| 1. |
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| 2. |
- Kondo, Y., et al.
(author)
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First observation of 28 O
- 2023
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In: Nature. - 0028-0836 .- 1476-4687. ; 620:7976, s. 965-970
-
Journal article (peer-reviewed)abstract
- Subjecting a physical system to extreme conditions is one of the means often used to obtain a better understanding and deeper insight into its organization and structure. In the case of the atomic nucleus, one such approach is to investigate isotopes that have very different neutron-to-proton (N/Z) ratios than in stable nuclei. Light, neutron-rich isotopes exhibit the most asymmetric N/Z ratios and those lying beyond the limits of binding, which undergo spontaneous neutron emission and exist only as very short-lived resonances (about 10−21s), provide the most stringent tests of modern nuclear-structure theories. Here we report on the first observation of 28O and 27O through their decay into 24O and four and three neutrons, respectively. The 28O nucleus is of particular interest as, with the Z = 8 and N = 20 magic numbers1,2, it is expected in the standard shell-model picture of nuclear structure to be one of a relatively small number of so-called ‘doubly magic’ nuclei. Both 27O and 28O were found to exist as narrow, low-lying resonances and their decay energies are compared here to the results of sophisticated theoretical modelling, including a large-scale shell-model calculation and a newly developed statistical approach. In both cases, the underlying nuclear interactions were derived from effective field theories of quantum chromodynamics. Finally, it is shown that the cross-section for the production of 28O from a 29F beam is consistent with it not exhibiting a closed N = 20 shell structure.
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| 3. |
- McGinn, Steven, et al.
(author)
-
New Technologies for DNA analysis-A review of the READNA Project.
- 2016
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In: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
-
Research review (peer-reviewed)abstract
- The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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| 4. |
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| 5. |
- Adler, Belinda, et al.
(author)
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Miniaturized and Automated High-Throughput Verification of Proteins in the ISET Platform with MALDI MS
- 2012
-
In: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 84:20, s. 8663-8669
-
Journal article (peer-reviewed)abstract
- A major bottleneck in high-throughput protein production is the validation step, which is why parallel and automated sample processing methods are highly desirable. Also, a miniaturized sample preparation format is preferred, as the reduction of reagent volumes significantly decreases the analysis cost per sample. We have developed an automated and miniaturized protein sequence verification protocol for recombinant proteins utilizing peptide mass fingerprinting and MS/MS analysis. The integrated selective enrichment target (ISET) platform, previously developed in our group, with its dual functionality, being both a sample preparation platform and a MALDI target plate, is employed. All steps including immobilized metal ion affinity chromatography of protein on cobalt-loaded beads, tryptic digestion, and MALDI MS analysis are performed in an array format, without any sample transfers, on the same ISET chip. The automated configuration reduced the sample preparation time significantly. Starting with crude lysate, a full plate of 48 purified, digested samples prepared for MALDI-MS can be generated in 4 h, with only 30 min of operator involvement. This paper demonstrates the utility of the method by parallel analysis of 45 His-tagged human recombinant proteins.
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| 6. |
- Adler, Belinda, et al.
(author)
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Optimizing nanovial outlet designs for improved solid-phase extraction in the integrated selective enrichment target-ISET.
- 2012
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In: Electrophoresis. - : Wiley. - 0173-0835. ; 33:21, s. 3143-3150
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Journal article (peer-reviewed)abstract
- The integrated selective enrichment target is a microfluidic platform for SPE sample preparation with integrated nanocolumns, which simultaneously offers direct MALDI MS read-out. Here, we present a study on the importance of different nanocolumn outlet hole geometries and hole areas in relation to MS signal intensity and reproducibility. A design solution that provides the flow characteristics required for robust sample preparation using automated liquid handling is reported.
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| 7. |
- Adler, Belinda, et al.
(author)
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Porous silicon immunoaffinity microarrays
- 2018. - 2
-
In: Handbook of Porous Silicon : Second Edition - Second Edition. - Cham : Springer International Publishing. - 9783319713793 - 9783319713816 ; 2-2, s. 1355-1367
-
Book chapter (peer-reviewed)abstract
- Porous silicon with immobilized recognition biomolecules is an attractive platform for many microfluidic chip-based bioanalytical applications. We review the progress in the field since its earliest developments in the 1990s. An improved assay for early detection of prostate cancer has reached clinical evaluation, but there are also exciting developments in both aptamer-based biosensing and mass spectrometry-based biosensing.
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| 8. |
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| 9. |
- Ahmad Tajudin, Asilah, et al.
(author)
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MALDI-target integrated platform for affinity-captured protein digestion.
- 2014
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In: Analytica Chimica Acta. - : Elsevier BV. - 1873-4324 .- 0003-2670. ; 807:Jan 7, s. 1-8
-
Journal article (peer-reviewed)abstract
- To address immunocapture of proteins in large cohorts of clinical samples high throughput sample processing is required. Here a method using the proteomic sample platform, ISET (integrated selective enrichment target) that integrates highly specific immunoaffinity capture of protein biomarker, digestion and sample cleanup with a direct interface to mass spectrometry is presented. The robustness of the on-ISET protein digestion protocol was validated by MALDI MS analysis of model proteins, ranging from 40fmol to 1pmol per nanovial. On-ISET digestion and MALDI MS/MS analysis of immunoaffinity captured disease-associated biomarker PSA (prostate specific antigen) from human seminal plasma are presented.
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| 10. |
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| 11. |
- Arnshav, Mirja, 1977-
(author)
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De små båtarna och den stora flykten : Arkeologi i spåren av andra världskrigets baltiska flyktbåtar
- 2020
-
Doctoral thesis (other academic/artistic)abstract
- The Baltic states, Estonia, Latvia and Lithuania, were occupied no less than three times during the Second World War. Faced with a reign of terror, the threat of deportation, and compulsory conscription, over 30,000 people fled over the Baltic Sea to Sweden. On their arrival in Sweden, most escape boats were confiscated by the authorities and in 1945 were returned to the Soviet Union.This study, which began as an attempt to find out about the Baltic escape boats that ended up in Sweden, is inspired by a foreign boat in a small fishing harbour on the island of Gotland. My curiosity was piqued when I caught sight of the boat and heard that it had probably been an escape boat.The purpose of this thesis is to establish which, if any, Baltic escape boats survive in Sweden, in which contexts they remain, and to review their state of preservation, as well as to answer the question of their significance for the memory of the escape. It is an archaeology of the escape and its aftermath, based on the surviving escape boats – what the boats say about the escape, what happened to them afterwards, and how people relate to them and their historical legacy today.The study looks at 35 boats that have been described as Baltic escape boats in various contexts. It shows that they are found in a multitude of environments and in a range of different states of preservation. The boats illustrate experiences that few other source materials can convey, in a manner pertinent to the archaeological understanding of flight. In addition, the boats are rare traces of an earlier Estonian coastal culture eradicated by the second Soviet occupation.One of the most important outcomes of the study is the documentation from the survey and examinations carried out. Few of the boats were known outside their local context. A national compilation has been lacking, which has impeded research and ultimately our understanding of the breadth and complexity of the Swedish historical landscape when it comes to ship remains.
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| 12. |
- Augustsson, Per, et al.
(author)
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Acoustophoretic microfluidic chip for sequential elution of surface bound molecules from beads or cells
- 2012
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In: Biomicrofluidics. - : AIP Publishing. - 1932-1058. ; 6:3
-
Journal article (peer-reviewed)abstract
- An acoustophoresis-based microfluidic flow-chip is presented as a novel platform to facilitate analysis of proteins and peptides loosely bound to the surface of beads or cells. The chip allows for direct removal of the background surrounding the beads or cells, followed by sequential treatment and collection of a sequence of up to five different buffer conditions. During this treatment, the beads/cells are retained in a single flow by acoustic radiation force. Eluted peptides are collected from the outlets and subsequently purified by miniaturized solid-phase extraction and analyzed with matrix assisted laser desorption mass spectrometry. Fundamental parameters such as the system fluidics and dispersion are presented. The device was successfully applied for wash and sequential elution of peptides bound to the surface of microbeads and human spermatozoa, respectively. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4749289]
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| 13. |
- Augustsson, Per, et al.
(author)
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Decomplexing biofluids using microchip based acoustophoresis
- 2009
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In: Lab on a Chip. - 1473-0189. ; 9:6, s. 810-818
-
Journal article (peer-reviewed)abstract
- Highly efficient washing and extraction of microbeads to decomplex analytes ranging from small peptides to large viruses was realised in a microscaled continuous flow format. The bead washing principle reported herein is based on acoustophoresis, i.e. the primary acoustic radiation force in an ultrasonic standing wave and laminar flow properties are utilised to translate bioanalytes trapped on functionalised microbeads from one carrier fluid to another. The carry-over of non-specific material ranges from 1 to 50 ppm relative to input levels depending on application, making acoustophoresis suitable for extraction of rare species from complex environments. Selective extraction of a phosphopeptide relative to its unphosphorylated counterpart is demonstrated using metal oxide affinity capture (MOAC) beads and MALDI-TOF MS readout. Acoustophoresis of microbeads activated with specific binders could be used to capture phage viral particles. The efficiency of the acoustophoretic washing principle was demonstrated by an unspecific phage cross contamination level of only 10(-6) of that in the input bead/phage mixture. The continuous flow format makes acoustophoretic washing flexible regarding sample volume and also allows for easy integration into a sequence of particle handling and analytical unit operations.
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| 14. |
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| 15. |
- Awad, Wael, et al.
(author)
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Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx
- 2019
-
In: Structure. - : Elsevier BV. - 0969-2126. ; 27:6, s. 6-936
-
Journal article (peer-reviewed)abstract
- YjbH is a bacterial adaptor protein required for efficient proteolysis of the RNA polymerase-binding transcription factor Spx by the ClpXP protease. We report the structure of YjbH in complex with Spx. YjbH comprises a DsbA-like thioredoxin domain connected via a linker to a C-terminal domain reminiscent of the winged helix-turn-helix fold. The interaction between YjbH and Spx involves a large surface area. Binding to YjbH stabilizes the C-terminal ClpX recognition region of Spx. We show that mutation of critical YjbH contact residues abrogates Spx recognition. Small-angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry analyses determined the existence of a stable heterodimeric complex in solution and provide evidence that binding of Spx to YjbH reduces the overall conformational flexibility of Spx. Our findings provide insights into the molecular basis for Spx recognition and suggest a model for how YjbH stabilizes Spx and displays the C terminus of Spx for engagement by ClpXP. Awad et al. determined the crystal structure of the ClpXP adaptor protein YjbH in complex with the transcription factor Spx. Structural dynamics of the complex were investigated by hydrogen-deuterium exchange mass spectrometry. The insights provided in this work add molecular details to the recognition of Spx by YjbH.
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| 16. |
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| 17. |
- Bengtsson, Martin, et al.
(author)
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Improved performance in silicon enzyme microreactors obtained by homogeneous porous silicon carrier matrix
- 2002
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In: Talanta. - 1873-3573. ; 56:2, s. 341-353
-
Journal article (peer-reviewed)abstract
- The catalytic performance of porous silicon (PS) micro enzyme reactors (muIMER) is strongly dependent on the PS matrix morphology for enzyme immobilisation. PS was achieved in the muIMER by anodisation in a HF-ethanol mixture. PS etching of structured silicon surfaces commonly results in an inhomogeneous pore formation. The deep channel microreactors described herein have previously suffered from these phenomena, yielding non-optimised muIMERs. In order to obtain a homogeneous PS layer on the deep microreactor channel walls, different reactor geometries (channel wall thicknesses of 50 and 75 mum) were anodised at 10 and 50 mA cm(-2) for anodisation times ranging between 0 and 50 min. The muIMERs were evaluated by immobilising two types of enzymes, glucose oxidase (GOx) and trypsin, and the resulting catalytic turnover was monitored by a colorimetric assay. It was found that reactors with a homogeneous PS matrix displayed improved performance. The trypsin muIMERs were used to digest a protein, beta-casein, in an on-line format and the digest was analysed by MALDI-TOF MS. The importance of tailoring the muIMER geometry and the PS-matrix is crucial for the protein digestion. Successful protein identification after only 12 s. digestion was demonstrated for the best reactor, 75 mum channel wall, 25 mum channel width, anodised at 50 mA cm(-2) for 10 min. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 18. |
- Bergkvist, Jonas, et al.
(author)
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Improved chip design for integrated solid-phase microextraction in on-line proteomic sample preparation
- 2002
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In: Proteomics. - 1615-9861. ; 2:4, s. 422-429
-
Journal article (peer-reviewed)abstract
- A recently introduced silicon microextraction chip (SMEC), used for on-line proteomic sample preparation, has proved to facilitate the process of protein identification by sample clean up and enrichment of peptides. It is demonstrated that a novel grid-SMEC design improves the operating characteristics for solid-phase microextraction, by reducing dispersion effects and thereby improving the sample preparation conditions. The structures investigated in this paper are treated both numerically and experimentally. The numerical approach is based on finite element analysis of the micro-fluidic flow in the microchip. The analysis is accomplished by use of the computational fluid dynamics-module FLOTRAN in the ANSYS(R) software package. The modeling and analysis of the previously reported weir-SMEC design indicates some severe drawbacks, that can be reduced by changing the microextraction chip geometry to the grid-SMEC design. The overall analytical performance was thereby improved and also verified by experimental work. Matrix-assisted laser desorption/ionization mass spectra of model peptides extracted from both the weir-SMEC and the new grid-SMEC support the numerical analysis results. Further use of numerical modeling and analysis of the SMEC structures is also discussed and suggested in this work.
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| 19. |
- Bergwik, Jesper, et al.
(author)
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Binding of the human antioxidation protein α1-microglobulin (A1M) to heparin and heparan sulfate. Mapping of binding site, molecular and functional characterization, and co-localization in vivo and in vitro
- 2021
-
In: Redox Biology. - : Elsevier BV. - 2213-2317. ; 41
-
Journal article (peer-reviewed)abstract
- Heparin and heparan sulfate (HS) are linear sulfated disaccharide polymers. Heparin is found mainly in mast cells, while heparan sulfate is found in connective tissue, extracellular matrix and on cell membranes in most tissues. α1-microglobulin (A1M) is a ubiquitous protein with thiol-dependent antioxidant properties, protecting cells and matrix against oxidative damage due to its reductase activities and radical- and heme-binding properties. In this work, it was shown that A1M binds to heparin and HS and can be purified from human plasma by heparin affinity chromatography and size exclusion chromatography. The binding strength is inversely dependent of salt concentration and proportional to the degree of sulfation of heparin and HS. Potential heparin binding sites, located on the outside of the barrel-shaped A1M molecule, were determined using hydrogen deuterium exchange mass spectrometry (HDX-MS). Immunostaining of endothelial cells revealed pericellular co-localization of A1M and HS and the staining of A1M was almost completely abolished after treatment with heparinase. A1M and HS were also found to be co-localized in vivo in the lungs, aorta, kidneys and skin of mice. The redox-active thiol group of A1M was unaffected by the binding to HS, and the cell protection and heme-binding abilities of A1M were slightly affected. The discovery of the binding of A1M to heparin and HS provides new insights into the biological role of A1M and represents the basis for a novel method for purification of A1M from plasma.
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| 20. |
- Bimai, Ornella, et al.
(author)
-
Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding
- 2024
-
In: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 12
-
Journal article (peer-reviewed)abstract
- A small, nucleotide-binding domain, the ATP-cone, is found at the N- terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerisation and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical, and structural information on the effects of ATP and dATP binding to the anaerobic RNR from Prevotella copri. The enzyme exists in a dimertetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP- cone and tetramers when two dATP molecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully ordered glycyl radical domain ( GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it cannot be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 A away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation.
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| 21. |
- Bimai, Ornella, et al.
(author)
-
Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding
- 2024
-
In: eLife. - 2050-084X. ; 12
-
Journal article (peer-reviewed)abstract
- A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerisation and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical, and structural information on the effects of ATP and dATP binding to the anaerobic RNR from Prevotella copri. The enzyme exists in a dimer– tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it cannot be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation.
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| 22. |
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| 23. |
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| 24. |
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| 25. |
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| 26. |
- Currow, David C., et al.
(author)
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Missed opportunity? Worsening breathlessness as a harbinger of death : A cohort study
- 2018
-
In: European Respiratory Journal. - : European Respiratory Society (ERS). - 0903-1936 .- 1399-3003. ; 52:3
-
Journal article (peer-reviewed)abstract
- The aim of the study was to explore trajectories of breathlessness intensity by function and life-limiting illness diagnosis in the last 3 weeks of life in palliative care patients. A prospective, consecutive cohort study obtained point-of-care data of patients of Silver Chain Hospice Care Service (Perth, Australia) over the period 2011–2014 (n=6801; 51494 data-points). Breathlessness intensity (0–10 numerical rating scale) and physical function (Australia-modified Karnofsky Performance Status (AKPS)) were measured at each visit. Time was anchored at death. Breathlessness trajectory was analysed by physical function and diagnosis using mixed effects regression. Mean±SD age was 71.5±15.1 years and 55.2% were male, most with cancer. The last recorded AKPS was >40 for 26.8%. Breathlessness was worst in people with cardiorespiratory disease and AKPS >40, and breathlessness in the last week of life increased most in this group (adjusted mean 2.92 versus all others 1.51; p=0.0001). The only significant interaction was with diagnosis and function in the last week of life (p<0.0001). Breathlessness is more intense and increases more in people with better function and cardiorespiratory disease immediately before death. Whether there are reversible causes for these people should be explored prospectively. Omitting function from previous population estimates may have overestimated breathlessness intensity for many patients in the days preceding death.
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| 27. |
-
Djur : Berörande möten och kulturella smärtpunkter
- 2018
-
Editorial collection (peer-reviewed)abstract
- I denna antologi skriver åtta etnologer utifrån ett kulturvetenskapligt perspektiv om människors varierade och komplexa relationer till andra arter. Bidragen är tydligt vinklade mot vilda djur, alltså sådana som sällan ingår i det egna hushållet eller rör sig i vår omedelbara närhet. Med utgångspunkt i pågående forskning diskuterar författarna teman som konflikter och glädjeämnen i fågelskådarvärlden, karismatiska djur i olika utställningskontexter, barns rädslor, morbida djurskämt och levande djurs rituella omvandling till ätbart kött. Texterna spänner från det innerliga, komiska och gulliga till död och existentiell utsatthet. Boken inleds med att redaktörerna presenterar en översikt av hur djur har framställts, uppmärksammats och studerats inom humanistisk forskning. Därefter följer artiklarna. Här följer Elin Lundquist på plats bevakningen av den fågeljakt som årligen äger rum på Malta, utifrån de ”affektiva logiker” som motiverar fågelskådare att bege sig dit. Mattias Frihammar skriver om hur ett vildmarkgalleri låter såväl levande som monterade djur bli utgångspunkt för hanterandet av frågor om lokal identitet. Lars Kaijser visar i sin undersökning av offentliga akvarier hur kunskap om hajar gestaltas och hur dessa iscensättningar samtidigt ofta rymmer ambivalenta och motstridiga drag. Sverker Hyltén-Cavallius riktar blicken mot förevisandet av utdöda djur på naturhistoriska museer, med ett särskilt fokus på hur själva dödsögonblicken skildras. Susanne Nylund Skog undersöker fågelskådares berättelser som uttryck för ett samlande och visar på de olika statusmarkeringar som detta samlande rymmer. Simon Ekström skriver om hur skämtteckningar föreställande humrar tangerar både djurrättsfrågor och mänsklig ångest. Helena Hörnfeldt uppehåller sig kring hur olika djurrädslor många gånger kan spåras till den diffusa gränsdragningen mellan människa och djur. Michelle Zethson undersöker hur slakt och tillredning av döda djur resulterar i ett "köttblivande" avsett för mänsklig konsumtion. Antologin avslutas med en kommenterande epilog från redaktörerna.
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| 28. |
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| 29. |
- Ekström, Erik, et al.
(author)
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Microstructure control and property switching in stress-free van der Waals epitaxial VO2 films on mica
- 2023
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In: Materials & design. - : Elsevier. - 0264-1275 .- 1873-4197. ; 229
-
Journal article (peer-reviewed)abstract
- Realizing stress-free inorganic epitaxial films on weakly bonding substrates is of importance for applications that require film transfer onto surfaces that do not seed epitaxy. Film-substrate bonding is usually weakened by harnessing natural van der Waals layers (e.g., graphene) on substrate surfaces, but this is difficult to achieve in non-layered materials. Here, we demonstrate van der Waals epitaxy of stress-free films of a non-layered material VO2 on mica. The films exhibit out-of-plane 010 texture with three in-plane orientations inherited from the crystallographic domains of the substrate. The lattice parameters are invariant with film thickness, indicating weak film-substrate bonding and complete interfacial stress relaxation. The out-of-plane domain size scales monotonically with film thickness, but the in-plane domain size exhibits a minimum, indicating that the nucleation of large in-plane domains supports subsequent island growth. Complementary ab initio investigations suggest that VO2 nucleation and van der Waals epitaxy involves subtle polarization effects around, and the active participation of, surface potassium atoms on the mica surface. The VO2 films show a narrow domain-size-sensitive electrical-conductivity-temperature hysteresis. These results offer promise for tuning the properties of stress-free van der Waals epitaxial films of non-layered materials such as VO2 through microstructure control.
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| 30. |
- Ekström, Simon, 1966-
(author)
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Alfred Nobels känsla för hummer
- 2021
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In: Svenska dagbladet. - 1101-2412.
-
Journal article (pop. science, debate, etc.)abstract
- Att läsa menyerna för de drygt hundra Nobelmiddagarna som hittills ordnats är att ta del av en veritabel kulinarisk teater. Inte minst belyser hummerns förändrade närvaro vid banketten en viktig förskjutning av idén om hur Sverige ska representeras vid dessa tillfällen.
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| 31. |
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| 32. |
- Ekström, Simon, 1966-
(author)
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Begrepp i bur : Om kulturbruk och kulturbråk
- 2010
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In: Kulturella perspektiv - Svensk etnologisk tidskrift. - 1102-7908. ; 19:3, s. 5-17
-
Journal article (peer-reviewed)abstract
- The Swedish debate concerning honour killings has largely revolved around the concept of “culture” – or more specifically, it has revolved around the ways in which different writers have criticized some other debaters for misusing the concept. Hence, this debate sheds light on how the concept of culture has come to occupy a position in something one might call a linguistic quarantine. Cultural explanations are often considered an issue which must be handled with great caution in order not to explode into cultural racism, or to an undesired exaggeration of cultural difference. Moreover, the most serious objections against the con- cept of culture seem to occur in the very field which the concept has traditionally been regarded as most suitable for. Recent controversies around phenomena such as honour killings, structural dis- crimination and cultural racism reveals that it first and foremost is in relation to the “exotic other” that cultural explanations nowadays are becoming questioned. On the other hand, few debaters and researchers are ready to seriously do away with a concept they continue to understand as applicable for their own analyses. The aim of this article is, therefore, to highlight some of the critical arguments in this debate, so as to discuss the ambivalences that distinguish contemporary public disputes about culture and cultural explanations. keywords: the concept of culture, honour killing, linguistic quarantine, culture racism.
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| 33. |
- Ekström, Simon, 1991-, et al.
(author)
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Deformable Image Registration of Volumetric Whole-body MRI: An Evaluation
-
Other publication (other academic/artistic)abstract
- Whole-body imaging presents a variety of interesting applications and combining these information rich images with image registration enables detailed large scale analysis. Whole-body image registration, with the large variability present in human anatomy, introduces a range of challenges that need to be dealt with. This paper aims to present two new extensions to a previously published registration method based on compositive updates and voxel-wise regularization. The new extensions are evaluated against a previously presented pipeline for whole-body registration and a learning-based approach using the Voxel Morph framework. The methods are evaluated on Dice overlap, smoothness of produced displacement fields, and the inverse consistency error. The presented extensions are shown to improve upon previous method both in terms of computation time and registration quality. The voxel-wise regularization produces a mean Dice overlap of 0.828 for the 10 segmented regions and a mean computation time of 320 seconds per subject. The learning-based approach had an inference time of only 3 seconds but a training time of 16 hours per reference subject. This approach produced a mean Dice overlap of only 0.797 but it was shown that the issues in overlap score were limited to the kidneys. In conclusion, both the extensions and VoxelMorph has presented great promise for the task of whole-body registration compared to previous method. However, the choice of method will be highly dependent upon the task. VoxelMorph provides results of lower quality and reduced flexibility but a computation time of only a few seconds.
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| 34. |
- Ekström, Simon, 1966-
(author)
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Den flyktiga fjärilen
- 2014
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In: Svenska sjömanstatueringar. - Stockholm : Medströms Bokförlag. - 9789173291170 ; , s. 129-138
-
Book chapter (other academic/artistic)
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| 35. |
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| 36. |
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| 37. |
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| 38. |
- Ekström, Simon, 1991-
(author)
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Efficient GPU-based Image Registration : for Detailed Large-Scale Whole-body Analysis
- 2020
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Doctoral thesis (other academic/artistic)abstract
- Imaging has become an important aspect of medicine, enabling visualization of internals in a non-invasive manner. The rapid advancement and adoption of imaging techniques have led to a demand for tools able to take advantage of the information that is produced. Medical image analysis aims to extract relevant information from acquired images to aid diagnostics in healthcare and increase the understanding within medical research. The main subject of this thesis, image registration, is a widely used tool in image analysis that can be employed to find a spatial transformation aligning a set of images. One application, that is described in detail in this thesis, is the use of image registration for large-scale analysis of whole-body images through the utilization of the correspondences defined by the resulting transformations. To produce detailed results, the correspondences, i.e. transformations, need to be of high resolution and the quality of the result has a direct impact on the quality of the analysis. Also, this type of application aims to analyze large cohorts and the value of a registration method is not only weighted by its ability to produce an accurate result but also by its efficiency. This thesis presents two contributions on the subject; a new method for efficient image registration with the ability to produce dense deformable transformations, and the application of the presented method in large-scale analysis of a whole-body dataset acquired using an integrated positron emission tomography (PET) and magnetic resonance imaging (MRI) system. In this thesis, it is shown that efficient and detailed image registration can be performed by employing graph cuts and a heuristic where the optimization is performed on subregions of the image. The performance can be improved further by the efficient utilization of a graphics processing unit (GPU). It is also shown that the method can be employed to produce a model on health based on a PET-MRI dataset which can be utilized to automatically detect pathology in the imaging.
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| 41. |
- Ekström, Simon, 1991-, et al.
(author)
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Fast graph-cut based optimization for practical dense deformable registration of volume images
- 2020
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In: Computerized Medical Imaging and Graphics. - : Elsevier. - 0895-6111 .- 1879-0771. ; 84
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Journal article (peer-reviewed)abstract
- Deformable image registration is a fundamental problem in medical image analysis, with applications such as longitudinal studies, population modeling, and atlas-based image segmentation. Registration is often phrased as an optimization problem, i.e., finding a deformation field that is optimal according to a given objective function. Discrete, combinatorial, optimization techniques have successfully been employed to solve the resulting optimization problem. Specifically, optimization based on α-expansion with minimal graph cuts has been proposed as a powerful tool for image registration. The high computational cost of the graph-cut based optimization approach, however, limits the utility of this approach for registration of large volume images. Here, we propose to accelerate graph-cut based deformable registration by dividing the image into overlapping sub-regions and restricting the α-expansion moves to a single sub-region at a time. We demonstrate empirically that this approach can achieve a large reduction in computation time - from days to minutes - with only a small penalty in terms of solution quality. The reduction in computation time provided by the proposed method makes graph-cut based deformable registration viable for large volume images. Graph-cut based image registration has previously been shown to produce excellent results, but the high computational cost has hindered the adoption of the method for registration of large medical volume images. Our proposed method lifts this restriction, requiring only a small fraction of the computational cost to produce results of comparable quality.
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| 42. |
- Ekström, Simon, 1991-, et al.
(author)
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Faster dense deformable image registration by utilizing both CPU and GPU
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Other publication (other academic/artistic)abstract
- Purpose: Image registration is an important aspect of medical image analysis and a key component in many analysis concepts. Applications include fusion of multimodal images, multi-atlas segmentation, and whole-body analysis. Deformable image registration is often computationally expensive, and the need for efficient registration methods is highlighted by the emergence of large-scale image databases, e.g., the UK Biobank, providing imaging from 100 000 participants.Approach: We present a heterogeneous computing approach, utilizing both the CPU and the GPU, to accelerate a previously proposed image registration method. The parallelizable task of computing the matching criterion is offloaded to the GPU, where it can be computed efficiently, while the more complex optimization task is performed on the CPU. To lessen the impact of data synchronization between the CPU and GPU we propose a pipeline model, effectively overlapping computational tasks with data synchronization. The performance is evaluated on a brain labeling task and compared with a CPU implementation of the same method and the popular Advanced Normalization Tools (ANTs) software.Results: The proposed method presents a speed-up by a factor of 4 and 8 against the CPU implementation and the ANTs software respectively. A significant improvement in labeling quality was also observed, with measured mean Dice overlaps of 0.712 and 0.701 for our method and ANTs respectively.Conclusions: We showed that the proposed method compares favorably to the ANTs software yielding both a significant speed-up and an improvement in labeling quality. The registration method together with the proposed parallelization strategy is implemented as an open-source software package, deform.
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| 43. |
- Ekström, Simon, 1991-, et al.
(author)
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Faster dense deformable image registration by utilizing both CPU and GPU
- 2021
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In: Journal of Medical Imaging. - 2329-4302 .- 2329-4310. ; 8:1
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Journal article (peer-reviewed)abstract
- Purpose: Image registration is an important aspect of medical image analysis and a key component in many analysis concepts. Applications include fusion of multimodal images, multi-atlas segmentation, and whole-body analysis. Deformable image registration is often computationally expensive, and the need for efficient registration methods is highlighted by the emergence of large-scale image databases, e.g., the UK Biobank, providing imaging from 100,000 participants. Approach: We present a heterogeneous computing approach, utilizing both the CPU and the graphics processing unit (GPU), to accelerate a previously proposed image registration method. The parallelizable task of computing the matching criterion is offloaded to the GPU, where it can be computed efficiently, while the more complex optimization task is performed on the CPU. To lessen the impact of data synchronization between the CPU and GPU, we propose a pipeline model, effectively overlapping computational tasks with data synchronization. The performance is evaluated on a brain labeling task and compared with a CPU implementation of the same method and the popular advanced normalization tools (ANTs) software. Results: The proposed method presents a speed-up by factors of 4 and 8 against the CPU implementation and the ANTs software, respectively. A significant improvement in labeling quality was also observed, with measured mean Dice overlaps of 0.712 and 0.701 for our method and ANTs, respectively. Conclusions: We showed that the proposed method compares favorably to the ANTs software yielding both a significant speed-up and an improvement in labeling quality. The registration method together with the proposed parallelization strategy is implemented as an open-source software package, deform.
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| 44. |
- Ekström, Simon, 1966-
(author)
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From Excerpt to Cosplay : Paths of Knowledge in the Nordic Museum Archive
- 2020
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In: Culture Unbound. - : Linkoping University Electronic Press. - 2000-1525. ; 12:1, s. 116-140
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Journal article (peer-reviewed)abstract
- The aim of this article is to shed some light on the situation that occurs when scholarly knowledge, once highly valued, is successively undermined, while elements of the same learning live on as attractive resources to other stakeholders. More accurately, the research question relates to the process that starts with many ethnologists who, over time, come to increasingly view formerly important materials as less relevant to their own academic issues. For the sake of the argument, the Nordic Museum’s extensive collection of excerpts concerning folk customs and beliefs is used as an eye-opening case study. During the 1960s and 1970s, folklore researchers and ethnologists retreated from researching those lingering traces of the past—of which the Nordic Museum’s excerpt collection constitutes a powerful material centre—and thus this field was left free for others to claim. By drawing attention to both the productive force of the Nordic Museum’s collection of excerpts, and a number of contemporary and popular representations of ancient folklore, this article actualises a set of questions that deal with the relationship between new and old knowledge; for what becomes of previously sought after academic learning, once treasured in the Nordic Museum Archive, when the vast majority of the discipline heads for new materials, methods and theories?
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| 45. |
- Ekström, Simon, 1966-
(author)
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Följa hummer
- 2013
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In: RIG. - 0035-5267 .- 2002-3863. ; 96:2, s. 65-79
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Journal article (peer-reviewed)abstract
- Following the LobsterIn this article, lobsters serve as an analytical trace element for a further discussion about the mutual relation between materiality and meaning. Through keystrokes in different historical and contemporary contexts, the first part of the text presents a number of examples of what a lobster could be – and what it could also be expected to do. The second part discusses the act of following as a culture-analytical method, and indicates the benefits that concepts like frequency, density and population can have.Asking oneself what a lobster could be underlines that lobsters have more than one meaning. In other words, it is a way of helping us to see how the meaning we ascribe to a lobster is dependent on the kind of company it keeps. Lobsters seldom appear alone. On the contrary, they are almost always surrounded by other things, at the same time as they are objects for highly varying practices. For someone whose task it is to actively look for lobsters, i.e. what in the article is called following the lobster, this is especially clear. When lobsters are moved from one context to another, the setting is also changed. The earlier network of objects, people and physical environments that surrounded the lobsters changes shape. For lobsters, every new setting also means a new network.In this way, the following of lobsters illustrates how translations and meaning-making should be understood as both material and cultural phenomenon. In the analysis, the object is always one and the same – lobsters – while the setting and the network can change several times by simply twisting the lens. All this can be regarded as a kaleidoscopic cultural analysis, where the ambition is to discover something new about the lobster by searching for it in expected as well as unexpected places. At the same time, the intention is also to generate new knowledge about the contexts and activities that are actualised by the presence of the lobsters. This is why the article’s recurring question – which is posed in the presence of every specific lobster population – is, what is the work that the lobsters are expected to do, right there and then?
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| 46. |
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| 49. |
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| 50. |
- Ekström, Simon, 1966-
(author)
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Hockeybockarna, skandalen och moralen.
- 2005
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In: Tankar från baslinjen.. - Eslöv : Brutus Östlings Bokförlag Symposion, Stockholm. ; , s. 119-136
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Book chapter (other academic/artistic)
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