiPSC-derived endothelial-like and astrocyte-like cells. Clear cellular disruption is observed when exposing the BBB-on-chip to the nitrosative stressor linsidomine, and the barrier permeability and barrier-protective effects of the antioxidant N-acetylcysteine amide are reported. Using metabolomic network analysis reveals further drug-induced changes consistent with prior literature regarding, e.g., cysteine and glutathione involvement. A model like this opens new possibilities for drug screening studies and personalized medicine, relying solely on isogenic human-derived cells and providing high-resolution temporal readouts that can help in pharmacodynamic studies. QC 20220330

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    Authors: Brigita Dalecka; Martins Strods; Talis Juhna; Gunaratna Kuttuva Rajarao;

    Discharge of organic load from treated wastewater may cause environmental eutrophication. Recently, fungi have gained much attention due to their removal of pharmaceutical substances by enzymatic degradation and adsorption. However, the fungal effect in removing nutrients is less investigated. Therefore, two fungal species, the white-rot fungus T. versicolor as a laboratory strain and the mold A. luchuensis as an environmental isolate from the municipal wastewater treatment plant, were studied to determine the fungal potential for phosphorus, nitrogen, and the total organic carbon removal from municipal wastewater, carrying out a batch scale experiment to a fluidized bed pelleted bioreactor. During the batch scale experiment, the total removal (99.9 %) of phosphorus by T. versicolor was attained after a 6 hours-long incubation period while the maximal removal efficiency (99.9 %) for phosphorus from A. luchuensis was gained after an incubation period of 24 hours. Furthermore, both fungi showed that the pH adjustment to 5.5 kept the concentration of nitrogen constant and stabilized the total organic carbon reduction process for the entire incubation period. The results from the fluidized bed bioreactor demonstrated opposite tendencies on a nutrient removal comparing to a batch experiment where no significant effect on phosphorus, nitrogen, and total organics carbon reduction was observed. The obtained results from this study of batch and fluidized bed bioreactor experiments are a promising starting point for a successful fungal treatment optimization and application to wastewater treatment. QC 20210107

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    Microbiological Research
    Article . 2020 . Peer-reviewed
    License: Elsevier Non-Commercial
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Microbiological Rese...arrow_drop_down
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      Microbiological Research
      Article . 2020 . Peer-reviewed
      License: Elsevier Non-Commercial
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sjöbergh, Jonas; Kann, Viggo;

    We present an online API to access a number of Natural Language Processing services developed at KTH. The services work on Swedish text. They include tokenization, part-of-speech tagging, shallow parsing, compound word analysis, word inflection, lemmatization, spelling error detection and correction, grammar checking, and more. The services can be accessed in several ways, including a RESTful interface, direct socket communication, and premade Web forms. The services are open to anyone. The source code is also freely available making it possible to set up another server or run the tools locally. We have also evaluated the performance of several of the services and compared them to other available systems. Both the precision and the recall for the Granska grammar checker are higher than for both Microsoft Word and Google Docs. The evaluation also shows that the recall is greatly improved when combining all the grammar checking services in the API, compared to any one method, and combining services is made easy by the API. QC 20230328

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    https://doi.org/10.3384/ecp184...
    Conference object . 2021 . Peer-reviewed
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      https://doi.org/10.3384/ecp184...
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