| 1421. |
- Nilsson, Björn, et al.
(författare)
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An improved method for detecting and delineating genomic regions with altered gene expression in cancer
- 2008
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Ingår i: GENOME BIOL. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 9:1, s. R13-
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Tidskriftsartikel (refereegranskat)abstract
- Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method combines top-notch detection performance with an ability to delineate relevant regions without excessive over-segmentation, making it a significant advance over existing methods. Software (Rendersome) is provided.
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| 1422. |
- Nilsson, Björn, et al.
(författare)
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Cross-platform classification in microarray-based leukemia diagnostics
- 2006
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Ingår i: Haematologica. - 1592-8721 .- 0390-6078. ; 91:6, s. 821-824
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Tidskriftsartikel (refereegranskat)abstract
- Gene expression profiling is a powerful technique for classifying hematologic malignancies. Its clinical use is, however, currently hindered by the need to collect large sets of expression profiles at each diagnostic facility. To overcome this limitation, we introduced cross-platform classification, allowing classifier construction using pre-existing microarray datasets. As proof-of-principle, we performed cross-platform classification of acute myeloid leukemia and childhood acute lymphoblastic leukemia using expression data from four different facilities. We show that cross-platform classification of these disorders is achievable, and, strikingly, that the diagnostic accuracy can be retained. We conclude that cross-platform classification constitutes an effective and convenient way to implement microarray diagnostics.
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| 1423. |
- Nilsson, Björn, et al.
(författare)
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Threshold-free high-power methods for the ontological analysis of genome-wide gene expression studies
- 2007
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 8:5, s. R74-
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Tidskriftsartikel (refereegranskat)abstract
- Ontological analysis facilitates microarray data interpretation. We describe new ontological analysis methods which, unlike existing approaches, are threshold-free and statistically powerful. We perform extensive evaluations and introduce a new concept, detection spectra, to characterize methods. We show that different ontological analysis methods exhibit distinct detection spectra, and that it is critical to account for this diversity. Our results argue strongly against the continued use of existing methods, and provide directions towards an enhanced approach.
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| 1424. |
- Nilsson, Björn, et al.
(författare)
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Ultrasome : efficient aberration caller for copy number studies of ultra-high resolution
- 2009
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 25:8, s. 1078-1079
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Multimillion-probe microarrays allow detection of gains and losses of chromosomal material at unprecedented resolution. However, the data generated by these arrays are several-fold larger than data from earlier platforms, creating a need for efficient analysis tools that scale robustly with data size. Results: We developed a new aberration caller, Ultrasome, that delineates genomic changes-of-interest with dramatically improved efficiency. Ultrasome shows near-linear computational complexity and processes latest generation copy number arrays about 10 000 times faster than standard methods with preserved analytic accuracy.
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| 1425. |
- Nilsson, Carin, et al.
(författare)
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Bottenfauna i Gävleborgs län 2013 - Regional miljöövervakning och kalkeffektkontroll av nitton vattendrag
- 2014
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Medins Biologi AB har fått i uppdrag av Länsstyrelsen i Gävleborgs län att utföra analyserav bottenfauna vid 19 lokaler i rinnande vatten (Tabell 1 och Figur 1). Provtagningenutfördes av personal från länsstyrelsen i Gävleborg samt Hudiksvalls kommun.Artbestämning samt utvärdering av resultaten gjordes av Medins Biologi. Det övergripandesyftet med undersökningarna var att undersökta och beskriva lokalernas bottenfaunasamt bedöma vilka miljöförhållanden nämnda djursamhällen speglar. Årets undersökningarkan även fungera som referenser till framtida undersökningar.Åtta av de provtagna lokalerna ingår i ett RMÖ- program (Regional Miljö Övervakning)som länsstyrelsen kallar ”Omdrevsvattendrag” (Tabell 1 och Figur 1). Programmet omfattarvissa utvalda vattendrag som planeras att provtas vid upprepade tillfällen. Programmetlöper över en sexårscykel där varje vattendrag provtas en gång per sexårsperiod.Bottenfaunan har inte undersökts tidigare vid dessa lokaler. Syftet är främst att geunderlag för statusklassning enligt Vattendirektivet. Hångelån (X8) är ett referensvattendragoch ingår i ett annat RMÖ-program som kallas ”Trendvattendrag”. Syftet meddetta program är att skapa tidserier och därmed kunna se om miljötillståndet i de utvaldavattendragen förändras. Hångelån undersöks årligen. De resterande tio vattendrageningår i kalkeffektuppföljningen (KEU). Syftet är främst att bedöma försurningens ochkalkningens effekter på bottenfaunan. Flera av dessa vattendrag har undersökts tidigare.
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| 1426. |
- Nilsson, Fritjof, Docent, 1978-, et al.
(författare)
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Modelling anti-icing of railway overhead catenary wires by resistive heating
- 2019
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Ingår i: International Journal of Heat and Mass Transfer. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0017-9310 .- 1879-2189. ; 143
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Tidskriftsartikel (refereegranskat)abstract
- Aggregation of ice on electrical cables and apparatus can cause severe equipment malfunction and is thus considered as a serious problem, especially in arctic climate zones. In particular, cable damage caused by ice accumulation on railway catenary wires is in wintertime a common origin for delayed trains in the northern parts of Europe. This study examines how resistive heating can be used for preventing formation of ice on metallic, non-insulated electrical cables. The heat equation and the Navier Stokes equations were solved simultaneously with FEM in 3D in order to predict the cable temperature as function of external temperature, applied voltage, wind speed, wind direction, and heating time. An analytical expression for the heat transfer coefficient was derived from the FEM simulations and it was concluded that the influence of wind direction can typically be neglected. Experimental validation measurements were performed on Kanthal cables in a climate chamber, giving temperature increase results in good agreement with the simulation predictions. The resistive heating efficiency, i.e. the ratio between applied electrical energy and resulting thermal energy, was found to be approximately 68% in this particular study.
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| 1427. |
- Nilsson, Fritjof, et al.
(författare)
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Predicting Solubility and Diffusivity of Gases in Polymers under High Pressure : N-2 in Polycarbonate and Poly(ether-ether-ketone)
- 2013
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Ingår i: Industrial & Engineering Chemistry Research. - : American Chemical Society (ACS). - 0888-5885 .- 1520-5045. ; 52:26, s. 8655-8663
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to develop a model that predicts the gas solubility and the sorption and desorption kinetics in polymer granulates over large temperature and pressure intervals. Besides the part predicting the solubility and diffusivity, the model involves the simultaneous solution of the diffusion equation and the heat equation in three dimensions using a finite element method (FEM). When the temperature- and pressure-dependent solubility of a specific polymer/gas combination is not known, an improved version of the non-equilibrium lattice fluid model (NELF) is used to predict the solubility. The improvement of the NELF model includes the use of Hansen's solubility parameters, and it uses pressure-volume-temperature (PVT) data from two new empirical models, which accurately estimate polymer densities over a wide range of temperatures and pressures. The new solubility model predicted the solubility-pressure data of N-2 in poly(ethyl methacrylate) and N-2 and CH4 in polycarbonate (PC) at pressures below 4.5 MPa, without using any adjustable interaction parameters. The model was used to predict the solubility of N-2 in poly(ether-ether-ketone) (PEEK) and PC at a very high pressure (67 MPa). Experimental N-2 solubility data were obtained with a specially built reactor yielding high pressure and temperature. For PEEK, it was possible to predict the very high pressure solubility using a gas-polymer interaction parameter obtained from data taken at low pressures In addition, a new free-volume-based diffusivity model requiring no adjustable interaction parameters was developed, and it successfully predicted the desorption kinetics of N-2 from PEEK and PC.
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| 1428. |
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| 1429. |
- Nilsson, Klara, et al.
(författare)
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Pasting and gelation of faba bean starch-protein mixtures
- 2023
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Ingår i: Food Hydrocolloids. - : Elsevier BV. - 0268-005X .- 1873-7137. ; 138, s. 108494-
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Tidskriftsartikel (refereegranskat)abstract
- Starch and protein are major components in many foods, contributing to nutritional and textural properties. Understanding how the behaviour and interactions of these components contribute to different textures is important. In this study, mixed gel systems were created with different ratios of starch to protein (constant solid content 12%) extracted from faba bean, a promising crop for locally produced plant-based foods in cold climate regions. The mixed starch-protein gels were characterised in terms of pasting, texture and microstructure. Starch-rich mixtures showed higher water binding and water absorption than samples with higher protein content. A tendency for more efficient hydration in starch-rich samples was confirmed by NMR. Iodine affinity appeared to be lower for high-protein samples, particularly at higher temperatures. Mixtures with high starch content also showed higher viscosity during pasting, higher storage modulus throughout gelation, lower tan delta and lower frequency dependence of the final gel. Characterisation by compression tests showed stronger and more elastic gels with increasing starch content. Light microscopy revealed that starch granules were tightly packed, espe-cially at higher starch content, with protein filling the spaces between starch granules. SEM micrographs revealed a network structure with larger pores and thicker strands in samples with higher starch content. Overall, increasing protein content reduced viscosity during pasting and caused softer gels, likely owing to different gelation and hydration properties of starch and protein.
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| 1430. |
- Nilsson, Lars, et al.
(författare)
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The molecular signature of MDS stem cells supports a stem-cell origin of 5q-myelodysplastic syndromes
- 2007
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 110:8, s. 3005-3014
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Tidskriftsartikel (refereegranskat)abstract
- Global gene expression profiling of highly purified 5q-deleted CD34+CD38–Thy1+ cells in 5q– myelodysplastic syndromes (MDSs) supported that they might originate from and outcompete normal CD34+CD38–Thy1+ hematopoietic stem cells. Few but distinct differences in gene expression distinguished MDS and normal stem cells. Expression of BMI1, encoding a critical regulator of self-renewal, was up-regulated in 5q– stem cells. Whereas multiple previous MDS genetic screens failed to identify altered expression of the gene encoding the myeloid transcription factor CEBPA, stage-specific and extensive down-regulation of CEBPA was specifically observed in MDS progenitors. These studies establish the importance of molecular characterization of distinct stages of cancer stem and progenitor cells to enhance the resolution of stage-specific dysregulated gene expression.
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