| 1. |
- Wöhri, Annemarie, 1976, et al.
(author)
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A Lipidic-Sponge Phase Screen for Membrane Protein Crystallization
- 2008
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In: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 16:7, s. 1003-1009
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Journal article (peer-reviewed)abstract
- A major current deficit in structural biology is the lack of high-resolution structures of eukaryotic membrane proteins, many of which are key drug targets for the treatment of disease. Numerous eukaryotic membrane proteins require specific lipids for their stability and activity, and efforts to crystallize and solve the structures of membrane proteins that do not address the issue of lipids frequently end in failure rather than success. To help address this problem, we have developed a sparse matrix crystallization screen consisting of 48 lipidic-sponge phase conditions. Sponge phases form liquid lipid bilayer environments which are suitable for conventional hanging- and sitting-drop crystallization experiments. Using the sponge phase screen, we obtained crystals of several different membrane proteins from bacterial and eukaryotic sources. We also demonstrate how the screen may be manipulated by incorporating specific lipids such as cholesterol; this modification led to crystals being recovered from a bacterial photosynthetic core complex.
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| 2. |
- Adesam, Yvonne, 1975, et al.
(author)
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Defining the Eukalyptus forest – the Koala treebank of Swedish
- 2015
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In: Proceedings of the 20th Nordic Conference of Computational Linguistics, NODALIDA 2015, May 11-13, 2015, Vilnius, Lithuania. Edited by Beáta Megyesi. - 1650-3686 .- 1650-3740. - 9789175190983 ; , s. 1-9
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Conference paper (peer-reviewed)abstract
- This paper details the design of the lexical and syntactic layers of a new annotated corpus of Swedish contemporary texts. In order to make the corpus adaptable into a variety of representations, the annotation is of a hybrid type with head-marked constituents and function-labeled edges, and with a rich annotation of non-local dependencies. The source material has been taken from public sources, to allow the resulting corpus to be made freely available.
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| 3. |
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| 4. |
- Adesam, Yvonne, 1975, et al.
(author)
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Multiwords, Word Senses and Multiword Senses in the Eukalyptus Treebank of Written Swedish
- 2015
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In: Proceedings of the Fourteenth International Workshop on Treebanks and Linguistic Theories (TLT14), 11–12 December 2015 Warsaw, Poland. - 9788363159184 ; , s. 3-12
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Conference paper (peer-reviewed)abstract
- Multiwords reside at the intersection of the lexicon and syntax and in an annotation project, they will affect both levels. In the Eukalyptus treebank of written Swedish, we treat multiwords formally as syntactic objects, which are assigned a lexical type and sense. With the help of a simple dichotomy, analyzed vs unanalyzed multiwords, and the expressiveness of the syntactic annotation formalism employed, we are able to flexibly handle most multiword types and usages.
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| 5. |
- Adesam, Yvonne, 1975, et al.
(author)
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The Eukalyptus Treebank of Written Swedish
- 2018
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In: Seventh Swedish Language Technology Conference (SLTC), Stockholm, 7–9 November 2018.
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Conference paper (other academic/artistic)
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| 6. |
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| 7. |
- Brändén, Gisela, 1975, et al.
(author)
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Coherent diffractive imaging of microtubules using an X-ray laser.
- 2019
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Journal article (peer-reviewed)abstract
- X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.
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| 8. |
- Dods, Robert, 1989, et al.
(author)
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Ultrafast structural changes within a photosynthetic reaction centre.
- 2021
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 589:7841, s. 310-314
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Journal article (peer-reviewed)abstract
- Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.
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| 9. |
- Forsberg, Markus, 1974, et al.
(author)
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From construction candidates to constructicon entries: An experiment using semi-automatic methods for identifying constructions in corpora
- 2014
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In: Constructions and Frames. - : John Benjamins Publishing Company. - 1876-1933 .- 1876-1941. ; 6:1, 2014, s. 114-135
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Journal article (peer-reviewed)abstract
- We present an experiment where natural language processing tools are used to automatically identify potential constructions in a corpus. e experiment was conducted as part of the ongoing efforts to develop a Swedish constructicon. Using an automatic method to suggest constructions has advantages not only for efficiency but also methodologically: it forces the analyst to look more objec-tively at the constructions actually occurring in corpora, as opposed to focusing on “interesting” constructions only. As a heuristic for identifying potential con-structions, the method has proved successful, yielding about 200 (out of 1,200) highly relevant construction candidates.
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| 10. |
- Hagström, Lovisa, 1995, et al.
(author)
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The Effect of Scaling, Retrieval Augmentation and Form on the Factual Consistency of Language Models
- 2023
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In: Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing, pages 5457–5476, Singapore. - : Association for Computational Linguistics.
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Conference paper (peer-reviewed)abstract
- Large Language Models (LLMs) make natural interfaces to factual knowledge, but their usefulness is limited by their tendency to deliver inconsistent answers to semantically equivalent questions. For example, a model might supply the answer “Edinburgh” to “Anne Redpath passed away in X.” and “London” to “Anne Redpath’s life ended in X.” In this work, we identify potential causes of inconsistency and evaluate the effectiveness of two mitigation strategies: up-scaling and augmenting the LM with a passage retrieval database. Our results on the LLaMA and Atlas models show that both strategies reduce inconsistency but that retrieval augmentation is considerably more efficient. We further consider and disentangle the consistency contributions of different components of Atlas. For all LMs evaluated we find that syntactical form and task artifacts impact consistency. Taken together, our results provide a better understanding of the factors affecting the factual consistency of language models.
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