| 1. |
- Jernheden, Elinor, et al.
(författare)
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Comparison of Exact and Approximate methods for the Vehicle Routing Problem with Time Windows
- 2020
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Ingår i: IEEE International Conference on Automation Science and Engineering. - 2161-8070 .- 2161-8089. ; 2020-August, s. 378-383
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Konferensbidrag (refereegranskat)abstract
- This paper presents a comparison of two approaches for solving the vehicle routing problem with time windows (VRPTW). Scheduling of vehicles for pickup and delivery is a common problem in logistics and may be expressed as VRPTW, for which both exact and approximate techniques are available. It is therefore interesting to compare such techniques to evaluate their performance and figure what is the best option based on the instance features and size. In this work, we compared Mixed Integer Linear Programming (MILP) with Set-Based Particle Swarm optimization (S-PSO). Both algorithms are tested on the full 56 instances of the Solomon dataset. The results show that the two algorithms perform similarly for lower number of customers while there are significant differences for the cases with higher number of customers. For higher number of customers MILP consistently performs as good as or better than S-PSO for the clustered data, both with short and long scheduling horizons, while the S-PSO outperforms MILP in most cases with random and mixed random clustered data with long scheduling horizons. Furthermore when the algorithms perform the same with regards to the main objective (number of vehicles), MILP generally achieves a better result in the second objective (distance traveled).
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| 2. |
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| 3. |
- Lantz, Jonas, 1982-, et al.
(författare)
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Impact of Pulmonary Venous Inflow on Cardiac Flow Simulations : Comparison with In Vivo 4D Flow MRI
- 2019
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Ingår i: Annals of Biomedical Engineering. - : Springer-Verlag New York. - 0090-6964 .- 1573-9686. ; 47:2, s. 413-424
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Tidskriftsartikel (refereegranskat)abstract
- Blood flow simulations are making their way into the clinic, and much attention is given to estimation of fractional flow reserve in coronary arteries. Intracardiac blood flow simulations also show promising results, and here the flow field is expected to depend on the pulmonary venous (PV) flow rates. In the absence of in vivo measurements, the distribution of the flow from the individual PVs is often unknown and typically assumed. Here, we performed intracardiac blood flow simulations based on time-resolved computed tomography on three patients, and investigated the effect of the distribution of PV flow rate on the flow field in the left atrium and ventricle. A design-of-experiment approach was used, where PV flow rates were varied in a systematic manner. In total 20 different simulations were performed per patient, and compared to in vivo 4D flow MRI measurements. Results were quantified by kinetic energy, mitral valve velocity profiles and root-mean-square errors of velocity. While large differences in atrial flow were found for varying PV inflow distributions, the effect on ventricular flow was negligible, due to a regularizing effect by mitral valve. Equal flow rate through all PVs most closely resembled in vivo measurements and is recommended in the absence of a priori knowledge.
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| 4. |
- Persson, Patrik, et al.
(författare)
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Parameterization of Ambiguity in Monocular Depth Prediction
- 2021
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Ingår i: Proceedings - 2021 International Conference on 3D Vision, 3DV 2021. - 9781665426886 ; , s. 761-770
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Konferensbidrag (refereegranskat)abstract
- Monocular depth estimation is a highly challenging problem that is often addressed with deep neural networks. While these use recognition of high level image features to predict reasonably looking depth maps,the result often has poor metric accuracy. Moreover,the standard feed forward architecture does not allow modification of the prediction based on cues other than the image.In this paper we relax the monocular depth estimation task by proposing a network that allows us to complement image features with a set of auxiliary variables. These allow disambiguation when image features are not enough to accurately pinpoint the exact depth map and can be thought of as a low dimensional parameterization of the surfaces that are reasonable monocular predictions. By searching the parameterization we can combine monocular estimation with traditional photoconsistency or geometry based methods to achieve both visually appealing and metrically accurate surface estimations. Since we relax the problem we are able to work with smaller networks than current architectures. In addition we design a self-supervised training scheme,eliminating the need for ground truth image depth-map pairs. Our experimental evaluation shows that our method generates more accurate depth maps and generalizes better than competing state-of-the-art approaches.
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| 5. |
- Frost, Rickard, 1979, et al.
(författare)
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Core−Shell Nanoplasmonic Sensing for Characterization of Biocorona Formation and Nanoparticle Surface Interactions
- 2016
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Ingår i: ACS Sensors. - : American Chemical Society (ACS). - 2379-3694. ; 1:6, s. 798-806
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Tidskriftsartikel (refereegranskat)abstract
- Surface properties of nanoparticles imposed by particle size, shape, and surface chemistry are key features that largely determine their environmental fate and effects on biological systems. Consequently, development of analytical tools to characterize surface properties of nanomaterials and their relation to toxicological properties must occur in parallel with applications. As a contribution to this quest, we present a nanoplasmonic sensing strategy that enables systematic in situ characterization of molecule−nanoparticle interactions under well-controlled conditions, in terms of both nanoparticle size and surface chemistry, with particular focus on the importance of surface faceting in crystalline nanoparticles. We assess the performance of our sensing strategy by presenting two case studies. (i) The first is protein corona formation on faceted Au core−SiO2 shell nanoparticles of different sizes, and thus different surface facet-to-edge ratios. Based on 2D and 3D models of the investigated structures, we find that for small particles the curved regions between adjacent facets dominate the response of the corona formation process, whereas the facets dominate the response in the large particle regime. (ii) The second is in situ functionalization of Au core−SiO2 shell nanoparticle surfaces, and analysis of the subsequent protein repellent behavior. Due to the versatility of the presented sensing strategy in studies of nanoparticle surface properties, including in situ surface modifications, and their interactions with (bio)molecules during corona formation, we foresee it to become a valuable tool in the areas of nanomedicine and nanotoxicology.
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| 6. |
- Gantelius, Jesper, et al.
(författare)
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A lateral flow protein microarray for rapid determination of contagious bovine pleuropneumonia status in bovine serum
- 2010
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Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 82:1, s. 11-18
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Tidskriftsartikel (refereegranskat)abstract
- Novel analytical methods for a next generation of diagnostic devices combine attributes from sensitive, accurate, fast, simple and multiplexed analysis methods. Here, we describe a possible contribution to these by the application of a lateral flow microarray where a panel of recombinant protein antigens was used to differentiate bovine serum samples in the context of the lung disease contagious bovine pleuropneumonia (CBPP). Lateral flow arrays were produced by attaching nitrocellulose onto microscopic slides and spotting of the recombinant proteins onto the membranes. The developed assay included evaluations of substrate matrix and detection reagents to allow for short assay times and convenient read-out options, and to yield a total assay time from sample application to data acquisition of less than ten minutes. It was found that healthy and disease-affected animals could be discriminated (AUC = 97%), and we suggest that the use of an antigen panel in combination with the lateral flow device offers an emerging analytical tool towards a simplified but accurate on-site diagnosis.
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| 7. |
- Hamsten, Carl, 1981-, et al.
(författare)
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Expression and immunogenicity of six putative variable surface proteins in Mycoplasma mycoides subsp. mycoides SC.
- 2008
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Ingår i: Microbiology. - Reading : Society for General Microbiology. - 1350-0872 .- 1465-2080. ; 154, s. 539-549
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Tidskriftsartikel (refereegranskat)abstract
- Variable surface protein Vmm and five Vmm-type proteins from Mycoplasma mycoides subsp. mycoides SC were analysed to determine whether these proteins are expressed in vivo in animals affected by contagious bovine pleuropneumonia (CBPP) and in vitro. Recombinant versions of these proteins were constructed and expressed in Escherichia coli after mutation of the TGA Trp codons to TGG. These proteins were then analysed by dot and Western blotting with sera from CBPP-affected cattle. Furthermore, affinity-purified polyclonal antibodies to the recombinant proteins were used in Western and colony blotting to look for expression of the putative Vmm-type proteins in cultured M. mycoides SC. This study demonstrates that immunoglobulins in CBPP sera recognize all putative Vmm-type proteins tested, indicating that these proteins or their homologues are expressed by mycoplasmas during natural infections. Vmm and one of the putative Vmm-type proteins showed variable expression in vitro.
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| 8. |
- Hamsten, Carl, 1981-
(författare)
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Protein based approaches to understand and prevent contagious bovine pleuropneumonia
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Contagious bovine pleuropneumonia (CBPP) is a severe infectious disease caused by Mycoplasma mycoides subsp. mycoides small colony type (M. mycoides SC) and is a vast problem in Africa. Current CBPP prevention is based on attenuated live strain vaccines, but these are limited by factors such as short-term immunity, cold-chain dependence and retained virulence. CBPP can be diagnosed using post-mortem examination, identification of the agent using culture and PCR based methods as well as serological diagnostic methods, but the latter are generally not sensitive enough and there is also demand for an inexpensive, pen side field test.The research presented in this thesis was focused on using recombinantly expressed surface proteins from M. mycoides SC to characterize humoral immune responses to CBPP. Thereby candidate proteins to be used in development of serological diagnostic methods and possibly subunit vaccines could be identified. As a first step, five putative variable surface proteins of M. mycoides SC were expressed and purified from E. coli in Paper I. These proteins were analyzed using immunoblotting techniques and results showed that one protein, MSC_0364, was variably expressed on the surface of M. mycoides SC in vitro. Paper II presents expanded efforts including cloning and expression of 64 recombinant surface proteins and an assay for high throughput analysis of protein-specific IgG, IgA and IgM titers in hundreds of sera using a bead-based screening assay. The assay was evaluated by protein-specific inhibition experiments, comparisons to Western blotting and monitoring of immune responses over time in a study with sera taken from eight animals over 293 days from a previous vaccine trial.Papers III and IV present applications using the recombinant proteins and bead-based screening assay wherein proteins for diagnostic and vaccine development were identified. In Paper III, the assay was used to screen 61 proteins using well-characterized serum samples from cattle with CBPP and healthy controls, resulting in selection of eight proteins suitable for diagnostic use. These proteins were combined and evaluated in a proof-of-concept ELISA with a discriminative power that enabled 96% correct classification of sera from CBPP-affected and CBPP-free bovines. Paper IV reports the results and protein-specific analyses of a vaccine trial using the recombinant putative variable surface proteins presented in Paper I as a subunit vaccine. The vaccine conferred no protection, but a weak vaccine response could not be excluded as the cause of failure. In an effort to identity other protein candidates to be used in a subunit vaccine, protein-specific analysis of humoral immune responses elicited by the currently approved live strain vaccine, T1/44, were investigated. Here, five proteins with high IgG titers associated to immunity were identified: LppQ, MSC_02714, MSC_0136, MSC_0079 and MSC_0431. These proteins may be important in the development of a novel subunit vaccine against CBPP.
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| 9. |
- Hamsten, Carl, 1981-, et al.
(författare)
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Protein-Specific Analysis of Humoral Immune Responses in a Clinical Trial for Vaccines against Contagious Bovine Pleuropneumonia
- 2010
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Ingår i: Clinical and Vaccine Immunology. - 1556-6811 .- 1556-679X. ; 17:5, s. 853-861
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Tidskriftsartikel (refereegranskat)abstract
- Specific humoral immune responses in a clinical trial on cattle for vaccines against contagious bovine pleuropneumonia (CBPP) were investigated. The trial included a subunit vaccine consisting of five recombinant putative variable surface proteins of the infectious agent Mycoplasma mycoides subspecies mycoides small colony type (M. mycoides SC) compared to the currently approved attenuated vaccine strain T1/44 and untreated controls. Humoral immune responses to 65 individual recombinant surface proteins of M. mycoides SC were monitored by a recently developed bead based array assay. Responses to the subunit vaccine components were found to be weak. Animals vaccinated with this vaccine were not protected and had CBPP lesions similar to the untreated controls. In correlating protein-specific humoral responses to T1/44 induced immunity, five proteins associated with a protective immune response were identified,namely LppQ and those of ORFs MSC_0271, MSC_0136, MSC_0079 and MSC_0431. The five proteins may be important candidates in the development of a novel subunit vaccine against CBPP.
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| 10. |
- Hamsten, Carl, 1981-, et al.
(författare)
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Recombinant surface proteomics as a tool to analyze humoral immune responses in bovines infected by Mycoplasma mycoides subsp. mycoides SC
- 2009
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Ingår i: Molecular & Cellular Proteomics. - Stanford : HighWire Press. - 1535-9476 .- 1535-9484. ; 8:11, s. 2544-2554
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Tidskriftsartikel (refereegranskat)abstract
- A systematic approach to characterize the surface proteome of Mycoplasma mycoides subspecies mycoides small colony type (M. mycoides SC), the causing agent of contagious bovine pleuropneumonia (CBPP) in cattle, is presented. Humoral immune responses in 242 CBPP affected cattle and controls were monitored against one third of the surface proteins of M. mycoides SC in a high-throughput magnetic bead based assay. First, 64 surface proteins were selected from the genome sequence of M. mycoides SC and expressed as recombinant proteins in E. coli. Binding of antibodies to each individual protein could then be analyzed simultaneously in minute sample volumes with the Luminex suspension array technology. The assay was optimized on Namibian CBPP positive sera and Swedish negative controls to allow detection and 20-fold mean signal separation between CBPP positive and negative sera. Signals were proven to be protein-specific by inhibition experiments and results agreed with western blot experiments. The assay's potential to monitor IgG, IgM and IgA responses over time was shown in a proof-of-concept study with 116 sera from 8 animals in a CBPP vaccine study. In conclusion, a toolbox with recombinant proteins and a flexible suspension array assay that allows multiplex analysis of humoral immune responses to M mycoides SC, has been created.
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