| 11. |
- Lundqvist, Joakim, et al.
(författare)
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ATP-Induced Conformational Dynamics in the AAA plus Motor Unit of Magnesium Chelatase
- 2010
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 18:3, s. 354-365
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Tidskriftsartikel (refereegranskat)abstract
- Mg-chelatase catalyzes the first committed step of the chlorophyll biosynthetic pathway, the ATP-dependent insertion of Mg2+ into protoporphyrin IX (PPIX). Here we report the reconstruction using single-particle cryo-electron microscopy of the complex between subunits BchD and BchI of Rhodobacter capsulatus Mg-chelatase in the presence of ADP, the nonhydrolyzable ATP analog AMPPNP, and ATP at 7.5 angstrom, 14 angstrom, and 13 angstrom resolution, respectively. We show that the two AAA+ modules of the subunits form a unique complex of 3 dimers related by a three-fold axis. The reconstructions demonstrate substantial differences between the conformations of the complex in the presence of ATIP and ADP, and suggest that the C-terminal integrin-I domains of the BchD subunits play a central role in transmitting conformational changes of BchI to BchD. Based on these data a model for the function of magnesium chelatase is proposed.
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| 12. |
- Nielsen, Henrietta, et al.
(författare)
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NG2 cells, a new trail for Alzheimer's disease mechanisms?
- 2013
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Ingår i: Acta Neuropathologica Communications. - : Springer Science and Business Media LLC. - 2051-5960. ; 1:1
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Tidskriftsartikel (refereegranskat)abstract
- Neuron Glial 2 (NG2) cells are glial cells known to serve as oligodendrocyte progenitors as well as modulators of the neuronal network. Altered NG2 cell morphology and up-regulation as well as increased shedding of the proteoglycan NG2 expressed on the cell surface have been described in rodent models of brain injury. Here we describe alterations in the human NG2 cell population in response to pathological changes characteristic of Alzheimer's disease (AD).
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| 13. |
- Nyström, Helena Filipsson, 1966, et al.
(författare)
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Thyroid volume in Swedish school children: a national, stratified, population-based survey.
- 2010
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Ingår i: European journal of clinical nutrition. - : Springer Science and Business Media LLC. - 1476-5640 .- 0954-3007. ; 64:11, s. 1289-95
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Tidskriftsartikel (refereegranskat)abstract
- Sweden has had a salt iodination program since 1936. This first national surveillance study on iodine nutrition infers an adequate level of urinary iodine concentration (UIC 125μg/l) and the aim is now to evaluate thyroid volume (Tvol) in the same national sample.
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| 14. |
- O'Boyle, Noel, et al.
(författare)
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Open Data, Open Source and Open Standards in chemistry : The Blue Obelisk five years on
- 2011
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Ingår i: Journal of Cheminformatics. - : BioMed Central. - 1758-2946. ; 3, s. 37-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data,Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistryresearch by promoting interoperability between chemistry software, encouraging cooperation between OpenSource developers, and developing community resources and Open Standards. Results: This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveysprogress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions: We show that the Blue Obelisk has been very successful in bringing together researchers anddevelopers with common interests in ODOSOS, leading to development of many useful resources freely availableto the chemistry community
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| 15. |
- Staron, Miroslaw, 1977, et al.
(författare)
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Measuring and Visualizing Code Stability - A Case Study at Three Companies
- 2013
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Ingår i: IWSM/Mensura, Conference proceedings, IEEE. - : IEEE.
-
Konferensbidrag (refereegranskat)abstract
- Monitoring performance of software development organizations can be achieved from a number of perspectives – e.g. using such tools as Balanced Scorecards or corporate dashboards. However, automated monitoring through quantitative metrics usually gives the best cost-benefit trade-off. In this paper we present results from a study on using code stability indicators as a tool for product stability and organizational performance, conducted at three different software development companies – Ericsson AB, Saab AB Electronic Defense Systems (Saab) and Volvo Group Trucks Technology (Volvo Group). The results show that visualizing the source code changes using heatmaps and linking these visualizations to defect inflow profiles provide indicators of how stable the product under development is and whether quality assurance efforts should be directed to specific parts of the product. Observing the indicator and making decisions based on its visualization leads to shorter feedback loops between development and test, thus resulting in lower development costs, shorter lead time and increased quality. The industrial case study in the paper shows that the indicator and its visualization can show whether the modifications of software products are focused on parts of the code base or are spread widely throughout the product.
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| 16. |
- Vafadar-Isfahani, Baharak, et al.
(författare)
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Identification of SPARC-like 1 Protein as Part of a Biomarker Panel for Alzheimer's Disease in Cerebrospinal Fluid
- 2012
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Ingår i: Journal of Alzheimer's Disease. - 1387-2877. ; 28:3, s. 625-636
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Tidskriftsartikel (refereegranskat)abstract
- We have used proteomic fingerprinting to investigate diagnosis of Alzheimer's disease (AD). Samples of lumbar cerebrospinal fluid (CSF) from clinically-diagnosed AD cases (n = 33), age-matched controls (n = 20), and mild cognitive impairment (MCI) patients (n = 10) were used to obtain proteomic profiles, followed by bioinformatic analysis that generated a set of potential biomarkers in CSF samples that could discriminate AD cases from controls. The identity of the biomarker ions was determined using mass spectroscopy. The panel of seven peptide biomarker ions was able to discriminate AD patients from controls with a median accuracy of 95% (sensitivity 85%, specificity 97%). When this model was applied to an independent blind dataset from MCI patients, the intensity of signals was intermediate between the control and AD patients implying that these markers could potentially predict patients with early neurodegenerative disease. The panel were identified, in order of predictive ability, as SPARC-like 1 protein, fibrinogen alpha chain precursor, amyloid-beta, apolipoprotein E precursor, serum albumin precursor, keratin type I cytoskeletal 9, and tetranectin. The 7 ion ANN model was further validated using an independent cohort of samples, where the model was able to classify AD cases from controls with median accuracy of 84.5% (sensitivity 93.3%, specificity 75.7%). Validation by immunoassay was performed on the top three identified markers using the discovery samples and an independent sample cohort which was from postmortem confirmed AD patients (n = 17).
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| 17. |
- Wallnerström, Carl Johan, 1980-, et al.
(författare)
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Potential of dynamic rating in Sweden
- 2014
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Konferensbidrag (refereegranskat)abstract
- Power system owners are facing major challenges, for example with changed electricity consumption and production patterns; more distributed generation and increased demand of cost efficiency while maintaining high reliability. The concept of dynamic rating can act as a part solution and implies that the capacity of a component is dynamically varying as a function of external parameters such as weather and load history. This hence implies that a component can be better utilized. This can have both direct economic benefits for the utility, but also benefits for the society and the environment by lower tariff levels, faster and cheaper connection of local environmentally friendly electricity production and less climate impact associated with component production and installation. This paper gives a brief introduction to the concept of dynamic rating applied to power systems. Furthermore, results and conclusions from two workshops during 2013 are summarized, where representatives from Vattenfall and Fortum (distribution system operators), ABB (producer and developer that work with dynamic rating solutions), Swedish national grid and several persons from the academia contributed. This was complemented by interviews with the involved companies. The result is a mapping of knowledge, research, development interests, current situation and future visions. All parties show a great interest and see potential, but there are also challenges to be solved.
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| 18. |
- Zetterblad, Jenny, et al.
(författare)
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Genomics based analysis of interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication
- 2010
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11:108
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Tidskriftsartikel (refereegranskat)abstract
- Background: The use of functional genomics has largely increased our understanding of cell biology and promises to help the development of systems biology needed to understand the complex order of events that regulates cellular differentiation in vivo. One model system clearly dependent on the integration of extra and intra cellular signals is the development of B-lymphocytes from hematopoietic stem cells in the bone marrow. This developmental pathway involves several defined differentiation stages associated with specific expression of genes including surface markers that can be used for the prospective isolation of the progenitor cells directly from the bone marrow to allow for ex vivo gene expression analysis. The developmental process can be simulated in vitro making it possible to dissect information about cell/cell communication as well as to address the relevance of communication pathways in a rather direct manner. Thus we believe that B-lymphocyte development represents a useful model system to take the first steps towards systems biology investigations in the bone marrow. Results: In order to identify extra cellular signals that promote B lymphocyte development we created a database with approximately 400 receptor ligand pairs and software matching gene expression data from two cell populations to obtain information about possible communication pathways. Using this database and gene expression data from NIH3T3 cells (unable to support B cell development), OP-9 cells (strongly supportive of B cell development), pro-B and pre-B cells as well as mature peripheral B-lineage cells, we were able to identify a set of potential stage and stromal cell restricted communication pathways. Functional analysis of some of these potential ways of communication allowed us to identify BMP-4 as a potent stimulator of B-cell development in vitro. Further, the analysis suggested that there existed possibilities for progenitor B cells to send signals to the stroma. The functional consequences of this were investigated by co-culture experiments revealing that the co-incubation of stromal cells with B cell progenitors altered both the morphology and the gene expression pattern in the stromal cells. Conclusions: We believe that this gene expression data analysis method allows for the identification of functionally relevant interactions and therefore could be applied to other data sets to unravel novel communication pathways.
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