| 1. |
- Ahlberg, Malin, 1986, et al.
(författare)
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Korp and Karp – a bestiary of language resources: the research infrastructure of Språkbanken
- 2013
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Ingår i: Proceedings of the 19th Nordic Conference of Computational Linguistics (NODALIDA 2013), May 22–24, 2013, Oslo University, Norway. NEALT Proceedings Series 16. - Linköping : Linköping University Electronic Press. - 1650-3686 .- 1650-3740.
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Konferensbidrag (refereegranskat)abstract
- A central activity in Språkbanken, an R&D unit at the University of Gothenburg, is the systematic construction of a research infrastructure based on interoperability and widely accepted standards for metadata and data. The two main components of this infrastructure deal with text corpora and with lexical resources. For modularity and flexibility, both components have a backend, or server-side part, accessed through an API made up of a set of well-defined web services. This means that there can be any number of different user interfaces to these components, corresponding, e.g., to different research needs. Here, we will demonstrate the standard corpus and lexicon search interfaces, designed primarily for linguistic searches: Korp and Karp.
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| 2. |
- Bengtsson, Olof, 1969-
(författare)
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Design and Characterization of RF-Power LDMOS Transistors
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In mobile communication new applications like wireless internet and mobile video have increased the demand of data-rates. Therefore, new more wideband systems are being implemented. Power amplifiers in the base-stations that simultaneously handle these wideband signals for many terminals (handhelds) need to be highly linear with a considerable band-width. In the past decade LDMOS has been the dominating technology for use in these RF-power amplifiers. In this work LDMOS transistors possible to fabricate in a normal CMOS process have been optimized and analyzed for RF-power applications. Their non-linear behavior has been explored using load-pull measurements. The mechanisms of the non-linear input capacitance have been analyzed using 2D TCAD simulations. The investigation shows that the input capacitance is a large contributor to phase distortion in the transistor. Computational load-pull TCAD methods have been developed for analysis of RF-power devices in high-efficiency operation. Methods have been developed for class-F with harmonic loading and for bias-modulation. Load-pull measurements with drain-bias modulation in a novel measurement setup have also been conducted. The investigation shows that the combination of computational load-pull of physical transistor structures and direct measurement evaluation with modified load-pull is a viable alternative for future design of RF-power devices. Simulations and measurements on the designed LDMOS shows a 10 to 15 % increase in drain efficiency in mid-power range both in simulations and measurements. The computational load-pull method has also been used to investigate the power capability of LDMOS transistors on SOI. This study indicates that either a low-resistivity or high-resistivity substrate should be used in manufacturing of RF-power LDMOS transistors on SOI to achieve optimum efficiency. Based on a proper substrate selection these devices exhibit a 10 % higher drain-efficiency mainly due to lower dissipated power in the devices.
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| 3. |
- Borin, Lars, 1957, et al.
(författare)
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The lexical editing system of Karp
- 2013
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Ingår i: Kosem, I., Kallas, J., Gantar, P., Krek, S., Langemets, M., Tuulik, M. (eds.) 2013. Electronic lexicography in the 21st century: thinking outside the paper. Proceedings of the eLex 2013 conference, 17-19 October 2013, Tallinn, Estonia.. - Ljubljana/Tallinn : Trojina, Institute for Applied Slovene Studies / Eesti Keele Instituut. - 9789619359402
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Konferensbidrag (refereegranskat)abstract
- Karp is the open lexical infrastructure of Språkbanken (the Swedish Language Bank). The infrastructure has three main functions: (1) to support the work on creating, curating, and integrating our various lexical resources; (2) to publish the resources, making them searchable and downloadable; and (3) to offer advanced editing functionalities. An important feature of the lexical infrastructure is also that we maintain a strong bidirectional connection to our corpus infrastructure. At the heart of the infrastructure is the SweFN++ project with the goal to create free Swedish lexical resources geared towards language technology applications. The infrastructure currently hosts 23 Swedish lexical resources. The resources are integrated through links to a pivot lexical resource, SALDO, a large morphological and lexical-semantic resource for modern Swedish.
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| 4. |
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| 5. |
- 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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| 6. |
- 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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| 7. |
- 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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| 8. |
- 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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| 9. |
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| 10. |
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| 11. |
- 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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| 12. |
- 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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| 13. |
- 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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| 14. |
- Majumdar, Abhinav, et al.
(författare)
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Macromolecular characterization of high β-glucan oat lines
- 2024
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Ingår i: Heliyon. - 2405-8440. ; 10:2
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Tidskriftsartikel (refereegranskat)abstract
- Oat (Avena sativa) is a cereal grain rich in fibers, proteins, vitamins and minerals. Oats have been linked to several health benefits, such as lowering blood cholesterol levels, counteracting cardiovascular disease and regulating blood sugar levels. This study aimed to characterize two new oat lines with high β-glucan content emanating from ethyl methyl sulphonate mutagenesis on the Lantmännen elite variety Belinda. Two of the mutated lines, and the mother variety Belinda, were profiled for β-glucan, arabinoxylan, total dietary fiber and starch composition. In addition, total lipid and protein content, amino acid composition and β-glucan molecular weights were analyzed. The high levels of β-glucan resulted in a significant increase in total dietary fiber, but no correlation could be established between higher or lower levels of the assayed macromolecules, i.e., between arabinoxylan-, starch-, lipid- or protein levels in the mutated lines compared to the reference. The results indicate separate biosynthetic pathways for β-glucans and other macromolecules and an independent regulation of the different polysaccharides studied. Therefore, ethyl methyl sulphonate mutagenesis can be used to increase levels of multiple macromolecules in the same line.
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| 15. |
- Moberg, Christina, et al.
(författare)
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De unga gör helt rätt när de stämmer staten
- 2022
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Ingår i: Aftonbladet. - 1103-9000.
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- 1 620 forskare och lärare i forskarvärlden: Vi ställer oss bakom Auroras klimatkrav
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| 16. |
- Olsson, Lovisa A., 1950-, et al.
(författare)
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Subjective well-being in Swedish active seniors or seniors with cognitive complaints and its relation to commonly available biomarkers
- 2013
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Ingår i: Archives of gerontology and geriatrics (Print). - : Elsevier BV. - 0167-4943 .- 1872-6976. ; 56:2, s. 303-308
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Tidskriftsartikel (refereegranskat)abstract
- Well-being (WB) is a complex variable in its relation to physical health and other personal and social characteristics. The aim was to study subjective well-being (SWB) and its possible associations with traditional biomarkers of cardiovascular risk or dementia, in Swedish seniors. SWB was estimated by the Psychological General Well-Being (PGWB) index in two study groups. The active seniors (AS) group consisted of community-dwelling elderly Swedes leading an active life (n=389). The DGM cohort (n=300) consisted of subjects referred to the Memory Unit at the Department of Geriatrics, the cognitive problems had to be subjective, mild or moderate (MMSE≥10). There were differences in all six subdimensions of SWB or distress, and in the sum of PGWB scores, between the two study groups (p<0.001 for all), and adjustment for differences in biomarkers of somatic health (age, sex, blood pressure, BMI, HDL cholesterol, ApoB/ApoA1 ratio, creatinine, and homocysteine) did not attenuate these differences. In addition, cognition as assessed by the Clock-Drawing Test (CDT) showed independent associations with four of the PGWB subdimensions and with the PGWB sum. Among the subjects in the DGM cohort, SWB was equally low among subjects with an MCI (minor cognitive impairment) diagnosis or without a dementia diagnosis as among subjects diagnosed with dementia disorder. We conclude that the nosological grouping variable (AS vs. DGM cohort) and a cognitive factor were the main independent predictors of SWB in this sample of elderly Swedes, whereas biomarkers of somatic health played a subordinated role.
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| 17. |
- Sikora, P., et al.
(författare)
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Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding
- 2011
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Ingår i: International Journal of Plant Genomics. - : Hindawi Limited. - 1687-5389 .- 1687-5370. ; 2011
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Tidskriftsartikel (refereegranskat)abstract
- Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed.
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| 18. |
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| 19. |
- Aboul-Ata, Aboul-Ata E, et al.
(författare)
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Plant-based vaccines: novel and low-cost possible route for mediterranean innovative vaccination strategies.
- 2014
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Ingår i: Advances in Virus Research. - : Elsevier. - 1557-8399. ; 89, s. 1-37, s. 1-37
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Forskningsöversikt (refereegranskat)abstract
- A plant bioreactor has enormous capability as a system that supports many biological activities, that is, production of plant bodies, virus-like particles (VLPs), and vaccines. Foreign gene expression is an efficient mechanism for getting protein vaccines against different human viral and nonviral diseases. Plants make it easy to deal with safe, inexpensive, and provide trouble-free storage. The broad spectrum of safe gene promoters is being used to avoid risk assessments. Engineered virus-based vectors have no side effect. The process can be manipulated as follows: (a) retrieve and select gene encoding, use an antigenic protein from GenBank and/or from a viral-genome sequence, (b) design and construct hybrid-virus vectors (viral vector with a gene of interest) eventually flanked by plant-specific genetic regulatory elements for constitutive expression for obtaining chimeric virus, (c) gene transformation and/or transfection, for transient expression, into a plant-host model, that is, tobacco, to get protocols processed positively, and then moving into edible host plants, (d) confirmation of protein expression by bioassay, PCR-associated tests (RT-PCR), Northern and Western blotting analysis, and serological assay (ELISA), (e) expression for adjuvant recombinant protein seeking better antigenicity, (f) extraction and purification of expressed protein for identification and dosing, (g) antigenicity capability evaluated using parental or oral delivery in animal models (mice and/or rabbit immunization), and (h) growing of construct-treated edible crops in protective green houses. Some successful cases of heterologous gene-expressed protein, as edible vaccine, are being discussed, that is, hepatitis C virus (HCV). R9 mimotope, also named hypervariable region 1 (HVR1), was derived from the HVR1 of HCV. It was used as a potential neutralizing epitope of HCV. The mimotope was expressed using cucumber mosaic virus coat protein (CP), alfalfa mosaic virus CP P3/RNA3, and tobacco mosaic virus (TMV) CP-tobacco mild green mosaic virus (TMGMV) CP as expression vectors into tobacco plants. Expressed recombinant protein has not only been confirmed as a therapeutic but also as a diagnostic tool. Herpes simplex virus 2 (HSV-2), HSV-2 gD, and HSV-2 VP16 subunits were transfected into tobacco plants, using TMV CP-TMGMV CP expression vectors.
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| 20. |
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| 21. |
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| 22. |
- Ahlberg, Malin, 1986, et al.
(författare)
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Språkbanken’s Open Lexical Infrastructure
- 2016
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Ingår i: SLTC 2016. The Sixth Swedish Language Technology Conference. Umeå University, 17-18 November, 2016.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Karp is an open lexical infrastructure and a web based tool for searching, exploring and developing lexical resources. Språkbanken currently hosts a number of lexicons in Karp and on-going work aims at broadening the type of resources that can be developed in the system. This abstract gives a short overview of Karp's basic functionality, and describes some current projects and on-going work.
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| 23. |
- Alfredo Zambrano, José, et al.
(författare)
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Characterization of high Arabinoxylan oat lines identified from a mutagenized oat population
- 2023
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Ingår i: Food Chemistry. - : Elsevier BV. - 0308-8146. ; 404
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Tidskriftsartikel (refereegranskat)abstract
- Oat (Avena sativa) is a nutritionally important cereal crop that is rich in health-promoting dietary fibers, favorable proteins and polar lipids. In this work, ca. 500 random lines of a mutagenized oat population of high genetic variation were screened for arabinoxylan (AX) content. This identified lines with up to 60% higher AX levels in flour from whole seed and up to 100% higher in flour from dehulled seeds, as compared to the original Belinda variety. In addition, the cellular localization of AX was determined in cross-sections of dehulled seeds from three high and one low AX line using a xylan-specific antibody. This revealed variations in the amount and localization of AX between high and low AX lines. The high AX lines will now serve as a starting point in the development of oat varieties with superior health-promoting and rheological properties.
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| 24. |
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| 25. |
- Andersson, Kristina E., et al.
(författare)
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Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport
- 2017
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Ingår i: Molecular Nutrition and Food Research. - : Wiley. - 1613-4125 .- 1613-4133. ; 61:7
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Tidskriftsartikel (refereegranskat)abstract
- Scope: The molecular mechanisms underlying the cholesterol-lowering properties of oats are only partly known. To study possible pathways involved, we investigated gene expressions in the liver and small intestine of mice fed oats. Method and results: Cholesterol and bile acids were analyzed in plasma and feces from LDL-receptor deficient (LDLr-/-) mice fed Western diet with wholegrain oats. A transcriptome analysis of mRNA from liver and jejunum was performed together with quantitative RT-PCR. Oat-fed mice had lower levels of plasma lipids and increased levels of bile acids and cholesterol in feces compared with controls. Two hundred thirty nine genes in jejunum and 25 genes in liver were differentially expressed (FDR corrected p < 0.05). The most affected biological process in jejunum was lipid biosynthesis and regulation. The apical sodium-dependent bile acid transporter (ASBT, Slc10a) and the intracellular bile acid binding protein (Fabp6) were both upregulated, whereas small heterodimer partner-1 (Shp-1) and apolipoprotein CII (Apoc2) were downregulated. Conclusions: Whole oats attenuated responses typically induced by high-fat diet. Increased expression of genes for intestinal bile acid uptake following oat consumption suggests retention in the gut lumen rather than decreased uptake capacity as cause for the increased bile acid excretion and the concomitant reduction of plasma cholesterol.
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