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Search Results: 1 - 10 of 325586 matches for " S S Jakobsen "
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Quantized rank R matrices
Hans Plesner Jakobsen,S?ren J?ndrup
Mathematics , 1999,
Abstract: First some old as well as new results about P.I. algebras, Ore extensions, and degrees are presented. Then quantized $n\times r$ matrices as well as quantized factor algebras of $M_q(n)$ are analyzed. The latter are the quantized function algebra of rank $r$ matrices obtained by working modulo the ideal generated by all $(r+1)\times (r+1)$ quantum subdeterminants and a certain localization of this algebra is proved to be isomorphic to a more manageable one. In all cases, the quantum parameter is a primitive $m$th roots of unity. The degrees and centers of the algebras are determined when $m$ is a prime and the general structure is obtained for arbitrary $m$.
Efficient Estimation for Diffusions Sampled at High Frequency Over a Fixed Time Interval
Nina Munkholt Jakobsen,Michael S?rensen
Statistics , 2015,
Abstract: Parametric estimation for diffusion processes is considered for high frequency observations over a fixed time interval. The processes solve stochastic differential equations with an unknown parameter in the diffusion coefficient. We find easily verified conditions on approximate martingale estimating functions under which estimators are consistent, rate optimal, and efficient under high frequency (in-fill) asymptotics. The asymptotic distributions of the estimators are shown to be normal variance-mixtures, where the mixing distribution generally depends on the full sample path of the diffusion process over the observation time interval. Utilising the concept of stable convergence, we also obtain the more easily applicable result that for a suitable data dependent normalisation, the estimators converge in distribution to a standard normal distribution. The theory is illustrated by a small simulation study comparing an efficient and a non-efficient estimating function.
Effects of AS-cast and wrought cobalt-chrome-molybdenum and titanium-aluminium-vanadium alloys on cytokine gene expression and protein secretion in J774A.1 macrophages
S S Jakobsen,A Larsen,M Stoltenberg,J M Bruun
European Cells and Materials (ECM) , 2007,
Abstract: Insertion of metal implants is associated with a possible change in the delicate balance between pro- and anti-inflammatory proteins, probably leading to an unfavourable predominantly pro-inflammatory milieu. The most likely cause is an inappropriate activation of macrophages in close relation to the metal implant and wear-products. The aim of the present study was to compare surfaces of as-cast and wrought Cobalt-Chrome-Molybdenum (CoCrMo) alloys and Titanium-Aluminium-Vanadium (TiAlV) alloy when incubated with mouse macrophage J774A.1 cell cultures. Changes in pro- and anti-inflammatory cytokines [TNF-alpha, IL-6, IL-alpha, IL-1beta, IL-10] and proteins known to induce proliferation [M-CSF], chemotaxis [MCP-1] and osteogenesis [TGF-beta, OPG] were determined by ELISA and Real Time reverse transcriptase - PCR (Real Time rt-PCR). Lactate dehydrogenase (LDH) was measured in the medium to asses the cell viability. Surface properties of the discs were characterised with a profilometer and with energy dispersive X-ray spectroscopy. We here report, for the first time, that the prosthetic material surface (non-phagocytable) of as-cast high carbon CoCrMo reduces the pro-inflammatory cytokine IL-6 transcription, the chemokine MCP-1 secretion, and M-CSF secretion by 77 %, 36 %, and 62 %, respectively. Furthermore, we found that reducing surface roughness did not affect this reduction. The results suggest that as-cast CoCrMo alloy is more inert than wrought CoCrMo and wrought TiAlV alloys and could prove to be a superior implant material generating less inflammation which might result in less osteolysis.
NICMOS imaging search for damped Lya galaxies
S. J. Warren,P. Moller,S. M. Fall,P. Jakobsen
Physics , 2001, DOI: 10.1046/j.1365-8711.2001.04629.x
Abstract: We are engaged in a programme of imaging with the STIS and NICMOS (NIC2) instruments aboard the Hubble Space Telescope (HST), to search for the galaxy counterparts of 18 high-redshift z>1.75 damped Lya absorption lines and 5 Lyman-limit systems seen in the spectra of 16 target quasars. This paper presents the results of the imaging campaign with the NIC2 camera. We describe the steps followed in reducing the data and combining in mosaics, and the methods used for subtracting the image of the quasar in each field, and for constructing error frames that include the systematic errors associated with the psf subtraction. To identify candidate counterparts, that are either compact or diffuse, we convolved the image and variance frames with circular top-hat filters of diameter 0.45 and 0.90 arcsec respectively, to create frames of summed S/N within the aperture. For each target quasar we provide catalogues listing positions and aperture magnitudes of all sources within a square of side 7.5 arcsec centred on the quasar, detected at S/N>6. We find a total of 41 candidates of which three have already been confirmed spectroscopically as the counterparts. We provide the aperture magnitude detection limits as a function of impact parameter, for both detection filters, for each field. The average detection limit for compact (diffuse) sources is H(AB)=25.0 (24.4) at an angular separation of 0.56 arcsec (0.79 arcsec) from the quasar, improving to H(AB)=25.5 (24.8) at large angular separations. For the brighter sources we have measured the half-light radius and the n parameter of the best-fit deconvolved Sersic-law surface-brightness profile, and the ellipticity and orientation.
Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae)
Thomas Marcussen, Bengt Oxelman, Anna Skog, Kjetill S Jakobsen
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-45
Abstract: We sequenced a ~1500 bp NRPD2/E2-like fragment from 18 Viola species, mostly paleopolyploids, and 6 non-Viola Violaceae species. Incongruence between the NRPD2/E2-like gene phylogeny and species phylogeny indicates a first duplication of NRPD2 relatively basally in Violaceae, with subsequent sorting of paralogs in the descendants, followed by a second duplication in the common ancestor of Viola and Allexis. In Viola, the mutation pattern suggested (sub-) neofunctionalization of the two NRPD2/E2-like paralogs, NRPD2/E2-a and NRPD2/E2-b. The dN/dS ratios indicated that a 54 bp region exerted strong positive selection for both paralogs immediately following duplication. This 54 bp region encodes a domain that is involved in the binding of the Nrpd2 subunit with other Pol IV/V subunits, and may be important for correct recognition of subunits specific to Pol IV and Pol V. Across all Viola taxa 73 NRPD2/E2-like sequences were obtained, of which 23 (32%) were putative pseudogenes - all occurring in polyploids. The NRPD2 duplication was conserved in all lineages except the diploid MELVIO clade, in which NRPD2/E2-b was lost, and its allopolyploid derivates from hybridization with the CHAM clade, section Viola and section Melanium, in which NRPD2/E2-a occurred in multiple copies while NRPD2/E2-b paralogs were either absent or pseudogenized.Following the relatively recent split of Pol IV and Pol V, our data indicate that these two multi-subunit enzymes are still in the process of specialization and each acquiring fully subfunctionalized copies of their subunit genes. Even after specialization, the NRPD2/E2-like paralogs are prone to pseudogenization and gene conversion and NRPD2 and NRPE2 copy number is a highly dynamic process modulated by allopolyploidy and gene death.Eukaryotes normally possess three nuclear DNA-dependent RNA polymerases (Pols), Pol I-III, functionally specialized for synthesis of different types of RNA and thus essential for viability. The Pol holoenzymes
The predictive value of microRNA-126 in relation to first line treatment with capecitabine and oxaliplatin in patients with metastatic colorectal cancer
Torben Hansen, Flemming S?rensen, Jan Lindebjerg, Anders Jakobsen
BMC Cancer , 2012, DOI: 10.1186/1471-2407-12-83
Abstract: The study included 89 patients with mCRC. In situ hybridization (ISH) was performed to detect miRNA-126 in formalin-fixed paraffin embedded tissue from primary tumours. The expression of miRNA-126, area per image (μm2), was measured using image analysis. Clinical response was evaluated according to RECIST. Progression free survival (PFS) was compared using the Kaplan-Meier method and the log rank test. Tumours were classified as low or high miRNA-126 expressing tumours using the median value from the patients with response as cut-off.The median miRNA-126 expression level was significantly higher in patients responding to XELOX, 3629 μm2 (95% CI, 2566-4846), compared to the patients not responding, 1670 μm2 (95% CI, 1436-2041), p < 0.0001. The positive predictive value was 90%, and the negative predictive value was 71%. The median PFS of patients with high expressing tumours was 11.5 months (95% CI, 9.0-12.7 months) compared to 6.0 months (95% CI, 4.8-6.9 months) for patients with low expressing tumours, p < 0.0001.Angiogenesis quantified by ISH of miRNA-126 was related to response to first line XELOX in patients with mCRC, translating to a significant difference in PFS. The predictive value of miRNA-126 remains to be further elucidated in prospective studies.In the recent years, a rapidly growing number of treatment modalities have become available for the treatment of patients with metastatic colorectal cancer (mCRC). It is therefore more important than ever to identify the right patients for the right treatment. Combination chemotherapy constitutes the backbone of mCRC treatment and combined with anti-angiogenetic therapy this is a common first line choice.In the search for potential biomarkers, angiogenesis, the formation of new blood vessels from pre-existing vessels, has been addressed for obvious reasons, including the introduction of anti-angiogenetic treatment. Furthermore, the important role of angiogenesis in the growth and dissemination of malignant tumou
Recombination and selectional forces in cyanopeptolin NRPS operons from highly similar, but geographically remote Planktothrix strains
Trine B Rounge, Thomas Rohrlack, Tom Kristensen, Kjetill S Jakobsen
BMC Microbiology , 2008, DOI: 10.1186/1471-2180-8-141
Abstract: We have investigated two cyanopeptolin gene clusters from highly similar, but geographically remote strains of the same genus. Sequencing of a nonribosomal peptide synthetase (NRPS) cyanopeptolin gene cluster from the Japanese strain Planktothrix NIES 205 (205-oci), showed the 30 kb gene cluster to be highly similar to the oci gene cluster previously described in Planktothrix NIVA CYA 116, isolated in Norway. Both operons contained seven NRPS modules, a sulfotransferase (S) and a glyceric acid loading (GA)-domain. Sequence analyses showed a high degree of conservation, except for the presence of an epimerase domain in NIES 205 and the regions around the epimerase, showing high substitution rates and Ka/Ks values above 1. The two strains produce almost identical cyanopeptolins, cyanopeptolin-1138 and oscillapeptin E respectively, but with slight differences regarding the production of minor cyanopeptolin variants. These variants may be the result of relaxed adenylation (A)-domain specificity in the nonribosomal enzyme complex. Other genetic markers (16S rRNA, ntcA and the phycocyanin cpcBA spacer) were identical, supporting that these geographically separated Planktothrix strains are closely related.A horizontal gene transfer event resulting in exchange of a whole module-encoding region was observed. Nucleotide statistics indicate that both purifying selection and positive selection forces are operating on the gene cluster. The positive selection forces are acting within and around the epimerase insertion while purifying selection conserves the remaining (major) part of the gene cluster. The presence of an epimerase in the gene cluster is in line with the D-configuration of Htyr, determined experimentally in oscillapeptin E in a previous study.Cyanopeptolins are nonribosomally produced peptides with highly variable composition. The general structure of the cyanopeptolin peptide family encompasses 7 amino acids, including the residue 3-amino-6-hydroxy-2-piperidone (Ah
Biphenyl-4,4′-dicarboxylic acid N,N-dimethylformamide monosolvate
Søren Jakobsen,David Stephen Wragg,Karl Petter Lillerud
Acta Crystallographica Section E , 2010, DOI: 10.1107/s1600536810030515
Abstract: Biphenyl-4,4′-dicarboxylic acid was recrystallized from N,N-dimethylformamide (DMF) yielding the title compound, C14H10O4·2C3H7NO. The acid molecules are located on crystallographic centres of inversion and are hydrogen bonded to DMF molecules. These hydrogen-bonded units form infinite chains although there is no interaction between the methyl groups of neighboring DMF molecules.
Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure
Thomas H. A. Haverkamp, ?yvind Hammer, Kjetill S. Jakobsen
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0085990
Abstract: Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.
Caught in the act: a helium-reionizing quasar near the line of sight to Q0302-003
P. Jakobsen,R. A. Jansen,S. Wagner,D. Reimers
Physics , 2002, DOI: 10.1051/0004-6361:20021579
Abstract: We report the discovery of a quasar at z=3.050+/-0.003, closely coincident in redshift with the isolated low-opacity feature seen near z~3.056 in the otherwise black portion of the HeII Gunn-Peterson absorption trough seen toward the z=3.286 background quasar Q0302-003, located 6.5' away on the sky. We explore plausible models for the HeIII ionization zone created by this neighboring quasar and its interception with the line of sight toward Q0302-003. At its present brightness of V=20.5 and separation of D=3.2 Mpc, the quasar can readily account for the opacity gap in the HeII absorption spectrum of Q0302-003, provided it has been active for t_Q > 10^7 y. This is the first clear detection of the `transverse' proximity effect and imprint of a quasar on the intervening absorption detected along an adjacent line of sight.
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