| 1. |
- Hober, Sophia, Professor, 1965-, et al.
(författare)
-
Systematic evaluation of SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay
- 2021
-
Ingår i: Clinical & Translational Immunology. - : Wiley. - 2050-0068. ; 10:7
-
Tidskriftsartikel (refereegranskat)abstract
- Objective. The COVID-19 pandemic poses an immense need for accurate, sensitive and high-throughput clinical tests, and serological assays are needed for both overarching epidemiological studies and evaluating vaccines. Here, we present the development and validation of a high-throughput multiplex bead-based serological assay. Methods. More than 100 representations of SARS-CoV-2 proteins were included for initial evaluation, including antigens produced in bacterial and mammalian hosts as well as synthetic peptides. The five best-performing antigens, three representing the spike glycoprotein and two representing the nucleocapsid protein, were further evaluated for detection of IgG antibodies in samples from 331 COVID-19 patients and convalescents, and in 2090 negative controls sampled before 2020. Results. Three antigens were finally selected, represented by a soluble trimeric form and the S1-domain of the spike glycoprotein as well as by the C-terminal domain of the nucleocapsid. The sensitivity for these three antigens individually was found to be 99.7%, 99.1% and 99.7%, and the specificity was found to be 98.1%, 98.7% and 95.7%. The best assay performance was although achieved when utilising two antigens in combination, enabling a sensitivity of up to 99.7% combined with a specificity of 100%. Requiring any two of the three antigens resulted in a sensitivity of 99.7% and a specificity of 99.4%. Conclusion. These observations demonstrate that a serological test based on a combination of several SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay.
|
|
| 2. |
- Thul, Peter J., et al.
(författare)
-
A subcellular map of the human proteome
- 2017
-
Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 356:6340
-
Tidskriftsartikel (refereegranskat)abstract
- Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.
|
|
| 3. |
- Bachmann, Bernhard, et al.
(författare)
-
Parallel Multiple-Shooting and Collocation Optimization with OpenModelica
- 2012
-
Ingår i: Proceedings of the 9th International MODELICA Conference; September 3-5; 2012; Munich; Germany. - : Linköping University Electronic Press. - 9789175198262 ; , s. 659-668
-
Konferensbidrag (refereegranskat)abstract
- Nonlinear model predictive control (NMPC) has become increasingly important for today’s control engineers during the last decade. In order to apply NMPC a nonlinear optimal control problem (NOCP) must be solved which needs a high computational effort.State-of-the-art solution algorithms are based on multiple shooting or collocation algorithms; which are required to solve the underlying dynamic model formulation. This paper describes a general discretization scheme applied to the dynamic model description which can be further concretized to reproduce the mul-tiple shooting or collocation approach. Furthermore; this approach can be refined to represent a total collocation method in order to solve the underlying NOCP much more efficiently. Further speedup of optimization has been achieved by parallelizing the calculation of model specific parts (e.g. constraints; Jacobians; etc.) and is presented in the coming sections.The corresponding discretized optimization problem has been solved by the interior optimizer Ipopt. The proposed parallelized algorithms have been tested on different applications. As industrial relevant application an optimal control of a Diesel-Electric power train has been investigated. The modeling and problem description has been done in Optimica and Modelica. The simulation has been performed using OpenModelica. Speedup curves for parallel execution are presented.
|
|
| 4. |
- Ekberg, Kristoffer, et al.
(författare)
-
Cycle Beating - An Analysis of the Boundaries During Vehicle Testing
- 2016
-
Ingår i: IFAC PAPERS ONLINE. - : ELSEVIER SCIENCE BV. ; , s. 657-664
-
Konferensbidrag (refereegranskat)abstract
- Todays vehicle industry is strictly controlled by environmental legislations. The vehicle industry is spending much money out reducing the fuel consumption and fulfilling the emission requirements to make sales possible in different regions in the world. Before introducing; a vehicle on the market, it is tested according to standardized driving cycles to specify the vehicle pollutant emissions and fuel consumption. These cycles allow some deviation from the reference vehicle speed during tests, e.g. NEDC allows deviations of +/- 2 km/h and +/- 1 s. This paper uses dynamic programming to find fuel optimal velocity profiles, given the allowed deviations of +/- 2 km/h and +/- 1 s from reference speed during drive cycle test. By taking advantage of the allowed deviation, the fuel consumption can be reduced by up to 16.56 % according to model results, ruoriing NEDC if gear selections are unrestricted (i.e. using automatic gearbox), and up to 5.90 % if changing gears according to the specifications in the drive cycle. Two different optimization goals are investigated, minimum amount of mass fuel consumed and best mileage. (C) 2016, IFAC (International Federation of Automatic Control) Hosting by Elsevier Ltd. All rights reserved.
|
|
| 5. |
- Eriksson, Lars, et al.
(författare)
-
Calculation of Optimal Heat Release Rates under Constrained Conditions
- 2016
-
Ingår i: SAE International Journal of Engines. - : SAE International. - 1946-3936 .- 1946-3944. ; 9:2, s. 1143-1162
-
Tidskriftsartikel (refereegranskat)abstract
- The work extends a methodology, for searching for optimal heat release profiles, by adding complex constraints on states. To find the optimum heat release profile a methodology, that uses available theory and methods, was developed that enables the use of state of the art optimal control software to find the optimum combustion trace for a model. The methodology is here extended to include constraints and the method is then applied to study how sensitive the solution is to different effects such as heat transfer, crevice flow, maximum rate of pressure rise, maximum pressure, knock and NO generation. The Gatowski single zone model is extended to a pseudo two zone model, to get an unburned zone that is used to describe the knocking and a burned zone for NO generation. A modification of the extended Zeldovich mechanism that makes it continuously differentiable, is used for NO generation. Previous results showed that the crevice effect had a significant influence on the shape for the unconstrained case where a two mode combustion was seen, one initial pressure rise and one constant pressure phase. Here it is shown that it still has a significant influence on the appearance until the maximum pressure limit is reached and becomes the dominating constraint. In the unconstrained case no conditions had combustion before TDC all started after, but when limitations are considered and come into play the combustion can now start before TDC to avoid excessive losses during the expansion. When introducing constraints on the NO formation through the extended Zeldovich mechanism the combustion takes the shape of a three mode combustion, one initial rapid burning, one later rapid burning and a constant pressure phase. In summary it is shown that the methodology is able to cope with the introduced constraints.
|
|
| 6. |
- Eriksson, Lars, et al.
(författare)
-
Computing Optimal Heat Release Rates in Combustion Engines
- 2015
-
Ingår i: SAE International Journal of Engines. - Warrendale : SAE inc.. - 1946-3936 .- 1946-3944. ; 8:2
-
Tidskriftsartikel (refereegranskat)abstract
- The combustion process has a high impact on the engine efficiency, and in the search for efficient engines it is of interest to study the combustion. Optimization and optimal control theory is used to compute the most efficient combustion profiles for single zone model with heat transfer and crevice effects. A model is first developed and tuned to experimental data, the model is a modification of the well known Gatowski-model (Gatowski et.al 1984). This model is selected since it gives a very good description of the in-cylinder pressure, and thus the produced work, and achieves this with a low computational complexity. This enables an efficient search method that can maximize the work to be developed. First, smooth combustion profiles are studied where the combustion is modeled using the Vibe function, and parametric optimization is used to search for the optimal profile. Then, the most efficient combustion process with a completely free combustion is studied with theory and software for optimal control. A parameter study is performed to analyze the impact of crevice volume and air/fuel ratio λ. The results show that the losses have a high impact on the behavior, which is natural, and that the crevice effect has a very distinct effect on the optimal combustion giving a two mode appearance similar to the Seiliger cycle.
|
|
| 7. |
- Fagerberg, Linn, et al.
(författare)
-
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
- 2014
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 13:2, s. 397-406
-
Tidskriftsartikel (refereegranskat)abstract
- Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody- based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to 80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.
|
|
| 8. |
- Fagerberg, Linn, et al.
(författare)
-
Contribution of antibody-based protein profiling to the human chromosome-centric proteome project (C-HPP)
- 2013
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 12:6, s. 2439-2448
-
Tidskriftsartikel (refereegranskat)abstract
- A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few tissue-specific proteins and approximately half of the genes expressed in all the analyzed cells. The status for each gene with regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas (www.proteinatlas.org).
|
|
| 9. |
- Ganesan, Anand, 1985, et al.
(författare)
-
Effect of engine dynamics on optimal power-split control strategies in hybrid electric vehicles
- 2020
-
Ingår i: 2020 IEEE Vehicle Power and Propulsion Conference, VPPC 2020 - Proceedings.
-
Konferensbidrag (refereegranskat)abstract
- This paper presents a model predictive control (MPC) based supervisory power-split control strategy, which optimises fuel and energy consumption in Hybrid Electric Vehicles (HEVs) by incorporating powertrain actuator dynamic models. In HEVs, while distributing the driver demand to the powertrain actuators, a standard approach is to approximate the actuator energy conversion dynamics with steady-state maps, which leads to sub-optimal control policy and increased fuel energy consumption, especially for a driving mission with high transient demands. To address this shortfall, the control strategy proposed in this paper explicitly integrates an experimentally validated dynamic model of gasoline internal combustion engine (ICE) into an MPC based power-split controller. The proposed strategy is validated in a parallel HEV platform, where the sensitivity of the HEV energy consumption w.r.t. its actuator dynamics and the transients in its load demands, is also established. The results enable an understanding of the energy saving potential in HEVs that supports the inclusion of actuator dynamic models in optimal power-split controllers and it also establishes that the proposed control strategy realises higher energy and fuel savings in HEVs.
|
|
| 10. |
- Grapotte, Mathys, et al.
(författare)
-
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
- 2021
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723.
-
Tidskriftsartikel (refereegranskat)abstract
- Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
|
|
