| 1. |
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| 2. |
- Betancourt, Lazaro Hiram, et al.
(author)
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The human melanoma proteome atlas-Defining the molecular pathology
- 2021
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In: Clinical and Translational Medicine. - : Wiley. - 2001-1326. ; 11:7, s. 1-20
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Journal article (peer-reviewed)abstract
- The MM500 study is an initiative to map the protein levels in malignant melanoma tumor samples, focused on in-depth histopathology coupled to proteome characterization. The protein levels and localization were determined for a broad spectrum of diverse, surgically isolated melanoma tumors originating from multiple body locations. More than 15,500 proteoforms were identified by mass spectrometry, from which chromosomal and subcellular localization was annotated within both primary and metastatic melanoma. The data generated by global proteomic experiments covered 72% of the proteins identified in the recently reported high stringency blueprint of the human proteome. This study contributes to the NIH Cancer Moonshot initiative combining detailed histopathological presentation with the molecular characterization for 505 melanoma tumor samples, localized in 26 organs from 232 patients.
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| 3. |
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| 4. |
- Arnarson, Teitur, et al.
(author)
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On the size of the non-coincidence set of parabolic obstacle problems with applications to American option pricing
- 2007
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In: Mathematica Scandinavica. - : Det Kgl. Bibliotek/Royal Danish Library. - 0025-5521 .- 1903-1807. ; 101:1, s. 148-160
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Journal article (peer-reviewed)abstract
- The following paper is devoted to the study of the positivity set U = {L phi > 0} arising in parabolic obstacle problems. It is shown that U is contained in the non-coincidence set with a positive distance between the boundaries uniformly in the spatial variable if the boundary of U satisfies an interior C-1 -Dini condition in the space variable and a Lipschitz condition in the time variable. We apply our results to American option pricing and we thus show that the positivity set is strictly contained in the continuation region, which means that the option should not be exercised in U or on the boundary of U.
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| 5. |
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| 6. |
- Ben-Shabat, Ilan, et al.
(author)
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Characteristics of in-hospital stroke patients in Sweden : a nationwide register-based study
- 2023
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In: European Stroke Journal. - : Sage Publications. - 2396-9873 .- 2396-9881. ; 8:3, s. 777-783
-
Journal article (peer-reviewed)abstract
- INTRODUCTION: Few studies have reported the characteristics of patients with in-hospital stroke (IHS) including the reason for hospitalization and invasive procedures before the stroke. We aimed to extend current knowledge.PATIENTS AND METHODS: All adult patients with IHS in Sweden during 2010-2019 registered in the Swedish Stroke Register (Riksstroke) were included. The cohort was cross-linked to the National Patient Register and data extracted on background diagnoses, main discharge diagnoses, and procedure codes for the hospitalization when IHS occurred and any hospital-based healthcare contacts within 30 days before IHS.RESULTS: 231,402 stroke cases were identified of which 12,551 (5.4%) were in-hospital and had corresponding entries in the National Patient Register. Of the IHS patients, 11,420 (91.0%) had ischemic stroke and 1131 (9.0%) hemorrhagic stroke; 5860 (46.7%) of the IHS patients had at least one invasive procedure prior to ictus. 1696 (13.5%) had a cardiovascular procedure and 560 (4.5%) a neurosurgical procedure. 1319 (10.5%) patients only had minimally invasive procedures such as blood product transfusion, hemodialysis, or central line insertion. Common discharge diagnosis in patients with no invasive procedures were cardiovascular disorders, injuries, and respiratory disorders.DISCUSSION AND CONCLUSION: One in every 17 strokes in Sweden occur in a hospital. In this unselected large cohort the previously reported major causes for in-hospital stroke, cardiovascular and neurosurgical procedures, preceded IHS in only 18.0% of cases suggesting that other etiologies are more common than previously reported. Future studies should aim at determining absolute risks of stroke after surgical procedures and ways of risk reduction.
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| 7. |
- Betancourt, Lazaro Hiram, et al.
(author)
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Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data
- 2019
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
-
Journal article (peer-reviewed)abstract
- Metastatic melanoma is one of the most common deadly cancers, and robust biomarkers are still needed, e.g. to predict survival and treatment efficiency. Here, protein expression analysis of one hundred eleven melanoma lymph node metastases using high resolution mass spectrometry is coupled with in-depth histopathology analysis, clinical data and genomics profiles. This broad view of protein expression allowed to identify novel candidate protein markers that improved prediction of survival in melanoma patients. Some of the prognostic proteins have not been reported in the context of melanoma before, and few of them exhibit unexpected relationship to survival, which likely reflects the limitations of current knowledge on melanoma and shows the potential of proteomics in clinical cancer research.
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| 8. |
- Betancourt, Lazaro Hiram, et al.
(author)
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The hidden story of heterogeneous B-raf V600E mutation quantitative protein expression in metastatic melanoma—association with clinical outcome and tumor phenotypes
- 2019
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In: Cancers. - : MDPI AG. - 2072-6694. ; 11:12
-
Journal article (peer-reviewed)abstract
- In comparison to other human cancer types, malignant melanoma exhibits the greatest amount of heterogeneity. After DNA-based detection of the BRAF V600E mutation in melanoma patients, targeted inhibitor treatment is the current recommendation. This approach, however, does not take the abundance of the therapeutic target, i.e., the B-raf V600E protein, into consideration. As shown by immunohistochemistry, the protein expression profiles of metastatic melanomas clearly reveal the existence of inter-and intra-tumor variability. Nevertheless, the technique is only semi-quantitative. To quantitate the mutant protein there is a fundamental need for more precise techniques that are aimed at defining the currently non-existent link between the levels of the target protein and subsequent drug efficacy. Using cutting-edge mass spectrometry combined with DNA and mRNA sequencing, the mutated B-raf protein within metastatic tumors was quantitated for the first time. B-raf V600E protein analysis revealed a subjacent layer of heterogeneity for mutation-positive metastatic melanomas. These were characterized into two distinct groups with different tumor morphologies, protein profiles and patient clinical outcomes. This study provides evidence that a higher level of expression in the mutated protein is associated with a more aggressive tumor progression. Our study design, comprised of surgical isolation of tumors, histopathological characterization, tissue biobanking, and protein analysis, may enable the eventual delineation of patient responders/non-responders and subsequent therapy for malignant melanoma.
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| 9. |
- Bustamante, Mariana, et al.
(author)
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Atlas-based analysis of 4D flow CMR: Automated vessel segmentation and flow quantification
- 2015
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In: Journal of Cardiovascular Magnetic Resonance. - : BIOMED CENTRAL LTD. - 1097-6647 .- 1532-429X. ; 17:87
-
Journal article (peer-reviewed)abstract
- Background: Flow volume quantification in the great thoracic vessels is used in the assessment of several cardiovascular diseases. Clinically, it is often based on semi-automatic segmentation of a vessel throughout the cardiac cycle in 2D cine phase-contrast Cardiovascular Magnetic Resonance (CMR) images. Three-dimensional (3D), time-resolved phase-contrast CMR with three-directional velocity encoding (4D flow CMR) permits assessment of net flow volumes and flow patterns retrospectively at any location in a time-resolved 3D volume. However, analysis of these datasets can be demanding. The aim of this study is to develop and evaluate a fully automatic method for segmentation and analysis of 4D flow CMR data of the great thoracic vessels. Methods: The proposed method utilizes atlas-based segmentation to segment the great thoracic vessels in systole, and registration between different time frames of the cardiac cycle in order to segment these vessels over time. Additionally, net flow volumes are calculated automatically at locations of interest. The method was applied on 4D flow CMR datasets obtained from 11 healthy volunteers and 10 patients with heart failure. Evaluation of the method was performed visually, and by comparison of net flow volumes in the ascending aorta obtained automatically (using the proposed method), and semi-automatically. Further evaluation was done by comparison of net flow volumes obtained automatically at different locations in the aorta, pulmonary artery, and caval veins. Results: Visual evaluation of the generated segmentations resulted in good outcomes for all the major vessels in all but one dataset. The comparison between automatically and semi-automatically obtained net flow volumes in the ascending aorta resulted in very high correlation (r(2) = 0.926). Moreover, comparison of the net flow volumes obtained automatically in other vessel locations also produced high correlations where expected: pulmonary trunk vs. proximal ascending aorta (r(2) = 0.955), pulmonary trunk vs. pulmonary branches (r(2) = 0.808), and pulmonary trunk vs. caval veins (r(2) = 0.906). Conclusions: The proposed method allows for automatic analysis of 4D flow CMR data, including vessel segmentation, assessment of flow volumes at locations of interest, and 4D flow visualization. This constitutes an important step towards facilitating the clinical utility of 4D flow CMR.
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| 10. |
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| 11. |
- Cibis, Merih, et al.
(author)
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Creating Hemodynamic Atlases of Cardiac 4D Flow MRI
- 2017
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In: Journal of Magnetic Resonance Imaging. - : WILEY. - 1053-1807 .- 1522-2586. ; 46:5, s. 1389-1399
-
Journal article (peer-reviewed)abstract
- Purpose: Hemodynamic atlases can add to the pathophysiological understanding of cardiac diseases. This study proposes a method to create hemodynamic atlases using 4D Flow magnetic resonance imaging (MRI). The method is demonstrated for kinetic energy (KE) and helicity density (Hd). Materials and Methods: Thirteen healthy subjects underwent 4D Flow MRI at 3T. Phase-contrast magnetic resonance cardioangiographies (PC-MRCAs) and an average heart were created and segmented. The PC-MRCAs, KE, and Hd were nonrigidly registered to the average heart to create atlases. The method was compared with 1) rigid, 2) affine registration of the PC-MRCAs, and 3) affine registration of segmentations. The peak and mean KE and Hd before and after registration were calculated to evaluate interpolation error due to nonrigid registration. Results: The segmentations deformed using nonrigid registration overlapped (median: 92.3%) more than rigid (23.1%, P amp;lt; 0.001), and affine registration of PC-MRCAs (38.5%, P amp;lt; 0.001) and affine registration of segmentations (61.5%, P amp;lt; 0.001). The peak KE was 4.9 mJ using the proposed method and affine registration of segmentations (P50.91), 3.5 mJ using rigid registration (P amp;lt; 0.001), and 4.2 mJ using affine registration of the PC-MRCAs (P amp;lt; 0.001). The mean KE was 1.1 mJ using the proposed method, 0.8 mJ using rigid registration (P amp;lt; 0.001), 0.9 mJ using affine registration of the PC-MRCAs (P amp;lt; 0.001), and 1.0 mJ using affine registration of segmentations (P50.028). The interpolation error was 5.262.6% at mid-systole, 2.863.8% at early diastole for peak KE; 9.669.3% at mid-systole, 4.064.6% at early diastole, and 4.964.6% at late diastole for peak Hd. The mean KE and Hd were not affected by interpolation. Conclusion: Hemodynamic atlases can be obtained with minimal user interaction using nonrigid registration of 4D Flow MRI. Level of Evidence: 2 Technical Efficacy: Stage 1
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| 12. |
- Danielson, Mattias, et al.
(author)
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Neuroinflammatory markers associate with cognitive decline after major surgery: Findings of an explorative study
- 2020
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In: Annals of Neurology. - : Wiley. - 0364-5134 .- 1531-8249. ; 87:3, s. 370-382
-
Journal article (peer-reviewed)abstract
- Objective Long-term cognitive decline is an adverse outcome after major surgery associated with increased risk for mortality and morbidity. We studied the cerebrospinal fluid (CSF) and serum biochemical inflammatory response to a standardized orthopedic surgical procedure and the possible association with long-term changes in cognitive function. We hypothesized that the CSF inflammatory response pattern after surgery would differ in patients having long-term cognitive decline defined as a composite cognitive z score of >= 1.0 compared to patients without long-term cognitive decline at 3 months postsurgery. Methods Serum and CSF biomarkers of inflammation and blood-brain barrier (BBB) integrity were measured preoperatively and up to 48 hours postoperatively, and cognitive function was assessed preoperatively and at 2 to 5 days and 3 months postoperatively. Results Surgery was associated with a pronounced increase in inflammatory biomarkers in both CSF and blood throughout the 48-hour study period. A principal component (PC) analysis was performed on 52 inflammatory biomarkers. The 2 first PC (PC1 and PC2) construct outcome variables on CSF biomarkers were significantly associated with long-term cognitive decline at 3 months, but none of the PC construct serum variables showed a significant association with long-term cognitive decline at 3 months. Patients both with and patients without long-term cognitive decline showed early transient increases of the astroglial biomarkers S-100B and glial fibrillary acidic protein in CSF, and in BBB permeability (CSF/serum albumin ratio). Interpretation Surgery rapidly triggers a temporal neuroinflammatory response closely associated with long-term cognitive outcome postsurgery. The findings of this explorative study require validation in a larger surgical patient cohort.
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| 13. |
- Danielsson, Mattias, et al.
(author)
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Association between cerebrospinal fluid biomarkers of neuronal injury or amyloidosis and cognitive decline after major surgery.
- 2021
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In: British journal of anaesthesia. - : Elsevier BV. - 1471-6771 .- 0007-0912. ; 126:2, s. 467-76
-
Journal article (peer-reviewed)abstract
- Postoperative neurocognitive decline is a frequent complication in adult patients undergoing major surgery with increased risk for morbidity and mortality. The mechanisms behind cognitive decline after anaesthesia and surgery are not known. We studied the association between CSF and blood biomarkers of neuronal injury or brain amyloidosis and long-term changes in neurocognitive function.In patients undergoing major orthopaedic surgery (knee or hip replacement), blood and CSF samples were obtained before surgery and then at 4, 8, 24, 32, and 48 h after skin incision through an indwelling spinal catheter. CSF and blood concentrations of total tau (T-tau), neurofilament light, neurone-specific enolase and amyloid β (Aβ1-42) were measured. Neurocognitive function was assessed using the International Study of Postoperative Cognitive Dysfunction (ISPOCD) test battery 1-2 weeks before surgery, at discharge from the hospital (2-5 days after surgery), and at 3 months after surgery.CSF and blood concentrations of T-tau, neurone-specific enolase, and Aβ1-42 increased after surgery. A similar increase in serum neurofilament light was seen with no overall changes in CSF concentrations. There were no differences between patients having a poor or good late postoperative neurocognitive outcome with respect to these biomarkers of neuronal injury and Aβ1-42.The findings of the present explorative study showed that major orthopaedic surgery causes a release of CSF markers of neural injury and brain amyloidosis, suggesting neuronal damage or stress. We were unable to detect an association between the magnitude of biomarker changes and long-term postoperative neurocognitive dysfunction.
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| 14. |
- Dyverfeldt, Petter, et al.
(author)
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Extending 4D Flow Visualization to the Human Right Ventricle
- 2009
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In: Proceedings of International Society for Magnetic Resonance in Medicine: 17th Scientific Meeting 2009. - : International Society for Magnetic Resonance in Medicine. ; , s. 3860-3860
-
Conference paper (peer-reviewed)abstract
- The right ventricle has an important role in cardiovascular disease. However, because of the complex geometry and the sensitivity to the respiratory cycle, imaging of the right ventricle is challenging. We investigated whether 3D cine phase-contrast MRI can provide data with sufficient accuracy for visualizations of the 4D blood flow in the right ventricle. Whole-heart 4D flow measurements with optimized imaging parameters and post-processing tools were made in healthy volunteers. Pathlines emitted from the right atrium could be traced through the right ventricle to the pulmonary artery without leaving the blood pool and thereby met our criteria for sufficient accuracy.
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| 15. |
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| 16. |
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| 17. |
- Eriksson, Alexander, et al.
(author)
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Virtual factory layouts from 3D laser scanning – A novel framework to define solid model requirements
- 2018
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In: Procedia CIRP. - : Elsevier BV. - 2212-8271. ; 76, s. 36-41
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Conference paper (peer-reviewed)abstract
- In a world with increasing customer demands, manufacturing companies must develop and produce products more rapidly and adapt their production systems offline, to not disturb the ongoing processes. This creates a demand of using digital production development so that development can be performed in parallel with production. Virtual factory layouts (VFLs) are essential for companies in order to plan their factory layout and evaluate production scenarios. However, requirements for a VFL depends heavily on its purpose. For example, the requirements on a model for offline programming of robots are different from those on a model used to determine buffer locations. There is currently a lack of clear guidelines for how developed a VFL should be to fulfil said requirements, which contributes to unnecessary modelling time and variation in delivery quality. This paper aims to put the actual demands and requirements of a VFL in focus. By adapting a Level of Development-framework for establishment of Building Information Models (BIMs) and connecting it to the purpose of VFLs, development of a framework for detail and functionality level of VFLs is enabled. Such a purpose-oriented framework will help to define delivery packages suited for different circumstances, which will provide the modeler with knowledge of how much detail and functionality a specific model should contain. The increased clarity provided by the developed framework results in a clearer connection between expected result and actual output from a custom VFL project. Also, by connecting model properties or development to the model-purpose, the framework brings clarity and structure to a currently vague field. This provides means for a more efficient and accurate use of VFLs, which will support the rapid development of production facilities.
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| 18. |
- Eriksson, Gustav, et al.
(author)
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Boundary and interface methods for energy stable finite difference discretizations of the dynamic beam equation
- 2023
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In: Journal of Computational Physics. - : Elsevier. - 0021-9991 .- 1090-2716. ; 476
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Journal article (peer-reviewed)abstract
- We consider energy stable summation by parts finite difference methods (SBP-FD) for the homogeneous and piecewise homogeneous dynamic beam equation (DBE). Previously the constant coefficient problem has been solved with SBP-FD together with penalty terms (SBP-SAT) to impose boundary conditions. In this work, we revisit this problem and compare SBP-SAT to the projection method (SBP-P). We also consider the DBE with discontinuous coefficients and present novel SBP-SAT, SBP-P, and hybrid SBP-SAT-P discretizations for imposing interface conditions. To demonstrate the methodology for two-dimensional problems, we also present a discretization of the piecewise homogeneous dynamic Kirchoff-Love plate equation based on the hybrid SBP-SAT-P method. Numerical experiments show that all methods considered are similar in terms of accuracy, but that SBP-P can be more computationally efficient (less restrictive time step requirement for explicit time integration methods) for both the constant and piecewise constant coefficient problems.
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| 19. |
- Eriksson, Jonatan
(author)
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Algorithms and Methods for Robust Processing and Analysis of Mass Spectrometry Data
- 2021
-
Doctoral thesis (other academic/artistic)abstract
- Liquid chromatography-mass spectrometry (LC-MS) and mass spectrometry imaging (MSI) are two techniques that are routinely used to study proteins, peptides, and metabolites at a large scale. Thousands of biological compounds can be identified and quantified in a single experiment with LC-MS, but many studies fail to convert this data to a better understanding of disease biology. One of the primary reasons for this is low reproducibility, which in turn is partially due to inaccurate and/or inconsistent data processing. Protein biomarkers and signatures for various types of cancer are frequently discovered with LC-MS, but their behavior in independent cohorts is often inconsistent to that in the discovery cohort. Biomarker candidates must be thoroughly validated in independent cohorts, which makes the ability to share data across different laboratories crucial to the future success of the MS-based research fields. The emergence and growth of public repositories for MSI data is a step in the rightdirection. Still, many of those data sets remain incompatible one another due to inaccurate or incompatible preprocessing strategies. Ensuring compatibility between data generated in different labs is therefore necessary to gain access to the full potential of MS-based research. In two of the studies that I present in this thesis, we used LC-MS to characterize lymph node metastases from individuals with melanoma. Furthermore, my thesis work has resulted in two novel preprocessing methods for MSI data sets. The first one is a peak detection method that achieves considerably higher sensitivity for faintly expressed compounds than existing methods, and the second one is a accurate, robust, and general approach to mass alignment. Both algorithms deliberately rely on centroid spectra, which makes them compatible with most shared data sets. I believe that the improvements demonstrated by these methods can lead to a higher reproducibility in the MS-based research fields, and, ultimately, to a better understanding of disease processes.
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| 20. |
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| 21. |
- Eriksson, Jonatan, et al.
(author)
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Four-dimensional blood flow-specific markers of LV dysfunction in dilated cardiomyopathy
- 2013
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In: European Heart Journal Cardiovascular Imaging. - : Oxford University Press. - 2047-2404 .- 2047-2412. ; 14:5, s. 417-424
-
Journal article (peer-reviewed)abstract
- Aims : Patients with mild heart failure (HF) who are clinically compensated may have normal left ventricular (LV) stroke volume (SV). Despite this, altered intra-ventricular flow patterns have been recognized in these subjects. We hypothesized that, compared with normal LVs, flow in myopathic LVs would demonstrate a smaller proportion of inflow volume passing directly to ejection and diminished the end-diastolic preservation of the inflow kinetic energy (KE).Methods and results : In 10 patients with dilated cardiomyopathy (DCM) (49 ± 14 years, six females) and 10 healthy subjects (44 ± 17 years, four females), four-dimensional MRI velocity and morphological data were acquired. A previously validated method was used to separate the LV end-diastolic volume (EDV) into four flow components based on the blood's locations at the beginning and end of the cardiac cycle. KE was calculated over the cardiac cycle for each component. The EDV was larger (P = 0.021) and the ejection fraction smaller (P < 0.001) in DCM compared with healthy subjects; the SV was equivalent (DCM: 77 ± 19, healthy: 79 ± 16 mL). The proportion of the total LV inflow that passed directly to ejection was smaller in DCM (P = 0.000), but the end-diastolic KE/mL of the direct flow was not different in the two groups (NS).Conclusion : Despite equivalent LVSVs, HF patients with mild LV remodelling demonstrate altered diastolic flow routes through the LV and impaired preservation of inflow KE at pre-systole compared with healthy subjects. These unique flow-specific changes in the flow route and energetics are detectable despite clinical compensation, and may prove useful as subclinical markers of LV dysfunction.
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| 22. |
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| 23. |
- Eriksson, Jonatan, et al.
(author)
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Left ventricular hemodynamic forces as a marker of mechanical dyssynchrony in heart failure patients with left bundle branch block
- 2017
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In: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 7
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Journal article (peer-reviewed)abstract
- Left bundle branch block (LBBB) causes left ventricular (LV) dyssynchrony which is often associated with heart failure. A significant proportion of heart failure patients do not demonstrate clinical improvement despite cardiac resynchronization therapy (CRT). How LBBB-related effects on LV diastolic function may contribute to those therapeutic failures has not been clarified. We hypothesized that LV hemodynamic forces calculated from 4D flow MRI could serve as a marker of diastolic mechanical dyssynchrony in LBBB hearts. MRI data were acquired in heart failure patients with LBBB or matched patients without LBBB. LV pressure gradients were calculated from the Navier-Stokes equations. Integration of the pressure gradients over the LV volume rendered the hemodynamic forces. The findings demonstrate that the LV filling forces are more orthogonal to the main LV flow direction in heart failure patients with LBBB compared to those without LBBB during early but not late diastole. The greater the conduction abnormality the greater the discordance of LV filling force with the predominant LV flow direction (r(2) = 0.49). Such unique flow-specific measures of mechanical dyssynchrony may serve as an additional tool for considering the risks imposed by conduction abnormalities in heart failure patients and prove to be useful in predicting response to CRT.
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| 24. |
- Eriksson, Jonatan, et al.
(author)
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Merging clinical chemistry biomarker data with a COPD database - building a clinical infrastructure for proteomic studies
- 2017
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In: Proteome Science. - : Springer Science and Business Media LLC. - 1477-5956. ; 15:1
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Journal article (peer-reviewed)abstract
- Background: Data from biological samples and medical evaluations plays an essential part in clinical decision making. This data is equally important in clinical studies and it is critical to have an infrastructure that ensures that its quality is preserved throughout its entire lifetime. We are running a 5-year longitudinal clinical study, KOL-Örestad, with the objective to identify new COPD (Chronic Obstructive Pulmonary Disease) biomarkers in blood. In the study, clinical data and blood samples are collected from both private and public health-care institutions and stored at our research center in databases and biobanks, respectively. The blood is analyzed by Mass Spectrometry and the results from this analysis then linked to the clinical data. Method: We built an infrastructure that allows us to efficiently collect and analyze the data. We chose to use REDCap as the EDC (Electronic Data Capture) tool for the study due to its short setup-time, ease of use, and flexibility. REDCap allows users to easily design data collection modules based on existing templates. In addition, it provides two functions that allow users to import batches of data; through a web API (Application Programming Interface) as well as by uploading CSV-files (Comma Separated Values). Results: We created a software, DART (Data Rapid Translation), that translates our biomarker data into a format that fits REDCap's CSV-templates. In addition, DART is configurable to work with many other data formats as well. We use DART to import our clinical chemistry data to the REDCap database. Conclusion: We have shown that a powerful and internationally adopted EDC tool such as REDCap can be extended so that it can be used efficiently in proteomic studies. In our study, we accomplish this by using DART to translate our clinical chemistry data to a format that fits the templates of REDCap.
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| 25. |
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| 26. |
- Eriksson, Jonatan
(author)
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Monotonicity in the volatility of single-barrier option prices
- 2006
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In: International Journal of Theoretical and Applied Finance. - 0219-0249. ; 9:6, s. 987-996
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Journal article (peer-reviewed)abstract
- We generalize earlier results on barrier options for puts and calls and log-normal stock processes to general local volatility models and convex contracts. We show that Γ ≥ 0, that Δ has a unique sign and that the option price is increasing with the volatility for convex contracts in the following cases: If the risk-free rate of return dominates the dividend rate, then it holds for up-and-out options if the contract function is zero at the barrier and for down-and-in options in general. If the risk-free rate of return is dominated by the dividend rate, then it holds for down-and-out options if the contract function is zero at the barrier and for up-and-in options in general. We apply our results to show that a hedger who misspecifies the volatility using a time-and-level dependent volatility will super-replicate any claim satisfying the above conditions if the misspecified volatility dominates the true (possibly stochastic) volatility almost surely.
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| 27. |
- Eriksson, Jonatan O., et al.
(author)
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Clusterwise Peak Detection and Filtering Based on Spatial Distribution to Efficiently Mine Mass Spectrometry Imaging Data
- 2019
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In: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; , s. 11888-11896
-
Journal article (peer-reviewed)abstract
- Mass spectrometry imaging (MSI) has the potential to reveal the localization of thousands of biomolecules such as metabolites and lipids in tissue sections. The increase in both mass and spatial resolution of today's instruments brings on considerable challenges in terms of data processing; accurately extracting meaningful signals from the large data sets generated by MSI without losing information that could be clinically relevant is one of the most fundamental tasks of analysis software. Ion images of the biomolecules are generated by visualizing their intensities in 2-D space using mass spectra collected across the tissue section. The intensities are often calculated by summing each compound's signal between predefined sets of borders (bins) in the m/z dimension. This approach, however, can result in mixed signals from different compounds in the same bin or splitting the signal from one compound between two adjacent bins, leading to low quality ion images. To remedy this problem, we propose a novel data processing approach. Our approach consists of a sensitive peak detection method able to discover both faint and localized signals by utilizing clusterwise kernel density estimates (KDEs) of peak distributions. We show that our method can recall more ground-truth molecules, molecule fragments, and isotopes than existing methods based on binning. Furthermore, it automatically detects previously reported molecular ions of lipids, including those close in m/z, in an experimental data set.
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| 28. |
- Eriksson, Jonatan O., et al.
(author)
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MSIWarp : A General Approach to Mass Alignment in Mass Spectrometry Imaging
- 2020
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In: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 92:24, s. 16138-16148
-
Journal article (peer-reviewed)abstract
- Mass spectrometry imaging (MSI) is a technique that provides comprehensive molecular information with high spatial resolution from tissue. Today, there is a strong push toward sharing data sets through public repositories in many research fields where MSI is commonly applied; yet, there is no standardized protocol for analyzing these data sets in a reproducible manner. Shifts in the mass-to-charge ratio (m/z) of molecular peaks present a major obstacle that can make it impossible to distinguish one compound from another. Here, we present a label-free m/z alignment approach that is compatible with multiple instrument types and makes no assumptions on the sample's molecular composition. Our approach, MSIWarp (https://github.com/horvatovichlab/MSIWarp), finds an m/z recalibration function by maximizing a similarity score that considers both the intensity and m/z position of peaks matched between two spectra. MSIWarp requires only centroid spectra to find the recalibration function and is thereby readily applicable to almost any MSI data set. To deal with particularly misaligned or peak-sparse spectra, we provide an option to detect and exclude spurious peak matches with a tailored random sample consensus (RANSAC) procedure. We evaluate our approach with four publicly available data sets from both time-of-flight (TOF) and Orbitrap instruments and demonstrate up to 88% improvement in m/z alignment.
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| 29. |
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| 30. |
- Eriksson, Jonatan, 1975-
(author)
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On the pricing equations of some path-dependent options
- 2006
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Doctoral thesis (other academic/artistic)abstract
- This thesis consists of four papers and a summary. The common topic of the included papers are the pricing equations of path-dependent options. Various properties of barrier options and American options are studied, such as convexity of option prices, the size of the continuation region in American option pricing and pricing formulas for turbo warrants. In Paper I we study the effect of model misspecification on barrier option pricing. It turns out that, as in the case of ordinary European and American options, this is closely related to convexity properties of the option prices. We show that barrier option prices are convex under certain conditions on the contract function and on the relation between the risk-free rate of return and the dividend rate. In Paper II a new condition is given to ensure that the early exercise feature in American option pricing has a positive value. We give necessary and sufficient conditions for the American option price to coincide with the corresponding European option price in at least one diffusion model. In Paper III we study parabolic obstacle problems related to American option pricing and in particular the size of the non-coincidence set. The main result is that if the boundary of the set of points where the obstacle is a strict subsolution to the differential equation is C1-Dini in space and Lipschitz in time, there is a positive distance, which is uniform in space, between the boundary of this set and the boundary of the non-coincidence set. In Paper IV we derive explicit pricing formulas for turbo warrants under the classical Black-Scholes assumptions.
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| 31. |
- Eriksson, Jonatan, 1983-
(author)
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Quantification of 4D Left Ventricular Blood Flow in Health and Disease
- 2013
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Doctoral thesis (other academic/artistic)abstract
- The main function of the heart is to pump blood throughout the cardiovascular system by generating pressure differences created through volume changes. Although the main purpose of the heart and vessels is to lead the flowing blood throughout the body, clinical assessments of cardiac function are usually based on morphology, approximating the flow features by viewing the motion of the myocardium and vessels. Measurement of three-directional, three-dimensional and time-resolved velocity (4D Flow) data is feasible using magnetic resonance (MR). The focus of this thesis is the development and application of methods that facilitate the analysis of larger groups of data in order to increase our understanding of intracardiac flow patterns and take the 4D flow technique closer to the clinical setting.In the first studies underlying this thesis, a pathline based method for analysis of intra ventricular blood flow patterns has been implemented and applied. A pathline is integrated from the velocity data and shows the path an imaginary massless particle would take through the data volume. This method separates the end-diastolic volume (EDV) into four functional components, based on the position for each individual pathline at end-diastole (ED) and end-systole (ES). This approach enables tracking of the full EDV over one cardiac cycle and facilitates calculation of parameters such as e.g. volumes and kinetic energy (KE). Besides blood flow, pressure plays an important role in the cardiac dynamics. In order to study this parameter in the left ventricle, the relative pressure field was computed using the pressure Poisson equation. A comprehensive presentation of the pressure data was obtained dividing the LV blood pool into 17 pie-shaped segments based on a modification of the standard seventeen segment model. Further insight into intracardiac blood flow dynamics was obtained by studying the turbulent kinetic energy (TKE) in the LV. The methods were applied to data from a group of healthy subjects and patients with dilated cardiomyopathy (DCM). DCM is a pathological state where the cardiac function is impaired and the left ventricle or both ventricles are dilated.The validation study of the flow analysis method showed that a reliable user friendly tool for intra ventricular blood flow analysis was obtained. The application of this tool also showed that roughly one third of the blood that enters the LV, directly leaves the LV again in the same heart beat. The distribution of the four LV EDV components was altered in the DCM group as compared to the healthy group; the component that enters and leaves the LV during one cardiac cycle (Direct Flow) was significantly larger in the healthy subjects. Furthermore, when the kinetic energy was normalized by the volume for each component, at time of ED, the Direct Flow had the highest values in the healthy subjects. In the DCM group, however, the Retained Inflow and Delayed Ejection Flow had higher values. The relative pressure field showed to be highly heterogeneous, in the healthy heart. During diastole the predominate pressure differences in the LV occur along the long axis from base to apex. The distribution and variability of 3D pressure fields differ between early and late diastolic filling phases, but common to both phases is a relatively lower pressure in the outflow segment. In the normal LV, TKE values are low. The highest TKE values can be seen during early diastole and are regionally distributed near the basal LV regions. In contrast, in a heterogeneous group of DCM patients, total diastolic and late diastolic TKE values are higher than in normals, and increase with the LV volume.In conclusion, in this thesis, methods for analysis of multidirectional intra cardiac velocity data have been obtained. These methods allow assessment of data quality, intra cardiac blood flow patterns, relative pressure fields, and TKE. Using these methods, new insights have been obtained in intra cardiac blood flow dynamics in health and disease. The work underlying this thesis facilitates assessment of data from a larger population of healthy subjects and patients, thus bringing the 4D Flow MRI technique closer to the clinical setting.
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| 32. |
- Eriksson, Jonatan, et al.
(author)
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Quantification of presystolic blood flow organization and energetics in the human left ventricle
- 2011
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In: AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY. - : AMER PHYSIOLOGICAL SOC, 9650 ROCKVILLE PIKE, BETHESDA, MD 20814 USA. - 0363-6135 .- 1522-1539. ; 300:6, s. H2135-H2141
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Journal article (peer-reviewed)abstract
- Intracardiac blood flow patterns are potentially important to cardiac pumping efficiency. However, these complex flow patterns remain incompletely characterized both in health and disease. We hypothesized that normal left ventricular (LV) blood flow patterns would preferentially optimize a portion of the end-diastolic volume (LVEDV) for effective and rapid systolic ejection by virtue of location near and motion towards the LV outflow tract (LVOT). Three-dimensional cine velocity and morphological data were acquired in 12 healthy persons and 1 patient with dilated cardiomyopathy using MRI. A previously validated method was used for analysis in which the LVEDV was separated into four functional flow components based on the bloods locations at the beginning and end of the cardiac cycle. Each components volume, kinetic energy (KE), site, direction, and linear momentum relative to the LVOT were calculated. Of the four components, the LV inflow that passes directly to outflow in a single cardiac cycle (Direct Flow) had the largest volume. At the time of isovolumic contraction, Direct Flow had the greatest amount of KE and the most favorable combination of distance, angle, and linear momentum relative to the LVOT. Atrial contraction boosted the late diastolic KE of the ejected components. We conclude that normal diastolic LV flow creates favorable conditions for ensuing ejection, defined by proximity and energetics, for the Direct Flow, and that atrial contraction augments the end-diastolic KE of the ejection volume. The correlation of Direct Flow characteristics with ejection efficiency might be a relevant investigative target in cardiac failure.
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| 33. |
- Eriksson, Jonatan, et al.
(author)
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Semi-automatic quantification of 4D left ventricular blood flow
- 2010
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In: JOURNAL OF CARDIOVASCULAR MAGNETIC RESONANCE. - 1097-6647. ; 12:9
-
Journal article (peer-reviewed)abstract
- Background: The beating heart is the generator of blood flow through the cardiovascular system. Within the hearts own chambers, normal complex blood flow patterns can be disturbed by diseases. Methods for the quantification of intra-cardiac blood flow, with its 4D (3D+time) nature, are lacking. We sought to develop and validate a novel semi-automatic analysis approach that integrates flow and morphological data. Method: In six healthy subjects and three patients with dilated cardiomyopathy, three-directional, three-dimensional cine phase-contrast cardiovascular magnetic resonance (CMR) velocity data and balanced steady-state free-precession long- and short-axis images were acquired. The LV endocardium was segmented from the short-axis images at the times of isovolumetric contraction (IVC) and isovolumetric relaxation (IVR). At the time of IVC, pathlines were emitted from the IVC LV blood volume and traced forwards and backwards in time until IVR, thus including the entire cardiac cycle. The IVR volume was used to determine if and where the pathlines left the LV. This information was used to automatically separate the pathlines into four different components of flow: Direct Flow, Retained Inflow, Delayed Ejection Flow and Residual Volume. Blood volumes were calculated for every component by multiplying the number of pathlines with the blood volume represented by each pathline. The accuracy and inter- and intra-observer reproducibility of the approach were evaluated by analyzing volumes of LV inflow and outflow, the four flow components, and the end-diastolic volume. Results: The volume and distribution of the LV flow components were determined in all subjects. The calculated LV outflow volumes [ml] (67 +/- 13) appeared to fall in between those obtained by through-plane phase-contrast CMR (77 +/- 16) and Doppler ultrasound (58 +/- 10), respectively. Calculated volumes of LV inflow (68 +/- 11) and outflow (67 +/- 13) were well matched (NS). Low inter- and intra-observer variability for the assessment of the volumes of the flow components was obtained. Conclusions: This semi-automatic analysis approach for the quantification of 4D blood flow resulted in accurate LV inflow and outflow volumes and a high reproducibility for the assessment of LV flow components.
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| 34. |
- Eriksson, Jonatan, et al.
(author)
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Spatial heterogeneity of 4D relative pressure fields in the human left ventricle
- 2013
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Other publication (other academic/artistic)abstract
- Blood flow throughout the cardiovascular system is driven by pressure differences generated by the contraction and relaxation of the heart, where blood accelerates from high to low pressure areas. Absolute intracardiac pressure cannot be measured noninvasively, but relative pressure can be calculated. The aim of this study was to assess the spatial heterogeneity of the 4D relative pressure fields in the human left ventricle (LV).Twelve healthy subjects underwent MRI examination where 4D flow as well as morphological data were acquired. The morphological data were segmented, and the segmentation used as boundary condition when computing relative pressure fields from the pressure Poisson equation using a multi grid solver. The LV lumen was divided according to a seventeen segment model in order to assess spatial heterogeneity and present the extensive amount of data in a comprehensive manner.The basal anteroseptal segment shows a significantly lower median pressure than the opposite basal inferolateral segment during both early and late diastolic filling (p<0.0005 and p=0.0024, respectively). Along the long axis, the relative pressure in the apical segments are significantly higher relative to the basal segments (p<0.0005) along both the anteroseptal and inferolateral sides at and after the peaks of E-wave and A-wave.During diastole the main pressure differences in the LV occur along the basal-apical axis. However, pressure differences can also be found in the short-axis direction, and may also reflect important aspects of atrioventricular coupling.
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| 35. |
- Eriksson, Jonatan, et al.
(author)
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Spatial Heterogeneity of Four-Dimensional Relative Pressure Fields in the Human Left Ventricle
- 2015
-
In: Magnetic Resonance in Medicine. - : WILEY-BLACKWELL. - 0740-3194 .- 1522-2594. ; 74:6, s. 1716-1725
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Journal article (peer-reviewed)abstract
- Purpose: To assess the spatial heterogeneity of the four-dimensional (4D) relative pressure fields in the healthy human left ventricle (LV) and provide reference data for normal LV relative pressure. Methods: Twelve healthy subjects underwent a cardiac MRI examination where 4D flow and morphological data were acquired. The latter data were segmented and used to define the borders of the LV for computation of relative pressure fields using the pressure Poisson equation. The LV lumen was divided into 17 pie-shaped segments. Results: In the normal left ventricle, the relative pressure in the apical segments was significantly higher relative to the basal segments (P < 0.0005) along both the anteroseptal and inferolateral sides after the peaks of early (E-wave) and late (A-wave) diastolic filling. The basal anteroseptal segment showed significantly lower median pressure than the opposite basal inferolateral segment during both E-wave (P < 0.0005) and A-wave (P = 0.0024). Conclusion: Relative pressure in the left ventricle is heterogeneous. During diastole, the main pressure differences in the LV occur along the basal-apical axis. However, pressure differences were also found in the short axis direction and may reflect important aspects of atrioventricular coupling. Additionally, this study provides reference data on LV pressure dynamics for a group of healthy subjects. (C) 2014 Wiley Periodicals, Inc.
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| 36. |
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| 37. |
- Fredriksson, Alexandru G, et al.
(author)
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4-D blood flow in the human right ventricle
- 2011
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In: American Journal of Physiology. Heart and Circulatory Physiology. - : American Physiological Society. - 0363-6135 .- 1522-1539. ; 301:6, s. H2344-H2350
-
Journal article (peer-reviewed)abstract
- Right ventricular (RV) function is a powerful prognostic indicator in many forms of heart disease, but its assessment remains challenging and inexact. RV dysfunction may alter the normal patterns of RV blood flow, but those patterns have been incompletely characterized. We hypothesized that, based on anatomic differences, the proportions and energetics of RV flow components would differ from those identified in the left ventricle (LV) and that the portion of the RV inflow passing directly to outflow (Direct Flow) would be prepared for effective systolic ejection as a result of preserved kinetic energy (KE) compared with other RV flow components. Three-dimensional, time-resolved phase-contrast velocity, and balanced steady-state free-precession morphological data were acquired in 10 healthy subjects using MRI. A previously validated method was used to separate the RV and LV end-diastolic volumes into four flow components and measure their volume and KE over the cardiac cycle. The RV Direct Flow: 1) followed a smoothly curving route that did not extend into the apical region of the ventricle; 2) had a larger volume and possessed a larger presystolic KE (0.4 +/- 0.3 mJ) than the other flow components (P andlt; 0.001 and P andlt; 0.01, respectively); and 3) represented a larger part of the end-diastolic blood volume compared with the LV Direct Flow (P andlt; 0.01). These findings suggest that diastolic flow patterns distinct to the normal RV create favorable conditions for ensuing systolic ejection of the Direct Flow component. These flow-specific aspects of RV diastolic-systolic coupling provide novel perspectives on RV physiology and may add to the understanding of RV pathophysiology.
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| 38. |
- Fredriksson, Alexandru Grigorescu, et al.
(author)
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4D flow MRI can detect subtle right ventricular dysfunction in primary left ventricular disease.
- 2016
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In: Journal of Magnetic Resonance Imaging. - : Wiley-Blackwell. - 1053-1807 .- 1522-2586. ; 43:3, s. 558-565
-
Journal article (peer-reviewed)abstract
- PURPOSE: To investigate whether 4D flow magnetic resonance imaging (MRI) can detect subtle right ventricular (RV) dysfunction in primary left ventricular (LV) disease.MATERIALS AND METHODS: 4D flow and morphological 3T MRI data were acquired in 22 patients with mild ischemic heart disease who were stratified into two groups based on LV end-diastolic volume index (EDVI): lower-LVEDVI and higher-LVEDVI, as well as in 11 healthy controls. The RV volume was segmented at end-diastole (ED) and end-systole (ES). Pathlines were emitted from the ED volume and traced forwards and backwards in time to ES. The blood volume was separated into flow components. The Direct Flow (DF) component was defined as RV inflow passing directly to outflow. The kinetic energy (KE) of the DF component was calculated. Echocardiographic conventional RV indices were also assessed.RESULTS: The higher-LVEDVI group had larger LVEDVI and lower LV ejection fraction (98 ± 32 ml/m(2) ; 48 ± 13%) compared to the healthy (67 ± 12, P = 0.002; 64 ± 7, P < 0.001) and lower-LVEDI groups (62 ± 10; 68 ± 7, both P < 0.001). The RV 4D flow-specific measures "DF/EDV volume-ratio" and "DF/EDV KE-ratio at ED" were lower in the higher-LVEDVI group (38 ± 5%; 52 ± 6%) compared to the healthy (44 ± 6; 65 ± 7, P = 0.018 and P < 0.001) and lower-LVEDVI groups (44 ± 6; 64 ± 7, P = 0.011 and P < 0.001). There was no difference in any of the conventional MRI and echocardiographic RV indices between the three groups.CONCLUSION: We found that in primary LV disease mild impairment of RV function can be detected by 4D flow-specific measures, but not by the conventional MRI and echocardiographic indices. J. Magn. Reson. Imaging 2015.
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| 39. |
- Gaeta, Stephen, et al.
(author)
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Fixed volume particle trace emission for the analysis of left atrial blood flow using 4D Flow MRI
- 2018
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In: Magnetic Resonance Imaging. - : ELSEVIER SCIENCE INC. - 0730-725X .- 1873-5894. ; 47, s. 83-88
-
Journal article (peer-reviewed)abstract
- 4D Flow MRI has been used to quantify normal and deranged left ventricular blood flow characteristics on the basis of functionally distinct flow components. However, the application of this technique to the atria is challenging due to the presence of continuous inflow. This continuous inflow necessitates plane-based emission of particle traces from the inlet veins, leading to particles that represents different amounts of blood, and related quantification errors. The purpose of this study was to develop a novel fixed-volume approach for particle tracing and employ this method to develop quantitative analysis of 4D blood flow characteristics in the left atrium. 4D Flow MRI data were acquired during free-breathing using a navigator-gated gradient-echo sequence in three volunteers at 1.5 T. Fixed-volume particle traces emitted from the pulmonary veins were used to visualize left atrial blood flow and to quantitatively separate the flow into two functionally distinct flow components: Direct flow = particle traces that enter and leave the atrium in one heartbeat, Retained flow = particle traces that enter the atrium and remains there for one cardiac cycle. Flow visualization based on fixed-volume traces revealed that, beginning in early ventricular systole, flow enters the atrium and engages with residual blood volume to form a vortex. In early diastole during early ventricular filling, the organized vortical flow is extinguished, followed by formation of a second transient atrial vortex. Finally, in late diastole during atrial contraction, a second acceleration of blood into the ventricle is seen. The direct and retained left atrial flow components were between 44 and 57% and 43-56% of the stroke volume, respectively. In conclusion, fixed volume particle tracing permits separation of left atrial blood flow into different components based on the transit of blood through the atrium.
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| 40. |
- Gil, Jeovanis, et al.
(author)
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Clinical protein science in translational medicine targeting malignant melanoma
- 2019
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In: Cell Biology and Toxicology. - : Springer Science and Business Media LLC. - 0742-2091 .- 1573-6822. ; 35:4, s. 293-332
-
Journal article (peer-reviewed)abstract
- Melanoma of the skin is the sixth most common type of cancer in Europe and accounts for 3.4% of all diagnosed cancers. More alarming is the degree of recurrence that occurs with approximately 20% of patients lethally relapsing following treatment. Malignant melanoma is a highly aggressive skin cancer and metastases rapidly extend to the regional lymph nodes (stage 3) and to distal organs (stage 4). Targeted oncotherapy is one of the standard treatment for progressive stage 4 melanoma, and BRAF inhibitors (e.g. vemurafenib, dabrafenib) combined with MEK inhibitor (e.g. trametinib) can effectively counter BRAFV600E-mutated melanomas. Compared to conventional chemotherapy, targeted BRAFV600E inhibition achieves a significantly higher response rate. After a period of cancer control, however, most responsive patients develop resistance to the therapy and lethal progression. The many underlying factors potentially causing resistance to BRAF inhibitors have been extensively studied. Nevertheless, the remaining unsolved clinical questions necessitate alternative research approaches to address the molecular mechanisms underlying metastatic and treatment-resistant melanoma. In broader terms, proteomics can address clinical questions far beyond the reach of genomics, by measuring, i.e. the relative abundance of protein products, post-translational modifications (PTMs), protein localisation, turnover, protein interactions and protein function. More specifically, proteomic analysis of body fluids and tissues in a given medical and clinical setting can aid in the identification of cancer biomarkers and novel therapeutic targets. Achieving this goal requires the development of a robust and reproducible clinical proteomic platform that encompasses automated biobanking of patient samples, tissue sectioning and histological examination, efficient protein extraction, enzymatic digestion, mass spectrometry–based quantitative protein analysis by label-free or labelling technologies and/or enrichment of peptides with specific PTMs. By combining data from, e.g. phosphoproteomics and acetylomics, the protein expression profiles of different melanoma stages can provide a solid framework for understanding the biology and progression of the disease. When complemented by proteogenomics, customised protein sequence databases generated from patient-specific genomic and transcriptomic data aid in interpreting clinical proteomic biomarker data to provide a deeper and more comprehensive molecular characterisation of cellular functions underlying disease progression. In parallel to a streamlined, patient-centric, clinical proteomic pipeline, mass spectrometry–based imaging can aid in interrogating the spatial distribution of drugs and drug metabolites within tissues at single-cell resolution. These developments are an important advancement in studying drug action and efficacy in vivo and will aid in the development of more effective and safer strategies for the treatment of melanoma. A collaborative effort of gargantuan proportions between academia and healthcare professionals has led to the initiation, establishment and development of a cutting-edge cancer research centre with a specialisation in melanoma and lung cancer. The primary research focus of the European Cancer Moonshot Lund Center is to understand the impact that drugs have on cancer at an individualised and personalised level. Simultaneously, the centre increases awareness of the relentless battle against cancer and attracts global interest in the exceptional research performed at the centre.
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| 41. |
- Hellstrom, Per Anders Rickard, 1975-, et al.
(author)
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Intelligent Wireless Body Area Network System for Human Motion Analysis
- 2015
-
Conference paper (peer-reviewed)abstract
- Human motion analysis provides several important applications. Examples are fall risk assessment, sports biomechanics, physical activity monitoring and rehabilitation. This work in progress paper proposes an intelligent wireless body area network system for motion and gait symmetry analysis. A Bluetooth network with accelerometers, gyroscopes and in-shoe force sensing resistors gathers data and sends it to a web server after intelligent pre-processing and filtering. The system is flexible and adaptable for different use cases including combinations of gait analysis, gait symmetry and pressure measurements between foot and shoe.
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| 42. |
- Lundin, Jonatan, et al.
(author)
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An Investigation of Maintenance Technicians' Information-Seeking Behavior in a Repair Center
- 2018
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In: IEEE Transactions on Professional Communication. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 0361-1434 .- 1558-1500. ; 61:3, s. 257-274
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Journal article (peer-reviewed)abstract
- Research problem: When it comes to understanding certain aspects of a maintenance technician's information-seeking behavior, knowledge is lacking. For instance, little is known about what kinds of information needs that maintenance technicians exhibit while performing work tasks and what types of sources they employ to satisfy those needs. Understanding such information-seeking behavior is especially essential for technical communicators who endeavor to design useful and relevant technical information. Research questions: 1. What information needs do maintenance technicians show evidence of while performing maintenance work tasks? 2. Where do they go to satisfy these information needs? Literature review: Current knowledge on maintenance technicians' information-seeking behavior is very limited. The literature reviewed for this study covers the task-based information-seeking behavior of different types of engineers and is mainly found within the field of library and information science research. This literature was selected because maintenance technicians and engineers share many characteristics. One information-seeking characteristic exhibited by engineers is the tendency to rely on internal company information, such as colleagues and self-created sources, before external information sources are consulted. Methodology: This study utilized an ethnographic research approach where empirical data were collected, analyzed, and interpreted from a theoretical viewpoint-a synthesis of Bystrom and Hansen's conceptual framework and the Systemic-Structural Theory of Activity. Seven in-house aftermarket maintenance technicians were observed via participant observation at a repair center in Sweden while they performed maintenance tasks on machines that had been taken out of service. Results and conclusions: The results-based on empirical data collected over the course of 12 days, spread over 12 weeks in the autumn of 2012-reveal that the observed maintenance technicians exhibited 50 different types of information needs. They seldom sought instructions covering an entire work task. Instead, to satisfy their information needs, the maintenance technicians consulted four types of sources that, in the present study, have been designated as information source hosts.
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| 43. |
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| 44. |
- Lundin, Jonatan, et al.
(author)
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Design challenges for technical communicators
- 2016
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In: SIGDOC 2016 - 34th ACM International Conference on the Design of Communication. - New York, NY, USA : ACM. - 9781450344951
-
Conference paper (peer-reviewed)abstract
- Based on participant observation conducted for a total of 85 hours spread across two months, this paper investigates the different types of information maintenance technicians seek, and discusses which of those types are relevant and challenging for a technical communicator to design. In order to design useful technical information, the technical communicator must not only understand the information needs of a user, but also understand the various aspects of the user context. This paper highlights a gap that exists between the type of information maintenance technicians seek, and what is relevant for a technical communicator to design. Information about the construction of a machine and work task instructions are relevant for a technical communicator to design. However, information regarding business identities and numbers, the cause of errors, placement of equipment and tools, as well as information related to various aspects of task execution seem very challenging\- or even impossible\- for a technical communicator to design during product development. This paper contributes knowledge to user behavior research within the technical communication research field. The results provide technical communicators with an understanding of what type of information maintenance technicians seek and select in order to satisfy an expressed information need. This discussion enables technical communication practitioners and researchers to gain a better understanding of what type of information is relevant to design and which information is a challenge to design, thus which types of expressed information needs are suitable to focus on, and why.
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| 45. |
- Lundin, Jonatan
(author)
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Designing technical information : Challenges regarding service engineers’ information-seeking behaviour
- 2015
-
Licentiate thesis (other academic/artistic)abstract
- There is a gap of knowledge regarding relevant aspects of users’ information-seekingbehaviours. The research presented in this thesis aims at gaining a deeper knowledge about such behaviours and discussing the consequences the behaviours may have on the design practice of technical communicators when designing technical information during product development. The information needs of users, and where they go to obtain information to satisfy these needs, are considered relevant aspects. The research presented in this thesis is limited to service engineers performing maintenance in a workshop. The objective is to try to frame the information needs service engineers give evidence of in a work task and map where they go to satisfy these needs. An ethnographic research approach were selected where empirical data was collected, analysed and interpreted from a theoretical viewpoint: a synthesis of Byström and Hansen’s Conceptual Framework for Tasks in Information Studies and Systemic-Structural Theory of Activity. Seven in-house aftermarket service engineers where observed by means of participant observation while performing maintenance work tasks on machine equipment taken out of service in a maintenance workshop in Sweden.The results reveal that these service engineers gave evidence of fifty (50) different information needs, that they actively searched and selected four (4) types of sources of information to satisfy these needs, but also that service engineers seldom seek instructions.The consequence for technical communicators having the intention of designing to satisfy the cognitive information needs of individuals, is that it is a challenge to satisfy every information need. The information needs unique to any one individual and those depending on the work task context, as well as those that are specific to a work role in an organisation rather than to the machine equipment, are challenging to satisfy. This research indicates that the same type of information is used to satisfy different types of information needs. The information designed to satisfy a specific information need may thus be used to satisfy an entirely different need.
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| 46. |
- Lundin, Jonatan
(author)
-
Shaping thought through action : A study of the use and design of technical information
- 2020
-
Doctoral thesis (other academic/artistic)abstract
- This dissertation deals with the design of technical information, such as a user manual for an industrial device, based on the searching and reading behaviour of process operators and maintenance technicians. Such industrial professionals, who use tools like measuring equipment, are sometimes unable to get the support they need from searching and reading in a text- and image-based tool manual in order to perform work tasks. If such a manual is the only available source of information, the user will either give up or attempt a workaround which ends up compromising the safety, quality, satisfaction, efficiency or effectiveness of the work task. Research within technical communication and human-computer interaction suggests how manuals can be designed to support users in accomplishing tasks. These suggestions are based upon studies of how users approach the use of tools and tool manuals, as well as how the design of procedural and declarative information supports users. However, there is limited knowledge about how users search and read manuals, and how manuals can be designed to support such searching and reading behaviour. This dissertation aims to contribute knowledge to technical communicators about how technical information can be designed to support industrial professionals in accomplishing their work tasks. An ethnographic research method was selected to study the behaviour exhibited by process operators and maintenance technicians’ while they search and read sources of information in order to perform work tasks with tools. The results show that some participants were unable to perform a task after searching and reading the manual. The empirical material has been analysed using Vygotsky’s sociocultural theory. This was to gain a deeper understanding of how thought and language influence—and are influenced by—searching and reading behaviours, as well as the task behaviours during tool use. This dissertation's contribution is a design method for technical communicators that will enable them to support users in the shaping of mental representations about what results are possible to accomplish with a tool. The method involves the design of tangible tokens that signify the results and components of a tool. As the end-user arranges these symbols into a result model they are supported in their process of shaping a mental representation.
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| 47. |
- Mulder, Skander, et al.
(author)
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A metabolomics-based molecular pathway analysis of how the sodium-glucose co-transporter-2 inhibitor dapagliflozin may slow kidney function decline in patients with diabetes
- 2020
-
In: Diabetes, obesity and metabolism. - : WILEY. - 1462-8902 .- 1463-1326. ; 22:7, s. 1157-1166
-
Journal article (peer-reviewed)abstract
- Aim To investigate which metabolic pathways are targeted by the sodium-glucose co-transporter-2 inhibitor dapagliflozin to explore the molecular processes involved in its renal protective effects. Methods An unbiased mass spectrometry plasma metabolomics assay was performed on baseline and follow-up (week 12) samples from the EFFECT II trial in patients with type 2 diabetes with non-alcoholic fatty liver disease receiving dapagliflozin 10 mg/day (n = 19) or placebo (n = 6). Transcriptomic signatures from tubular compartments were identified from kidney biopsies collected from patients with diabetic kidney disease (DKD) (n = 17) and healthy controls (n = 30) from the European Renal cDNA Biobank. Serum metabolites that significantly changed after 12 weeks of dapagliflozin were mapped to a metabolite-protein interaction network. These proteins were then linked with intra-renal transcripts that were associated with DKD or estimated glomerular filtration rate (eGFR). The impacted metabolites and their protein-coding transcripts were analysed for enriched pathways. Results Of all measured (n = 812) metabolites, 108 changed (P < 0.05) during dapagliflozin treatment and 74 could be linked to 367 unique proteins/genes. Intra-renal mRNA expression analysis of the genes encoding the metabolite-associated proteins using kidney biopsies resulted in 105 genes that were significantly associated with eGFR in patients with DKD, and 135 genes that were differentially expressed between patients with DKD and controls. The combination of metabolites and transcripts identified four enriched pathways that were affected by dapagliflozin and associated with eGFR: glycine degradation (mitochondrial function), TCA cycle II (energy metabolism), L-carnitine biosynthesis (energy metabolism) and superpathway of citrulline metabolism (nitric oxide synthase and endothelial function). Conclusion The observed molecular pathways targeted by dapagliflozin and associated with DKD suggest that modifying molecular processes related to energy metabolism, mitochondrial function and endothelial function may contribute to its renal protective effect.
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| 48. |
- Nordin, Erik, et al.
(author)
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Smog Chamber Experiments of SOA Formation from Gasoline Exhaust and Light Aromatics
- 2010
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Conference paper (other academic/artistic)abstract
- Experiments where gasoline exhaust was exposed to UV-radiation to examine Secondary Organic Aerosol (SOA) formation were performed in a smog chamber. The Aerosol Mass Yield (formed SOA/reacted precursor mass) was determined and compared with the yield from a pure precursor experiment in the chamber and from results reported in literature. Preliminary results show that the majority of the organic aerosol mass emitted from idling gasoline cars is secondary. Further, the SOA yields when taking only C6-C10 light aromatics into account are within a similar range to pure precursor experiments, suggesting that light aromatics are dominating precursors in gasoline exhaust SOA.
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| 49. |
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| 50. |
- Nystrand, Thomas, et al.
(author)
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Coarse-Graining Approach to Atomistic SpinDynamics
- 2015
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In: ULTRAFAST MAGNETISM I. - Cham : Springer International Publishing. - 9783319077437 - 9783319077420 ; , s. 162-165
-
Conference paper (peer-reviewed)abstract
- We introduce a coarse-graining approach to study the movement of a Domain Wall (DW) under the influence of a spin polarized current, in the framework of atomistic spin dynamics. An increase in performance of up to 35% is obtained. We show the dependence of the method on both exchange range and temperature effects.
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