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| 6. |
- Bjarnason, Ragnar, 1959, et al.
(författare)
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Cartilage oligomeric matrix protein increases in serum after the start of growth hormone treatment in prepubertal children
- 2004
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Ingår i: Journal of Clinical Endocrinology and Metabolism. - : The Endocrine Society. - 0021-972X .- 1945-7197. ; 89:10, s. 5156-60
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Tidskriftsartikel (refereegranskat)abstract
- Both GH and IGF-I stimulate bone growth, but the molecular mechanisms mediating their effects on the growth plate are not fully understood. We measured gene expression by microarray analysis in primary cultured human chondrocytes treated with either GH or IGF-I. One of the genes found to be up-regulated by both GH and IGF-I was that encoding cartilage oligomeric matrix protein (COMP). This protein is predominantly found in the extracellular matrix of cartilage. Mutations in the COMP gene have been associated with syndromes of short stature. To verify that COMP is regulated by GH in vivo, we measured COMP levels in serum in short children treated with GH. The study included 113 short prepubertal children (14 girls and 99 boys) with a mean (+/- sd) age of 8.84 +/- 2.76 yr, height sd score of -2.74 +/- 0.67, and IGF-I sd score of -1.21 +/- 1.07 at the start of GH administration. Serum levels of COMP were 1.58 +/- 0.28, 1.83 +/- 0.28 (P < 0.0001), 1.91 +/- 0.28 (P < 0.0001), 1.78 +/- 0.28 (P < 0.001), and 1.70 +/- 0.24 (P < 0.05) microg/ml at baseline and after 1 wk and 1, 3, and 12 months, respectively.In conclusion, we have demonstrated that COMP expression is up-regulated by both GH and IGF-I in primary cultured human chondrocytes. Furthermore, serum levels of COMP increase after the start of GH treatment in short children.
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| 7. |
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| 8. |
- Bräutigam, Marcus, 1968, et al.
(författare)
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Development of Swedish winter oat with gene technology and molecular breeding
- 2006
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Ingår i: J. Seed Science. - 0039-6990. ; 116:1-2, s. 12-35
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Tidskriftsartikel (refereegranskat)abstract
- In Sweden, oat (Avena sativa) is only grown as a spring crop. A Swedish winter oat, on the other hand, would give increased yields and would secure oat in Swedish agriculture. During three consecutive winters we performed field trials with oat aiming at identifying potential winter material. More than 300 varieties, originating from breeding programs all over the world, were tested. Plants were rated according to winter survival, vigour and general performance during the following growth season and more than 20 lines were identified that were cold hardier than present commercial oat varieties. In parallel experiments a cDNA library was constructed from cold induced English winter oat (Gerald) and ca 10000 EST sequences were generated. After data mining a UniGene set of 2800 oat genes was obtained. By detailed analysis of microarray data from cold stressed Arabidopsis and by advanced bioinformatics, gene interactions in the complex cold induced signal transduction pathway were deduced. By comparison to the oat UniGene set, several genes potentially involved in the regulation of cold hardiness in oat were identified. An Agrobacterium mediated transformation protocol was developed for one oat genotype. Key regulatory genes in cold acclimation will be introduced to oat by genetic transformation or modified by TILLING. Such genes will be used as molecular markers in intogression of winter hardiness to commercial oat.
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| 9. |
- Bräutigam, Marcus, 1968, et al.
(författare)
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Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa
- 2005
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Ingår i: BMC Plant Biol. - : Springer Science and Business Media LLC. - 1471-2229. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Oat is an important crop in North America and northern Europe. In Scandinavia, yields are limited by the fact that oat cannot be used as a winter crop. In order to develop such a crop, more knowledge about mechanisms of cold tolerance in oat is required. RESULTS: From an oat cDNA library 9792 single-pass EST sequences were obtained. The library was prepared from pooled RNA samples isolated from leaves of four-week old Avena sativa (oat) plants incubated at +4 degrees C for 4, 8, 16 and 32 hours. Exclusion of sequences shorter than 100 bp resulted in 8508 high-quality ESTs with a mean length of 710.7 bp. Clustering and assembly identified a set of 2800 different transcripts denoted the Avena sativa cold induced UniGene set (AsCIUniGene set). Taking advantage of various tools and databases, putative functions were assigned to 1620 (58%) of these genes. Of the remaining 1180 unclassified sequences, 427 appeared to be oat-specific since they lacked any significant sequence similarity (Blast E values > 10(-10)) to any sequence available in the public databases. Of the 2800 UniGene sequences, 398 displayed significant homology (BlastX E values < or = 10(-10)) to genes previously reported to be involved in cold stress related processes. 107 novel oat transcription factors were also identified, out of which 51 were similar to genes previously shown to be cold induced. The CBF transcription factors have a major role in regulating cold acclimation. Four oat CBF sequences were found, belonging to the monocot cluster of DREB family ERF/AP2 domain proteins. Finally in the total EST sequence data (5.3 Mbp) approximately 400 potential SSRs were found, a frequency similar to what has previously been identified in Arabidopsis ESTs. CONCLUSION: The AsCIUniGene set will now be used to fabricate an oat biochip, to perform various expression studies with different oat cultivars incubated at varying temperatures, to generate molecular markers and provide tools for various genetic transformation experiments in oat. This will lead to a better understanding of the cellular biology of this important crop and will open up new ways to improve its agronomical properties.
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| 10. |
- Bucin, Dragan, et al.
(författare)
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Heart transplantation across the antibodies against HLA and ABO
- 2006
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Ingår i: Transplant International. - : Frontiers Media SA. - 1432-2277 .- 0934-0874. ; 19:3, s. 239-244
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Tidskriftsartikel (refereegranskat)abstract
- We have intentionally performed heart transplantation in a 5-year-old child, despite the most unfavourable risk factors for patient survival; the presence of high level of antibodies against donor's human leucocyte antigen (HLA) class I/II and blood group antigens. Pretransplant treatment by mycophenolate mofetil, prednisolone, tacrolimus, intravenous immunoglobulin, rituximab, protein-A immunoadsorption (IA) and plasma exchange reduced antibody titres against the donor's lymphocytes from 128 to 16 and against the donor's blood group antigen from 256 to 0. The patient was urgently transplanted with a heart from an ABO incompatible donor (A(1) to O). A standard triple-drug immunosuppressive protocol was used. No hyperacute rejection was seen. Antibodies against the donor's HLA antigens remained at a low level despite three acute rejections. Rising anti-A(1) blood group antibodies preceded the second rejection and were reduced by two blood group-specific IAs and remained at a low level. The patient is doing well despite the persistence of donor-reactive antibodies.
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| 11. |
- Chawade, Aakash, et al.
(författare)
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Global expression profiling of low temperature induced genes in the chilling tolerant japonica rice jumli marshi
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 8:12, s. e81729-
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Tidskriftsartikel (refereegranskat)abstract
- Low temperature is a key factor that limits growth and productivity of many important agronomical crops worldwide. Rice (Oryza sativa L.) is negatively affected already at temperatures below +10°C and is therefore denoted as chilling sensitive. However, chilling tolerant rice cultivars exist and can be commercially cultivated at altitudes up to 3,050 meters with temperatures reaching as low as +4°C. In this work, the global transcriptional response to cold stress (+4°C) was studied in the Nepalese highland variety Jumli Marshi (spp. japonica) and 4,636 genes were identified as significantly differentially expressed within 24 hours of cold stress. Comparison with previously published microarray data from one chilling tolerant and two sensitive rice cultivars identified 182 genes differentially expressed (DE) upon cold stress in all four rice cultivars and 511 genes DE only in the chilling tolerant rice. Promoter analysis of the 182 genes suggests a complex cross-talk between ABRE and CBF regulons. Promoter analysis of the 511 genes identified over-represented ABRE motifs but not DRE motifs, suggesting a role for ABA signaling in cold tolerance. Moreover, 2,101 genes were DE in Jumli Marshi alone. By chromosomal localization analysis, 473 of these cold responsive genes were located within 13 different QTLs previously identified as cold associated.
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| 12. |
- Chawade, Aakash, 1980, et al.
(författare)
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Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors
- 2007
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Ingår i: BMC GENOMICS. - : Springer Science and Business Media LLC. - 1471-2164. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background With the advent of microarray technology, it has become feasible to identify virtually all genes in an organism that are induced by developmental or environmental changes. However, relying solely on gene expression data may be of limited value if the aim is to infer the underlying genetic networks. Development of computational methods to combine microarray data with other information sources is therefore necessary. Here we describe one such method. Results By means of our method, previously published Arabidopsis microarray data from cold acclimated plants at six different time points, promoter motif sequence data extracted from ~24,000 Arabidopsis promoters and known transcription factor binding sites were combined to construct a putative genetic regulatory interaction network. The inferred network includes both previously characterised and hitherto un-described regulatory interactions between transcription factor (TF) genes and genes that encode other TFs or other proteins. Part of the obtained transcription factor regulatory network is presented here. More detailed information is available in the additional files. Conclusion The rule-based method described here can be used to infer genetic networks by combining data from microarrays, promoter sequences and known promoter binding sites. This method should in principle be applicable to any biological system. We tested the method on the cold acclimation process in Arabidopsis and could identify a more complex putative genetic regulatory network than previously described. However, it should be noted that information on specific binding sites for individual TFs were in most cases not available. Thus, gene targets for the entire TF gene families were predicted. In addition, the networks were built solely by a bioinformatics approach and experimental verifications will be necessary for their final validation. On the other hand, since our method highlights putative novel interactions, more directed experiments could now be performed.
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| 13. |
- Dura, Elzbieta, et al.
(författare)
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Towards Information Fusion in Pathway Evaluation : Encoding Relations in Biomedical Texts
- 2006
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Ingår i: 9th International Conference on Information Fusion. - : IEEE. - 9781424409532
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Konferensbidrag (refereegranskat)abstract
- The long-term goal of the research presented in this paper is to incorporate linguistic text analysis into a system for evaluation of biological pathways. In this system, relations extracted from biomedical texts will be compared with pathways encoded in existing specialized databases. In this way, the biologist's conclusions regarding the plausibility and/or novelty of a certain relation between genes, proteins, etc., can be supported by fused information from biological databases and biological literature. We aim at overcoming the shortcomings of existing systems for information retrieval by proposing a method based on thorough linguistic analysis of a large text corpus. In this paper, we present a comparative analysis of two corpora: one consisting of biomedical texts from PubMed, the other one of general English prose. The results stress the importance of taking multiword entries into account when constructing a system for extracting biological relations from texts
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| 14. |
- Ekroos, Johan, et al.
(författare)
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Sparing land for biodiversity at multiple spatial scales
- 2016
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- A common approach to the conservation of farmland biodiversity and the promotion of multifunctional landscapes, particularly in landscapes containing only small remnants of non-crop habitats, has been to maintain landscape heterogeneity and reduce land-use intensity. In contrast, it has recently been shown that devoting specific areas of non-crop habitats to conservation, segregated from high-yielding farmland (“land sparing”), can more effectively conserve biodiversity than promoting low-yielding, less intensively managed farmland occupying larger areas (“land sharing”). In the present paper we suggest that the debate over the relative merits of land sparing or land sharing is partly blurred by the differing spatial scales at which it is suggested that land sparing should be applied. We argue that there is no single correct spatial scale for segregating biodiversity protection and commodity production in multifunctional landscapes. Instead we propose an alternative conceptual construct, which we call “multiple-scale land sparing,” targeting biodiversity and ecosystem services in transformed landscapes. We discuss how multiple-scale land sparing may overcome the apparent dichotomy between land sharing and land sparing and help to find acceptable compromises that conserve biodiversity and landscape multifunctionality.
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| 15. |
- Gavali, Hamid, et al.
(författare)
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Outcome of Radical Surgical Treatment of Abdominal Aortic Graft and Endograft Infections Comparing Extra-anatomic Bypass with In Situ Reconstruction : A Nationwide Multicentre Study
- 2021
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Ingår i: European Journal of Vascular and Endovascular Surgery. - : Saunders Elsevier. - 1078-5884 .- 1532-2165. ; 62:6, s. 918-926
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Abdominal aortic graft and endograft infection (AGI) is primarily treated by resection of the infected graft and restoration of distal perfusion through extra-anatomic bypass (EAB) or in situ reconstruction/repair (ISR). The aim of this study was to compare these surgical strategies in a nationwide multicentre retrospective cohort study.Methods: The Swedish Vascular Registry (Swedvasc) was used to identify surgically treated abdominal AGIs in Sweden between January 1995 and May 2017. The primary aim was to compare short and long term survival, as well as complications for EAB and ISR.Results: Some 126 radically surgically treated AGI patients were identified – 102 graft infections and 24 endograft infections – treated by EAB: 71 and ISR: 55 (23 neo-aorto-iliac systems, NAISs). No differences in early 30 day (EAB 81.7% vs. ISR 76.4%, p =.46), or long term five year survival (48.2% vs. 49.9%, p =.87) were identified. There was no survival difference comparing NAIS to other ISR strategies. The frequency of recurrent graft infection during follow up was similar: EAB 20.3% vs. ISR 17.0% (p =.56). Survival and re-infection rates of the new conduit did not differ between NAIS and other ISR strategies. Age ≥ 75 years (odds ratio [OR] 4.0, confidence interval [CI] 1.1 – 14.8), coronary artery disease (OR 4.2, CI 1.2 – 15.1) and post-operative circulatory complications (OR 5.2, CI 1.2 – 22.5) were associated with early death. Prolonged antimicrobial therapy (> 3 months) was associated with reduced long term mortality (HR 0.3, CI 0.1 – 0.9).Conclusion: In this nationwide multicentre study comparing outcomes of radically treated AGI, no differences in survival or re-infection rate could be identified comparing EAB and ISR.
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| 16. |
- Gavali, Hamid, et al.
(författare)
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Semi-Conservative Treatment Versus Radical Surgery in Abdominal Aortic Graft and Endograft Infections
- 2023
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Ingår i: European Journal of Vascular and Endovascular Surgery. - : Elsevier. - 1078-5884 .- 1532-2165. ; 66:3, s. 397-406
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Abdominal aortic graft and endograft infections (AGIs) are rare complications following aortic surgery. Radical surgery (RS) with resection of the infected graft and reconstruction with extra-anatomical bypass or in situ reconstruction is the preferred therapy. For patients unfit for RS, a semi-conservative (SC), graft preserving strategy is possible. This paper aimed to compare survival and infection outcomes between RS and SC treatment for AGI in a nationwide cohort.Methods: Patients with abdominal AGI related surgery in Sweden between January 1995 and May 2017 were identified. The Management of Aortic Graft Infection Collaboration (MAGIC) criteria were used for the definition of AGI. Multivariable regression was performed to identify factors associated with mortality.Results: One hundred and sixty-nine patients with surgically treated abdominal AGI were identified, comprising 43 SC (14 endografts; 53% with a graft enteric fistula [GEF] in total) and 126 RS (26 endografts; 50% with a GEF in total). The SC cohort was older and had a higher frequency of cardiac comorbidities. There was a non-significant trend towards lower Kaplan -Meier estimated five year survival for SC vs. RS (30.2% vs. 48.4%; p = .066). A non-significant trend was identified towards worse Kaplan -Meier estimated five year survival for SC patients with a GEF vs. without a GEF (21.7% vs. 40.1%; p = .097). There were significantly more recurrent graft infections comparing SC with RS (45.4% vs. 19.3%; p < .001). In a Cox regression model adjusting for confounders, there was no difference in five year survival comparing SC vs. RS (HR 1.0, 95% CI 0.6 -1.5).Conclusion: In this national AGI cohort, there was no mortality difference comparing SC and RS for AGI when adjusting for comorbidities. Presence of GEF probably negatively impacts survival outcomes of SC patients. Rates of recurrent infection remain high for SC treated patients.
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| 17. |
- Gawronska, Barbara, et al.
(författare)
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Towards an Automated Analysis of Biomedical Abstracts
- 2006
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Ingår i: Data Integration in the Life Sciences. - Berlin, Heidelberg : Springer. - 9783540365938 ; , s. 50-65
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- An essential part of bioinformatic research concerns the iterative process of validating hypotheses by analyzing facts stored in databases and in published literature. This process can be enhanced by language technology methods, in particular by automatic text understanding. Since it is becoming increasingly difficult to keep up with the vast number of scientific articles being published, there is a need for more easily accessible representations of the current knowledge. The goal of the research described in this paper is to develop a system aimed to support the large-scale research on metabolic and regulatory pathways by extracting relations between biological objects from descriptions found in literature. We present and evaluate the procedures for semantico-syntactic tagging, dividing the text into parts concerning previous research and current research, syntactic parsing, and transformation of syntactic trees into logical representations similar to the pathway graphs utilized in the Kyoto Encyclopaedia of Genes and Genomes.
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| 18. |
- Gawronska, Barbara, et al.
(författare)
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Tracking biological relations in texts : a Referent Grammar based approach
- 2005
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Ingår i: Proceedings of the workshop Biomedical Ontologies and Text Processing, in connection to ECCB/05. ; , s. 15-22
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Konferensbidrag (refereegranskat)abstract
- In this paper, we describe a method for extracting biological relations (in the first place, relations used in the KEGG ontology of biological pathways) from scientific texts. The main assumption is that correct syntactic analysis combined with domain-specific heuristics provides a good basis for relation extraction. We propose an algorithm that searches through the syntactic trees produced by a parser based on a formalism called Referent Grammar (inspired by Categorial Grammar), identifies relations mentioned in the sentence, and classifies them with respect to their semantic class and epistemic status (facts, counterfactuals, hypotheses).
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| 19. |
- Grevholm, Barbro, 1941-, et al.
(författare)
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Inledning
- 2001
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Ingår i: Grevholm, Barbro (red.). Matematikdidaktik. - Lund : Studentlitteratur. - 9144018355 ; , s. 9-14, s. 13-21
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 20. |
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| 21. |
- Harbst, Katja, et al.
(författare)
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Molecular and genetic diversity in the metastatic process of melanoma.
- 2014
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Ingår i: Journal of Pathology. - : Wiley. - 0022-3417 .- 1096-9896. ; 233:1, s. 39-50
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Tidskriftsartikel (refereegranskat)abstract
- Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3 months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk.
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| 22. |
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| 23. |
- Hägg, Daniel, 1974, et al.
(författare)
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Expression profiling of macrophages from subjects with atherosclerosis to identify novel susceptibility genes.
- 2008
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Ingår i: International journal of molecular medicine. - 1107-3756. ; 21:6, s. 697-704
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Tidskriftsartikel (refereegranskat)abstract
- Although a number of environmental risk factors for atherosclerosis have been identified, heredity seems to be a significant independent risk factor. The aim of our study was to identify novel susceptibility genes for atherosclerosis. The screening process consisted of three steps. First, expression profiles of macrophages from subjects with atherosclerosis were compared to macrophages from control subjects. Secondly, the subjects were genotyped for promoter region polymorphisms in genes with altered gene expression. Thirdly, a population of subjects with coronary heart disease and control subjects were genotyped to test for an association with identified polymorphisms that affected gene expression. Twenty-seven genes were differentially expressed in both macrophages and foam cells from subjects with atherosclerosis. Three of these genes, IRS2, CD86 and SLC11A1 were selected for further analysis. Foam cells from subjects homozygous for the C allele at the -765C-->T SNP located in the promoter region of IRS2 had increased gene expression compared to foam cells from subjects with the nonCC genotype. Also, macrophages and foam cells from subjects homozygous for allele 2 at a repeat element in the promoter region of SLC11A1 had increased gene expression compared to macrophages and foam cells from subjects with the non22 genotype. Genotyping of 512 pairs of subjects with coronary heart disease (CHD) and matched controls revealed that subjects homozygous for C of the IRS2 SNP had an increased risk for CHD; odds ratio 1.43, p=0.010. Immunohistochemical staining of human carotid plaques showed that IRS2 expression was localised to macrophages and endothelial cells in vivo. Our method provides a reliable approach for identifying susceptibility genes for atherosclerosis, and we conclude that elevated IRS2 gene expression in macrophages may be associated with an increased risk of CHD.
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| 24. |
- Idström, Alexander, et al.
(författare)
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Dissolution of cellulose in tetrabutylammonium acetate/dimethyl sulfoxide
- 2016
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Ingår i: The 7th Workshop on cellulose, regenerated cellulose and cellulose derivatives. ; , s. 15-18
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The dissolution of cellulose in tetrabutylammonium acetate (TBAAc)/dimethyl sulfoxide (DMSO) was studied combining experimental and simulation techniques. It was found that the dissolution limit at 40 °C corresponded to a molar ratio close to one acetate per cellulose anhydroglucose units. MD simulations suggested that the acetate ions bind to cellulose by dual hydrogen bonds. This effectively turns cellulose into a polyelectrolyte, attracting the bulky tetrabutylammonium (TBA+) counter ions, which prevent close contact between chains in the dissolved state. This hypothesis was tested by 1H- and 13C-NMR spectroscopy, which confirmed that acetate forms hydrogen bonds to cellulose, and by diffusion NMR spectroscopy, which demonstrated a strong dynamic correlation between bound acetate and tetrabutylammonium in near-quantitative agreement with simulation. The present results suggest that offering hydrogen bonding to the acetate ions is the main driving force for dissolving cellulose and that the TBA+ counter ions form a diffuse layer around the acetate-decorated cellulose chains.
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| 25. |
- Idström, Alexander, et al.
(författare)
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On the dissolution of cellulose in tetrabutylammonium acetate/dimethyl sulfoxide : a frustrated solvent
- 2017
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Ingår i: Cellulose. - : Springer Science and Business Media LLC. - 0969-0239 .- 1572-882X. ; 24:9, s. 3645-3657
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Tidskriftsartikel (refereegranskat)abstract
- We have found that the dissolution of cellulose in the binary mixed solvent tetrabutylammonium acetate/dimethyl sulfoxide follows a previously overlooked near-stoichiometric relationship such that one dissolved acetate ion is able to dissolve an amount of cellulose corresponding to about one glucose residue. The structure and dynamics of the resulting cellulose solutions were investigated using small-angle X-ray scattering (SAXS) and nuclear magnetic resonance techniques as well as molecular dynamics simulation. This yielded a detailed picture of the dissolution mechanism in which acetate ions form hydrogen bonds to cellulose and causes a diffuse solvation sheath of bulky tetrabutylammonium counterions to form. In turn, this leads to a steric repulsion that helps to keep the cellulose chains apart. Structural similarities to previously investigated cellulose solutions in aqueous tetrabutylammonium hydroxide were revealed by SAXS measurement. To what extent this corresponds to similarities in dissolution mechanism is discussed.
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| 26. |
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| 27. |
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| 28. |
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| 29. |
- Lindlöf, Angelica, et al.
(författare)
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Evaluation of combining several statistical methods with a flexible cutoff for identifying differentially expressed genes in pairwise comparison of EST sets
- 2008
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Ingår i: Bioinformatics and Biology Insights. - : Libertas Academica. - 1177-9322. ; 2, s. 215-237
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Tidskriftsartikel (refereegranskat)abstract
- The detection of differentially expressed genes from EST data is of importance for the discovery of potential biological or pharmaceutical targets, especially when studying biological processes in less characterized organisms and where large-scale microarrays are not an option. We present a comparison of five different statistical methods for identifying up-regulated genes through pairwise comparison of EST sets, where one of the sets is generated from a treatment and the other one serves as a control. In addition, we specifically address situations where the sets are relatively small (~2,000– 10,000 ESTs) and may differ in size. The methods were tested on both simulated and experimentally derived data, and compared to a collection of cold stress induced genes identified by microarrays. We found that combining the method pro- posed by Audic and Claverie with Fisher’s exact test and a method based on calculating the difference in relative frequency was the best combination for maximizing the detection of up-regulated genes. We also introduced the use of a flexible cutoff, which takes the size of the EST sets into consideration. This could be considered as an alternative to a static cutoff. Finally, the detected genes showed a low overlap with those identified by microarrays, which indicates, as in previous studies, low overall concordance between the two platforms.
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| 30. |
- Lindlöf, Angelica, et al.
(författare)
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Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets
- 2007
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Ingår i: S. Hochreiter and R. Wagner (Eds.): BIRD, LNBI. - Berlin, Heidelberg : Springer. ; 4414, s. 48-65, s. 48-65
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Tidskriftsartikel (refereegranskat)abstract
- Freezing tolerance in plants is obtained during a period of low nonfreezing temperatures before the winter sets on, through a biological process known as cold acclimation. Cold is one of the major stress factors that limits the growth, productivity and distribution of plants, and understanding the mechanism of cold tolerance is therefore important for crop improvement. Expressed sequence tags (EST) analysis is a powerful, economical and timeefficient way of assembling information on the transcriptome. To date, several EST sets have been generated from cold-induced cDNA libraries from several different plant species. In this study we utilize the variation in the frequency of ESTs sampled from different cold-stressed plant libraries, in order to identify genes preferentially expressed in cold in comparison to a number of control sets. The species included in the comparative study are oat (Avena sativa), barley (Hordeum vulgare), wheat (Triticum aestivum), rice (Oryza sativa) and Arabidopsis thaliana. However, in order to get comparable gene expression estimates across multiple species and data sets, we choose to compare the expression of tentative ortholog groups (TOGs) instead of single genes, as in the normal procedure. We consider TOGs as preferentially expressed if they are detected as differentially expressed by a test statistic and up-regulated in comparison to all control sets, and/or uniquely expressed during cold stress, i.e., not present in any of the control sets. The result of this analysis revealed a diverse representation of genes in the different species. In addition, the derived TOGs mainly represent genes that are long-term highly or moderately expressed in response to cold and/or other stresses.
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| 31. |
- Lindlöf, Angelica, et al.
(författare)
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In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
- 2009
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 25:11, s. 1345-1348
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Cold acclimation involves a number of different cellular processes that together increase the freezing tolerance of an organism. The DREB1/CBFs are transcription factors (TFs) that are prominent in the regulation of cold responses in Arabidopsis thaliana, rice and many other crops. We investigated if the expression of DREB1/CBFs and co-expressed genes relies on combinatorial control by several TFs. Our results support this notion and indicate that methods for studying the regulation of complex cellular processes should include identification of combinations of motifs, in addition to searching for individual overrepresented binding sites.
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| 32. |
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| 33. |
- Melander, Björn, 1958-, et al.
(författare)
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Inledning
- 2001
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Ingår i: Verklighetens texter. - Lund : Studentlitteratur. - 9144017537 ; , s. 13-21
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 34. |
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| 35. |
- Nilsson, J, et al.
(författare)
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Variation in the content of glucosinolates, hydroxycinnamic acids, carotenoids, total antioxidant capacity and low-molecular-weight carbohydrates in Brassica vegetables
- 2006
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Ingår i: Journal of the Science of Food and Agriculture. - : Wiley. - 1097-0010 .- 0022-5142. ; 86:4, s. 528-538
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Tidskriftsartikel (refereegranskat)abstract
- Bioactive compounds were investigated in genotypes (cauliflower 10, white cabbage 10, curly kale 1) and plant parts of the three crops. The content of most of the major glucosinolates glucobrassicin, sinigrin and glucoiberin differed significantly between cultivars. Samples harvested in 2000 had higher amounts of several glucosinolates than samples from 1999. Within cauliflower the buds of the floret had 1.5 to 2.5-fold higher concentration of glucobrassicin and 4-methoxyglucobrassicin than the stalk. In white cabbage several glucosinolates had their highest content in the outer leaves (up to 2-fold higher). Upper leaves of curly kale contained 5-fold more of total glucosinolates than lower leaves. Chlorogenic acid was the dominating hydroxycinnamate in curly kale, which also contained at least ten times more of carotenoids (mainly lutein) than white cabbage. Total antioxidant capacity (TAC) assayed with the FRAP method was 0.76 (0.06) mu mol/g fw (mean (SD)) in water-soluble and 0.32 (0.04) in water-insoluble extracts of cauliflower which was 62-68% higher than in white cabbage. Curly kale contained 6.4 and 6.1 mu mol/g fw TAC in water-soluble and water-insoluble extracts. TAC did not differ between plant parts. Progoitrin and 4-hydroxyglucobrassicin were correlated to water-soluble TAC in white cabbage, probably reflecting a variation in other compounds. Cauliflower contained less glucose, fructose and sorbitol but more sucrose than white cabbage. Curly kale had lower contents of glucose (similar to 2 times), fructose (similar to 4-S times) and sucrose (20 and 36 times, respectively) than cauliflower and white cabbage, while inositol was only found in curly kale. Storage of white cabbage reduced the amount of sorbitol and sucrose. The study shows that cultivar, plant part and storage affect the content of bioactive compounds in Brassica vegetables. The variation between years, as in cauliflower, is due to environmental factors. Since the cultivar ranking order was rather stable for several components the data could provide a basis for the selection of cultivars optimised for valuable health components for fresh market consumption. (c) 2005 Society of Chemical Industry.
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| 36. |
- Olofsson, Louise, 1977, et al.
(författare)
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CCAAT/enhancer binding protein alpha (C/EBPalpha) in adipose tissue regulates genes in lipid and glucose metabolism and a genetic variation in C/EBPalpha is associated with serum levels of triglycerides.
- 2008
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Ingår i: The Journal of clinical endocrinology and metabolism. - : The Endocrine Society. - 0021-972X .- 1945-7197. ; 93:12, s. 4880-6
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Tidskriftsartikel (refereegranskat)abstract
- CONTEXT: CCAAT/enhancer binding protein alpha (C/EBPalpha) is a transcription factor involved in adipogenesis and hepatic glucose and lipid metabolism. OBJECTIVE: The aim of the study was to test the hypothesis that adipose tissue C/EBPalpha regulates genes in lipid and glucose metabolism and to test for an association between a polymorphism in C/EBPalpha and metabolic parameters. DESIGN AND METHODS: Adipose tissue C/EBPalpha mRNA expression was analyzed at four time points in obese subjects with (n = 12) and without (n = 12) the metabolic syndrome during caloric restriction (450 kcal/d for 16 wk) using DNA microarray and real-time PCR. Adenoviral overexpression of C/EBPalpha was used to identify genes regulated by C/EBPalpha in 3T3-L1 cells. Association between a genetic variation in C/EBPalpha (rs12691) and metabolic parameters was tested in the Swedish Obese Subjects (SOS) study (n = 528) and replicated in Finnish individuals from the Botnia type 2 diabetes study (n = 4,866). RESULTS: During caloric restriction, adipose tissue C/EBPalpha mRNA levels were reduced in subjects with the metabolic syndrome (P = 0.024) and correlated to metabolic parameters. In 3T3-L1 cells, C/EBPalpha regulated the expression of adiponectin; hexokinase 2; lipoprotein lipase; diacylglycerol O-acyltransferase 1 and 2; ATP-binding cassette, sub-family D, member 2; acyl-coenzyme A synthetase long-chain family member 1; CD36; and hydroxysteroid 11-beta dehydrogenase 1. Furthermore, the expression of the human homologs, except adiponectin, correlated to C/EBPalpha mRNA levels in human adipose tissue. The AA genotype of rs12691 was associated with higher serum triglyceride levels in the SOS study (P = 0.022), and this association was replicated in the Botnia study (P = 0.041). CONCLUSIONS: Adipose tissue C/EBPalpha regulates several genes in glucose and lipid metabolism, and a genetic variation in C/EBPalpha is associated with triglycerides in two independent populations.
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| 37. |
- Olsson, Björn, et al.
(författare)
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Automated text analysis of biomedical abstracts applied to the extraction of signaling pathways involved in plant cold-adaptation
- 2006
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Ingår i: Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure. - : Russian Academy of Sciences. - 5769208481 - 9785769208485 ; , s. 296-299
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Motivation: Automated text analysis is an important tool for facilitating the extraction of knowledge from biomedical abstracts, thereby enabling researchers to build pathway models that integrate and summarize information from a large number of sources. Advanced methods of in-depth analysis of texts using grammar-based approaches developed within the field of computational linguistics must be adapted to the special requirements and challenges posed by biomedical texts, so that these methods can be made available to the bioinformatics and computational biology communities. Results: Our system for automated text analysis and extraction of pathway information is here applied to a set of PubMed abstracts concerning the CBF signaling pathway, which is a key pathway involved in the cold-adaptation response of plants subjected to cold non-freezing temperatures. The system successfully and accurately re-discovers the main features of this pathway, while also pointing to interesting and plausible new hypotheses. The evaluation also reveals a number of issues which will be important targets in the continued development of the system, e.g. the need for an extended lexicon of taxonomic terms and an improved procedure for recognition of sentence boundaries.
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| 38. |
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| 39. |
- Olsson, Björn, et al.
(författare)
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Deriving pathway maps from automated text analysis using a grammar-based approach
- 2006
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Ingår i: Journal of Bioinformatics and Computational Biology. - : World Scientific. - 0219-7200 .- 1757-6334. ; 4:2, s. 483-501
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate how automated text analysis can be used to support the large-scale analysis of metabolic and regulatory pathways by deriving pathway maps from textual descriptions found in the scientific literature. The main assumption is that correct syntactic analysis combined with domain-specific heuristics provides a good basis for relation extraction. Our method uses an algorithm that searches through the syntactic trees produced by a parser based on a Referent Grammar formalism, identifies relations mentioned in the sentence, and classifies them with respect to their semantic class and epistemic status (facts, counterfactuals, hypotheses). The semantic categories used in the classification are based on the relation set used in KEGG (Kyoto Encyclopedia of Genes and Genomes), so that pathway maps using KEGG notation can be automatically generated. We present the current version of the relation extraction algorithm and an evaluation based on a corpus of abstracts obtained from PubMed. The results indicate that the method is able to combine a reasonable coverage with high accuracy. We found that 61% of all sentences were parsed, and 97% of the parse trees were judged to be correct. The extraction algorithm was tested on a sample of 300 parse trees and was found to produce correct extractions in 90.5% of the cases.
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| 40. |
- Olsson, Björn, et al.
(författare)
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Förutsättningar och styrmedel för ökad elsjöfart
- 2024
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Ingår i: Sammanställning av referat från Transportforum 2024. - Linköping : Statens väg- och transportforskningsinstitut. ; , s. 43-44
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Det finns potential att öka elektrifieringen i svensk sjöfart. Inom ramen för ett regeringsuppdrag föreslår Trafikanalys nya styrmedel för elsjöfart, bland annat skattereduktion för landström, klimatpremie för elfartyg och stöd till land- och laddinfrastruktur i hamnar. Under 2022 har Trafikanalys haft i uppdrag att dels utreda förutsättningarna för en ökad användning av helt eller delvis eldrivna fartyg i Sverige, dels utreda möjliga incitament för att åstadkomma ökad användning av land- och laddström. Resultaten från båda uppdragen redovisas här gemensamt.Vi har studerat litteraturen och utvecklingen avseende elektrifieringen av sjöfart inom Sverige, Norge och Nederländerna. Marknadspotentialen för elektrifieringen har analyserats genom energiförbrukningen för fartyg som anlöper svenska hamnar. Vi beskriver de tekniska förutsättningarna och vilka problem som är specifika för elektrifiering av sjöfart jämfört med andra trafikslag. Vi har också studerat vilka styrmedel som finns idag för elektrifiering inom sjöfart såväl som andra trafikslag. Baserat på detta har vi pekat på möjliga styrmedel med potential att öka användningen av land- och laddström, samt öka användningen av helt eller delvis eldrivna fartyg i Sverige. Vi har också låtit en referensgrupp med representanter från branschen ha synpunkter och kommentarer på vårt arbete och våra förslag till styrmedel. De förslag till styrmedel vi lyfter fram är:Skattereduktion för elanslutning för mindre fartygKlimatpremie för elfartygStöd till elanslutning för fartygUndantag från kravet på nätkoncession för hamnarTydligare klimatkrav på nationella fartygUnderlätta processen för certifiering av fartyg vid konvertering till eldriftInnovationsupphandling i regionalt upphandlad färjetrafikDet ingick i uppdraget att göra en bedömning av införande av miljözoner i hamnar. Vår uppfattning är att marknaden i Sverige idag inte är mogen för införande av miljözoner. Vi efterlyser en vidare diskussion om miljödifferentierade sjöfartsavgifter för att stimulera introduktionen av elsjöfart.
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| 41. |
- Olsson, Björn, 1962-, et al.
(författare)
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Running research-oriented final year projects for CS and IS students
- 2003
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Ingår i: SIGCSE '03. - New York, NY, USA : ACM Special Interest Group on Computer Science Education. - 158113648X ; , s. 79-83
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Konferensbidrag (refereegranskat)abstract
- In this paper we discuss the difficulties of designing and running a final year project course for computer science and information systems students. In particular, we present the design of a research-oriented final year project course, where the aim is to develop the student's critical thinking and research skills. We also discuss the lessons learnt during the seven years that the course has been given.
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| 42. |
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| 43. |
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| 44. |
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| 45. |
- Peterson, Pernilla, et al.
(författare)
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Knee dGEMRIC at 7 T : Comparison against 1.5 T and evaluation of T1-mapping methods
- 2018
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Ingår i: BMC Musculoskeletal Disorders. - : Springer Science and Business Media LLC. - 1471-2474. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: dGEMRIC (delayed Gadolinium Enhanced Magnetic Resonance Image of Cartilage) is a well-established technique for cartilage quality assessment in osteoarthritis at clinical field strengths. The method is robust, but requires injection of contrast agent and a cumbersome examination procedure. New non-contrast-agent-based techniques for cartilage quality assessment are currently being developed at 7 T. However, dGEMRIC remains an important reference technique during this development. The aim of this work was to compare T1 mapping for dGEMRIC at 7 T and 1.5 T, and to evaluate three T1-mapping methods at 7 T. Methods: The knee of 10 healthy volunteers and 9 patients with early signs of cartilage degradation were examined at 1.5 T and 7 T after a single (one) contrast agent injection (Gd-(DTPA)2-). Inversion recovery (IR) sequences were acquired at both field strengths, and at 7 T variable flip angle (VFA) and Look-Locker (LL) sequences were additionally acquired. T1 maps were calculated and average T1 values were estimated within superficial and deep regions-of-interest (ROIs) in the lateral and medial condyles, respectively. Results: T1 values were 1.8 (1.4-2.3) times longer at 7 T. A strong correlation was detected between 1.5 T and 7 T T1 values (r = 0.80). For IR, an additional inversion time was required to avoid underestimation (bias±limits of agreement - 127 ± 234 ms) due to the longer T1 values at 7 T. Out of the two 3D sequences tested, LL resulted in more accurate and precise T1 estimation compared to VFA (average bias±limits of agreement LL: 12 ± 202 ms compared to VFA: 25 ± 622 ms). For both, B1 correction improved agreement to IR. Conclusion: With an adapted sampling scheme, dGEMRIC T1 mapping is feasible at 7 T and correlates well to 1.5 T. If 3D is to be used for T1 mapping of the knee at 7 T, LL is preferred and VFA is not recommended. For VFA and LL, B1 correction is necessary for accurate T1 estimation.
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| 46. |
- Rahm, Henrik, et al.
(författare)
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Rösterna i texterna
- 2001
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Ingår i: Verklighetens texter : Sjutton fallstudier. - 9144017537
-
Bokkapitel (refereegranskat)
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| 47. |
- Saiki, Atsuhito, et al.
(författare)
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Tenomodulin is highly expressed in adipose tissue, increased in obesity, and down-regulated during diet-induced weight loss.
- 2009
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Ingår i: The Journal of clinical endocrinology and metabolism. - : The Endocrine Society. - 1945-7197 .- 0021-972X. ; 94:10, s. 3987-94
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Tidskriftsartikel (refereegranskat)abstract
- CONTEXT: Tenomodulin (TNMD), a putative angiogenesis inhibitor, is expressed in hypovascular connective tissues. Global gene expression scans show that the TNMD gene also is expressed in human adipose tissue and that its expression is regulated in response to weight reduction; however, more detailed information is lacking. OBJECTIVE: The aim of this study was to investigate TNMD tissue distribution and TNMD gene expression in human adipose tissue in relation to obesity and metabolic disease. DESIGN, PATIENTS, AND INTERVENTIONS: TNMD gene expression, tissue distribution, and TNMD gene expression in adipose tissue from different depots, from lean and obese subjects, and during diet-induced weight reduction were analyzed by DNA microarray and real-time PCR. MAIN OUTCOME MEASURE: We primarily measured TNMD gene expression. RESULTS: The TNMD gene was predominantly expressed in sc adipose tissue. TNMD gene expression was higher in sc than omental adipose tissue both in lean (P = 0.002) and obese subjects (P = 0.014). In both women and men, TNMD gene expression was significantly higher in the obese subjects compared to the lean subjects (P = 1.1 x 10(-26) and P = 0.010, respectively). In a multiple linear regression analysis, BMI was a significant independent predictor of TNMD gene expression. TNMD gene expression was down-regulated during diet-induced weight loss, with a 65% decrease after 18 wk of diet (P < 0.0001). CONCLUSIONS: We conclude that human adipose tissue TNMD gene expression is highly affected by obesity, adipose tissue location, and weight loss, indicating that TNMD may play a role in adipose tissue function.
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| 48. |
- Sondell, Björn, et al.
(författare)
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Altered walking pattern in a virtual environment
- 2005
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Ingår i: Presence - Teleoperators and Virtual Environments. - Cambridge : MIT Press. - 1054-7460 .- 1531-3263. ; 14:2, s. 191-197
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Tidskriftsartikel (refereegranskat)abstract
- Falls and fractures among elderly persons constitute a major health problem. Many falls occur while walking and falls that occur during turning often result in a fracture. Methods aimed at understanding the complex mechanisms involved in walking should therefore assess tested individuals during walks and turns. In order to identify persons at risk and take the correct preventive measures, it is important to find methods that quantify movements as the tested persons are processing multisensory input. In a clinical setting this is sometimes difficult to achieve in a controlled manner, since tests are difficult to set exactly the same from one time to another. Using a virtual environment (VE) and a tracker system, conditions such as light, sound, events, body movements, and room size can be controlled and measured. Tests in VE can therefore be identically reproduced over and over again to evaluate if a person can withstand changing outer demands at any given moment. In order to perform quantitative measures 8 persons (21-74 years) were tested in immersive virtual reality. The VE was a corridor in which expected and unexpected events could be produced. Events studied were doors swinging open in front of the subjects during a walk and a virtual tilting of the environment. Trackers were used for collecting and analyzing the movement data. Our results show that the system was well tolerated among the subjects and that there was a clear tendency that the system could generate fall tendency among the subjects. There was also a difference among the subjects regarding walking strategies when subjected to the various events.
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| 49. |
- Steineck, I., et al.
(författare)
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Insulin pump therapy, multiple daily injections, and cardiovascular mortality in 18 168 people with type 1 diabetes: observational study
- 2015
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Ingår i: Bmj-British Medical Journal. - : BMJ. - 1756-1833. ; 350
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE To investigate the long term effects of continuous subcutaneous insulin infusion (insulin pump therapy) on cardiovascular diseases and mortality in people with type 1 diabetes. Design Observational study. 18 168 people with type 1 diabetes, 2441 using insulin pump therapy and 15 727 using multiple daily insulin injections. Cox regression analysis was used to estimate hazard ratios for the outcomes, with stratification of propensity scores including clinical characteristics, risk factors for cardiovascular disease, treatments, and previous diseases. Follow-up was for a mean of 6.8 years until December 2012, with 114 135 person years. With multiple daily injections as reference, the adjusted hazard ratios for insulin pump treatment were significantly lower: 0.55 (95% confidence interval 0.36 to 0.83) for fatal coronary heart disease, 0.58 (0.40 to 0.85) for fatal cardiovascular disease (coronary heart disease or stroke), and 0.73 (0.58 to 0.92) for all cause mortality. Hazard ratios were lower, but not significantly so, for fatal or non-fatal coronary heart disease and fatal or non-fatal cardiovascular disease. Unadjusted absolute differences were 3.0 events of fatal coronary heart disease per 1000 person years; corresponding figures were 3.3 for fatal cardiovascular disease and 5.7 for all cause mortality. When lower body mass index and previous cardiovascular diseases were excluded, results of subgroup analyses were similar to the results from complete data. A sensitivity analysis of unmeasured confounders in all individuals showed that an unmeasured confounders with hazard ratio of 1.3 would have to be present in > 80% of the individuals treated with multiple daily injections versus not presence in those treated with pump therapy to invalidate the significantly lower hazard ratios for fatal cardiovascular disease. Data on patient education and frequency of blood glucose monitoring were missing, which might have influenced the observed association. Among people with type 1 diabetes use of insulin pump therapy is associated with lower cardiovascular mortality than treatment with multiple daily insulin injections.
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| 50. |
- Synnergren, Jane, 1967, et al.
(författare)
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Cardiomyogenic gene expression profiling of differentiating human embryonic stem cells.
- 2008
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Ingår i: Journal of biotechnology. - : Elsevier BV. - 0168-1656 .- 1873-4863. ; 134:1-2, s. 162-70
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Tidskriftsartikel (refereegranskat)abstract
- Human embryonic stem cells (hESCs) can differentiate into a variety of specialized cell types. Thus, they provide a model system for embryonic development to investigate the molecular processes of cell differentiation and lineage commitment. The development of the cardiac lineage is easily detected in mixed cultures by the appearance of spontaneously contracting areas of cells. We performed gene expression profiling of undifferentiated and differentiating hESCs and monitored 468 genes expressed during cardiac development and/or in cardiac tissue. Their transcription during early differentiation of hESCs through embryoid bodies (EBs) was investigated and compared with spontaneously differentiating hESCs maintained on feeders in culture without passaging (high-density (HD) protocol). We observed a larger variation in the gene expression between cells from a single cell line that were differentiated using two different protocols than in cells from different cell lines that were cultured according to the same protocol. Notably, the EB protocol resulted in more reproducible transcription profiles than the HD protocol. The results presented here provide new information about gene regulation during early differentiation of hESCs with emphasis on the cardiomyogenic program. In addition, we also identified regulatory elements that could prove critical for the development of the cardiomyocyte lineage.
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