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| 3. |
- Malmberg, Maja, et al.
(författare)
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Genetic characterization of a novel adenovirus detected in captive bottlenose dolphin (Tursiops truncates) suffering from self-limiting gastroenteritis
- 2016
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Adenoviruses have a wide host range and are common pathogens in vertebrates. In cetaceans, adenoviruses have only rarely been detected and correlated with disease. A novel adenovirus was recently detected in captive bottlenose dolphin (Tursiops truncates) suffering from self-limiting gastroenteritis. The initial analysis of partial pol and hexon gene sequences indicated that this was a hitherto unknown adenovirus with less than 80% sequence identity to previously published sequences. The aim of this study was to further genetically characterize this novel adenovirus using a high-throughput sequencing approach for whole-genome sequencing. Fecal samples from affected bottlenose dolphins were collected as previously described. Samples were homogenized and centrifuged through filters with 0.22 μm pores. To remove non-viral DNA the filtrate was treated with DNase and RNase prior to DNA extraction. Nextera XT sequencing libraries were sequenced at the MiSeq platform. Sequence reads were assembled using the MIRA assembler. The longest contigs were used to identify the most similar reference genome using BLASTn. To generate a draft consensus sequence, matching contigs were aligned against the reference genome using CodonCode Aligner software. The complete genome sequence was verified using PCR and Sanger sequencing. The analysis of phylogenetic relationships was conducted in MEGA 5 [2]. Gene prediction and annotation were used using PROKKA, MAKER and GeneMark.hmm with heuristic models. High-throughput sequencing allowed the recovery of the complete sequence of Bottlenose dolphin Adenovirus-1 (BdAdV-1). The sequence is 34 040bp and has an ITR of about 220bp. A total of 26 coding sequences were identified out of which 3 were assigned as hypothetical and 23 were functionally annotated. The homology analysis indicates that the most similar genome is the Bottlenose dolphin Adenovirus 2 (KR024710) (71% identity), followed by the California sea lion adenovirus 1 (KJ563221), and then Bovine adenovirus type 2 (AF252854). We here describe the complete sequence of a recently identified adenovirus associated with gastroenteritis in dolphins. This virus is clearly different from previously published adenoviruses, demonstrating less than 72% sequence identity. A more in-depth analysis of the obtained sequence data and predicted proteins should allow predictions to be made regarding e.g. tropism. The study also demonstrate the usefulness of high-throughput sequencing to obtain full-length genomes of genetically divergent viruses.
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- Parsmo, Rasmus, et al.
(författare)
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BRAVE ECO – Benchmark for Reduction of Anchoring Vessels’ Emissions – Enabling Change of Operation
- 2021
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This feasibility study aims to evaluate the possibilities to reduce air emissions from ships anchored in port areas and, then especially the Port of Gothenburg. For this purpose, the study uses two main approaches. Firstly, it analyses the reasons and legal/business aspects for anchoring. Secondly, this study develops a reproducible calculation model for anchored vessels' CO2 emissions. Regulation of anchoring sites are not entirely clear since international regulation partly applies, also it is not clear who is responsible for the anchoring sites. This implies that the port´s scope of action is limited mainly to the ships that are calling the port. However, also emission from other ships at in the port area has been evaluated in this study to get a broader perspective. This pre-study provides both qualitative and quantitative findings and it is produced using mixed methods, including workshops with relevant port stakeholders. It also involves different scientific disciplines and several authors from the Port of Gothenburg Authority, IVL Swedish Environmental Research Institute, Maritime Studies at Chalmers University of Technology and the School of Business, Economics and Law at the University of Gothenburg. Furthermore, in connection to this study, one bachelor's thesis and two master's theses have been carried out. The results show that it is mainly tanker ships that are anchoring in Gothenburg and that their main reasons for anchoring are related to awaiting Laycan or waiting for an available berth. The companies involved in the study generally combine time charter and voyage charter contracts to access vessel capacity. The inputs from the workshops, the interviews conducted with stakeholders and the international literature are “rather” consistent: combining just in time arrival with slow steaming has a great potential for making a business case and to reduce fuel consumption and thereby emissions. However, there are many barriers which needs to be addressed, such as: lack of trust, improving information sharing (actors now communicate via phone or email), loss of income (due to demurrage), attitudes in the industry, the “first come, first serve” concept, risk of missing estimated time of arrival and port infrastructure. Even if there are many barriers, several actors in the port already have experience of combining just in time arrival and slow steaming. In this study, we develop a reproducible emission calculation model that calculates CO2eq emissions. The emissions are partly calculated by using the ships’ positions (AIS-data) from 2019, to extract the time spent at anchor. The emission model calculates the anchored vessels' total CO2eq emissions, but the model also calculates the theoretical potential for avoiding emission by using the time at anchor to slow steam. The results show that all tanker ships that anchored outside the port in 2019, could theoretically have reduced their emissions with about 30 ktonnes CO2eq, if they would have been notified of delays 24 hours before arrival and then reduced their speed to 10 knots. The results also show that using time to slow steam have a much greater potential to reduce emissions than if the ships would only reduce the time at anchor (by using fewer ships to perform the same transport work). This is especially true for the initial speed reductions (10-14 knots). This study also evaluates the emission calculation methods and assesses the uncertainties, by comparing different sources and underlying assumptions with real world data. The study argues that it is problematic to just use default values proposed in the global emission inventory issued by the International Maritime Organization (IMO). Using default values for estimating emission makes it harder to estimate the real effect of a new policy, regulation, or incentive in the port. However, a better emission inventory requires that on-board visits are made or that data is obtained digitally. The largest calculation uncertainties now are for boiler fuel consumption and bunker ships fuel consumption at the anchorage areas.
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- Andersson, Niclas, et al.
(författare)
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Competition and barriers to entry the construction sector
- 2003
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Ingår i: Construction Innovation and Global Competitiveness. - 0849314496 ; , s. 461-475
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Konferensbidrag (refereegranskat)abstract
- In 1999 Sweden and Denmark were physically, linked for the first time by, a bridge bringing the countries even closer. The bridge connects the capital area of Denmark and the south part of Sweden in an area called the Oresund region. At a national level there is a mutual political interest to create an integrated market in the Oresund region and in a wider perspective the bridge is a physical contribution to the common market within the European Union. The objectives of this study, are to describe the characteristics of competition in Sweden and Denmark as a means to identify, barriers for companies in one country to entry, the construction market In the other country. The paper is principally based on two separate meso-economic analyses of the Swedish and Danish construction sectors presenting some basic characteristics in figures and facts.
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- Arvidsson, Anna, 1973, et al.
(författare)
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Early interactions between leukocytes and three different potentially bioactive titanium surface modifications
- 2011
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Ingår i: Journal of Biomedical Materials Research. Part B - Applied biomaterials. - : Wiley. - 1552-4973 .- 1552-4981. ; 97:2, s. 364-72
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Tidskriftsartikel (refereegranskat)abstract
- The aim of the present study was to compare the early interactions between leukocytes and three different surface modifications, suggested as bioactive. Blasted titanium discs were modified by alkali and heat treatment, sodium fluoride treatment, or hydroxyapatite coating. A number of these discs were also immersed in simulated body fluid (SBF) for a week, a treatment which yielded high levels of calcium and phosphate on each surface type. The specimens were exposed for human venous blood for 32 minutes and the respiratory burst response was measured in terms of reactive oxygen species with a luminometer, and coverage of viable cells with a fluorescence microscope after staining steps. The topography, morphology, and chemistry of the surfaces were evaluated with optical interferometry and scanning electron microscopy/energy dispersive X-ray analysis (SEM/EDX). A high respiratory burst response was found for HA coated titanium in comparison with the other surface groups (p < 0.0005). The SBF immersion resulted in an increased respiratory burst response (p < 0.0005) and removed statistically significant differences between the surface groups. Thus, the results in the present study indicate that different titanium surface modifications influence the early inflammatory response differently, and that calcium phosphate compounds increase the inflammatory response.
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- Blache, Ludovic, et al.
(författare)
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SoftCut: : A Virtual Planning Tool for Soft Tissue Resection on CT Images
- 2018
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Ingår i: Medical Image Understanding and Analysis. - Cham : Springer. - 9783319959207 ; , s. 299-310
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Konferensbidrag (refereegranskat)abstract
- With the increasing use of three-dimensional (3D) models and Computer Aided Design (CAD) in the medical domain, virtual surgical planning is now frequently used. Most of the current solutions focus on bone surgical operations. However, for head and neck oncologic resection, soft tissue ablation and reconstruction are common operations. In this paper, we propose a method to provide a fast and efficient estimation of shape and dimensions of soft tissue resections. Our approach takes advantage of a simple sketch-based interface which allows the user to paint the contour of the resection on a patient specific 3D model reconstructed from a computed tomography (CT) scan. The volume is then virtually cut and carved following this pattern. From the outline of the resection defined on the skin surface as a closed curve, we can identify which areas of the skin are inside or outside this shape. We then use distance transforms to identify the soft tissue voxels which are closer from the inside of this shape. Thus, we can propagate the shape of the resection inside the soft tissue layers of the volume. We demonstrate the usefulness of the method on patient specific CT data.
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| 9. |
- Borgegard, Tomas, et al.
(författare)
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Alzheimers Disease: Presenilin 2-Sparing gamma-Secretase Inhibition Is a Tolerable A beta Peptide-Lowering Strategy
- 2012
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Ingår i: Journal of Neuroscience. - : Society for Neuroscience. - 0270-6474 .- 1529-2401. ; 32:48, s. 17297-17305
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Tidskriftsartikel (refereegranskat)abstract
- gamma-Secretase inhibition represents a major therapeutic strategy for lowering amyloid beta (A beta) peptide production in Alzheimers disease (AD). Progress toward clinical use of gamma-secretase inhibitors has, however, been hampered due to mechanism-based adverse events, primarily related to impairment of Notch signaling. The gamma-secretase inhibitor MRK-560 represents an exception as it is largely tolerable in vivo despite displaying only a small selectivity between A beta production and Notch signaling in vitro. In exploring the molecular basis for the observed tolerability, we show that MRK-560 displays a strong preference for the presenilin 1(PS1) over PS2 subclass of gamma-secretases and is tolerable in wild-type mice but causes dose-dependent Notch-related side effect in PS2-deficient mice at drug exposure levels resulting in a substantial decrease in brain A beta levels. This demonstrates that PS2 plays an important role in mediating essential Notch signaling in several peripheral organs during pharmacological inhibition of PS1 and provide preclinical in vivo proof of concept for PS2-sparing inhibition as a novel, tolerable and efficacious gamma-secretase targeting strategy for AD.
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| 10. |
- Borgegård, Tomas, et al.
(författare)
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Alzheimer's Disease : Presenilin 2-Sparing γ-Secretase Inhibition Is a Tolerable Aβ Peptide-Lowering Strategy
- 2012
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Ingår i: Journal of Neuroscience. - 0270-6474 .- 1529-2401. ; 32:48, s. 17297-17305
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Tidskriftsartikel (refereegranskat)abstract
- γ-Secretase inhibition represents a major therapeutic strategy for lowering amyloid β (Aβ) peptide production in Alzheimer's disease (AD). Progress toward clinical use of γ-secretase inhibitors has, however, been hampered due to mechanism-based adverse events, primarily related to impairment of Notch signaling. The γ-secretase inhibitor MRK-560 represents an exception as it is largely tolerable in vivo despite displaying only a small selectivity between Aβ production and Notch signaling in vitro. In exploring the molecular basis for the observed tolerability, we show that MRK-560 displays a strong preference for the presenilin 1 (PS1) over PS2 subclass of γ-secretases and is tolerable in wild-type mice but causes dose-dependent Notch-related side effect in PS2-deficient mice at drug exposure levels resulting in a substantial decrease in brain Aβ levels. This demonstrates that PS2 plays an important role in mediating essential Notch signaling in several peripheral organs during pharmacological inhibition of PS1 and provide preclinical in vivo proof of concept for PS2-sparing inhibition as a novel, tolerable and efficacious γ-secretase targeting strategy for AD.
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