| 1. |
- Abdellah, Tebani, et al.
(författare)
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Integration of molecular profiles in a longitudinal wellness profiling cohort.
- 2020
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.
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| 2. |
- Nyberg, Lena, 1979, et al.
(författare)
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A single-step competitive binding assay for mapping of single DNA molecules
- 2012
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
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| 3. |
- Sjöblom, Ted, et al.
(författare)
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REEDS : Reference data and algorithms for research and development of smart ships
- 2023
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The Swedish Transport Administration Research and Innovation fund for Maritime research funded the project "Reference data and algorithms to support research and development of smart ships". The project goes by the working name, and is communicated as, Reeds. It responds to a synthesis of a number of different needs identified in previous projects and studies. The background to the project is that in recent years the focus has been on developing algorithms to interpret and act on the physical environment around different types of craft. In order to be able to develop and evaluate these algorithms, it has become clear that open datasets and a fair benchmarking platform are required that allow various developers in industries and researchers to evaluate algorithms. In the road vehicle sector, Kitti, as of 2013, is the largest dataset used as a reference dataset. The dataset in this project contains sensor data from several data collection occasions within a maritime context, from high-precision sensors such as cameras, radar, lidar, and IMU. For marine applications, there has been no similar dataset with anywhere near the same amount of data and time synchronisation between sensors. The reference data and reference algorithms were available periodically during the project through an online service where researchers and developers could upload their algorithms to use the dataset.In addition to the dataset itself, Reeds adds additional strengths compared to other reference datasets:- New approach to comparing algorithms fairly, where new algorithms are always compared on a centralised hardware in a cloud service and re-evaluated when new data is added, i.e. an unbiased algorithm evaluation service.- Method that combines NTP and PTP time protocols for synchronisation between the sensors with microsecond accuracy- More types and more modern sensors that can be used at a higher level of abstraction and can thus be applied in more areas.- Sensor fusion of both onboard and land-side sensors- Identify areas of application for navigation and surveillance on land based on the algorithms developed during the project and the use of new sensor types not established in shipping.- The project built up a maritime reference data set that enables the creation of a digital description for the ship's surrounding environment and developed reference algorithms to demonstrate new navigation and monitoring methodology in the area of "enhanced navigation"."Enhanced navigation" is defined under the project as the use of new technology based on developments in digitisation and autonomous functions, where new navigation methods use sensors both on board and ashore to increase maritime safety and robustness. The project has built a web-based user interface referred to in the report as "Crowsnest" that handles these new sensors and visualises this data in a familiar interface similar to an overlay in ECDIS that is openly available for the public to build on. Which was used for the evaluation and concept development of new user interfaces based on feedback from pilots and VTS operators.By providing reference datasets and reference algorithms with demonstrations, researchers and companies now have the opportunity to develop algorithms for the intelligent and autonomous ships of the future.
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| 4. |
- Adeboye, Peter, 1982, et al.
(författare)
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Catabolism of coniferyl aldehyde, ferulic acid and p-coumaric acid by Saccharomyces cerevisiae yields less toxic products
- 2015
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Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 14:1, s. 149-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Lignocellulosic substrates and pulping process streams are of increasing relevance to biorefineries for second generation biofuels and biochemical production. They are known to be rich in sugars and inhibitors such as phenolic compounds, organic acids and furaldehydes. Phenolic compounds are a group of aromatic compounds known to be inhibitory to fermentative organisms. It is known that inhibition of Sacchromyces cerevisiae varies among phenolic compounds and the yeast is capable of in situ catabolic conversion and metabolism of some phenolic compounds. In an approach to engineer a S. cerevisiae strain with higher tolerance to phenolic inhibitors, we selectively investigated the metabolic conversion and physiological effects of coniferyl aldehyde, ferulic acid, and p-coumaric acid in Saccharomyces cerevisiae. Aerobic batch cultivations were separately performed with each of the three phenolic compounds. Conversion of each of the phenolic compounds was observed on time-based qualitative analysis of the culture broth to monitor various intermediate and final metabolites. Result: Coniferyl aldehyde was rapidly converted within the first 24 h, while ferulic acid and p-coumaric acid were more slowly converted over a period of 72 h. The conversion of the three phenolic compounds was observed to involved several transient intermediates that were concurrently formed and converted to other phenolic products. Although there were several conversion products formed from coniferyl aldehyde, ferulic acid and p-coumaric acid, the conversion products profile from the three compounds were similar. On the physiology of Saccharomyces cerevisiae, the maximum specific growth rates of the yeast was not affected in the presence of coniferyl aldehyde or ferulic acid, but it was significantly reduced in the presence of p-coumaric acid. The biomass yields on glucose were reduced to 73 and 54 % of the control in the presence of coniferyl aldehyde and ferulic acid, respectively, biomass yield increased to 127 % of the control in the presence of p-coumaric acid. Coniferyl aldehyde, ferulic acid and p-coumaric acid and their conversion products were screened for inhibition, the conversion products were less inhibitory than coniferyl aldehyde, ferulic acid and p-coumaric acid, indicating that the conversion of the three compounds by Saccharomyces cerevisiae was also a detoxification process. Conclusion: We conclude that the conversion of coniferyl aldehyde, ferulic acid and p-coumaric acid into less inhibitory compounds is a form of stress response and a detoxification process. We hypothesize that all phenolic compounds are converted by Saccharomyces cerevisiae using the same metabolic process. We suggest that the enhancement of the ability of S. cerevisiae to convert toxic phenolic compounds into less inhibitory compounds is a potent route to developing a S. cerevisiae with superior tolerance to phenolic compounds.
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| 5. |
- Andersson, Mats, et al.
(författare)
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Road Friction Estimation
- 2007
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This project is part of the Swedish IVSS program. The aim of IVSS is to stimulate research and development for the road safety of the future. Road conditions with low friction have been identified as a frequent cause of traffic accidents. Therefore, technology to automaticallydetect changes in road conditions and alert the driver or take proper actions with active driver support systems would be a key contribution to increased road safety.The aim of this project was to investigate the possibilities to estimate the tire to road friction.Three different approaches have been developed and evaluated, from concept to early prototypes in test vehicles. In the first method, the estimation of the coefficient of friction is based on the forces and torques that are produced at the front tires at cornering maneuvers.The second method is based on a physical model of the tire behavior and estimates road friction from information on the forces that are produced at straight driving. The third method is based on an optical sensor that classifies the road surface ahead of the vehicle.The three methods have been successfully evaluated in proving ground and public road tests in summer and winter conditions with different tires, and have been compared with reference measurements. The conclusion is that all three methods can be used for tire to road frictionestimation and are recommended for further development and industrialization.
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| 6. |
- Bereczky-Veress, Biborka, et al.
(författare)
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Host strain-dependent difference in susceptibility in a rat model of herpes simplex type 1 encephalitis.
- 2008
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Ingår i: Journal of neurovirology. - : Springer Science and Business Media LLC. - 1538-2443 .- 1355-0284. ; 14:2, s. 102-18
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Tidskriftsartikel (refereegranskat)abstract
- Herpes simplex encephalitis (HSE) is characterized by severe focal brain inflammation leading to substantial loss of nervous tissue. The authors established a model of Herpes simplex virus type 1 (HSV)-1-induced acute encephalitis in the rat by injecting into the whiskers' area a virus strain isolated from a fatal human HSE case. The model might resemble natural propagation of HSV-1 in humans; spreading from the mouth and lips via the trigeminal nerve to trigeminal ganglia and subsequently entering the central nervous system (CNS). HSV-1 infected Dark Agouti (DA) rats developed a well-synchronized disease and died 5 days after inoculation. HSV-1 detection by quantitative polymerase chain reaction (qPCR), virus isolation and immunohistochemistry, magnetic resonance imaging, and histopathological examination verified dramatic encephalitis mainly in the brainstem, but also in the olfactory bulb and other segments of the brain of diseased rats. In contrast, Piebald Virol Glaxo (PVG) rats were completely resistant to disease, displaying a more rapid clearance of peripheral infection and no evidence of virus entering into neither the trigeminal ganglia nor the CNS. These results suggest a regulation of susceptibility to HSV-1-induced encephalitis at the level of peripheral infection and subsequent neuronal uptake/transport of the virus. This provides a basis for future positioning of genetic polymorphisms regulating HSE and for dissection of important pathogenetic mechanisms of this severe human disease.
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| 7. |
- Bill, Susanna, et al.
(författare)
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Rethinking User Involvement in the Front End of Healthcare Innovation
- 2011
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Konferensbidrag (refereegranskat)abstract
- The purpose of this paper is to share insights from an empirical study within the Swedish healthcare system, based on a case study of the largest business unit of a Swedish medical technology company and its key customer segment. The study involving a Swedish medical technology company and three Swedish hospitals indicates need to move away from an archetypical, largely homogeneous view of the user, towards a more flexible, heterogeneous user perspective. Following from that insight the paper outlines a preliminary model aimed at improving the conditions of the firm for user involvement in the front end of healthcare innovation. In the proposed model, different users are brought to the foreground in different parts of the front-end innovation process. The research performed aimed at putting the business unit in a more beneficial position to involve users in the front end of innovation by increasing their understanding of a) which user types they actually have access to, b) which roles that different user types may take in the various stages of the innovation front-end.
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| 8. |
- Bylow, Erik, et al.
(författare)
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Robust online 3D reconstruction combining a depth sensor and sparse feature points
- 2016
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Ingår i: Proceedings - International Conference on Pattern Recognition. - 1051-4651. - 9781509048472 ; , s. 3709-3714
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Konferensbidrag (refereegranskat)abstract
- Online 3D reconstruction has been an active research area for a long time. Since the release of the Microsoft Kinect Camera and publication of KinectFusion [11] attention has been drawn how to acquire dense models in real-time. In this paper we present a method to make online 3D reconstruction which increases robustness for scenes with little structure information and little texture information. It is shown empirically that our proposed method also increases robustness when the distance between the camera positions becomes larger than what is commonly assumed. Quantitative and qualitative results suggest that this approach can handle situations where other well-known methods fail. This is important in, for example, robotics applications like when the camera position and the 3D model must be created online in real-time.
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| 9. |
- Christiansen, Evald H, et al.
(författare)
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Instantaneous Wave-free Ratio versus Fractional Flow Reserve to Guide PCI.
- 2017
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Ingår i: The New England journal of medicine. - : Massachussetts Medical Society. - 1533-4406 .- 0028-4793. ; 376:19, s. 1813-1823
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Tidskriftsartikel (refereegranskat)abstract
- The instantaneous wave-free ratio (iFR) is an index used to assess the severity of coronary-artery stenosis. The index has been tested against fractional flow reserve (FFR) in small trials, and the two measures have been found to have similar diagnostic accuracy. However, studies of clinical outcomes associated with the use of iFR are lacking. We aimed to evaluate whether iFR is noninferior to FFR with respect to the rate of subsequent major adverse cardiac events.We conducted a multicenter, randomized, controlled, open-label clinical trial using the Swedish Coronary Angiography and Angioplasty Registry for enrollment. A total of 2037 participants with stable angina or an acute coronary syndrome who had an indication for physiologically guided assessment of coronary-artery stenosis were randomly assigned to undergo revascularization guided by either iFR or FFR. The primary end point was the rate of a composite of death from any cause, nonfatal myocardial infarction, or unplanned revascularization within 12 months after the procedure.A primary end-point event occurred in 68 of 1012 patients (6.7%) in the iFR group and in 61 of 1007 (6.1%) in the FFR group (difference in event rates, 0.7 percentage points; 95% confidence interval [CI], -1.5 to 2.8; P=0.007 for noninferiority; hazard ratio, 1.12; 95% CI, 0.79 to 1.58; P=0.53); the upper limit of the 95% confidence interval for the difference in event rates fell within the prespecified noninferiority margin of 3.2 percentage points. The results were similar among major subgroups. The rates of myocardial infarction, target-lesion revascularization, restenosis, and stent thrombosis did not differ significantly between the two groups. A significantly higher proportion of patients in the FFR group than in the iFR group reported chest discomfort during the procedure.Among patients with stable angina or an acute coronary syndrome, an iFR-guided revascularization strategy was noninferior to an FFR-guided revascularization strategy with respect to the rate of major adverse cardiac events at 12 months. (Funded by Philips Volcano; iFR SWEDEHEART ClinicalTrials.gov number, NCT02166736 .).
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| 10. |
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