| 1. |
- Frazier-Wood, Alexis C., et al.
(författare)
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Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses
- 2016
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Ingår i: Nature Genetics. - : Nature Research (part of Springer Nature). - 1061-4036 .- 1546-1718. ; 48, s. 624-
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Tidskriftsartikel (refereegranskat)abstract
- Very few genetic variants have been associated with depression and neuroticism, likely because of limitations on sample size in previous studies. Subjective well-being, a phenotype that is genetically correlated with both of these traits, has not yet been studied with genome-wide data. We conducted genome-wide association studies of three phenotypes: subjective well-being (n = 298,420), depressive symptoms (n = 161,460), and neuroticism (n = 170,911). We identify 3 variants associated with subjective well-being, 2 variants associated with depressive symptoms, and 11 variants associated with neuroticism, including 2 inversion polymorphisms. The two loci associated with depressive symptoms replicate in an independent depression sample. Joint analyses that exploit the high genetic correlations between the phenotypes (vertical bar(p) over cap vertical bar approximate to 0.8) strengthen the overall credibility of the findings and allow us to identify additional variants. Across our phenotypes, loci regulating expression in central nervous system and adrenal or pancreas tissues are strongly enriched for association.
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| 2. |
- Botling, Johan, et al.
(författare)
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Biomarker Discovery in Non-Small Cell Lung Cancer : Integrating Gene Expression Profiling, Meta-analysis, and Tissue Microarray Validation
- 2013
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Ingår i: Clinical Cancer Research. - 1078-0432 .- 1557-3265. ; 19:1, s. 194-204
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis and therapy response. So far, the value of these multigene signatures in clinical practice is unclear, and the biologic importance of individual genes is difficult to assess, as the published signatures virtually do not overlap.Experimental Design: Here, we describe a novel single institute cohort, including 196 non-small lung cancers (NSCLC) with clinical information and long-term follow-up. Gene expression array data were used as a training set to screen for single genes with prognostic impact. The top 450 probe sets identified using a univariate Cox regression model (significance level P < 0.01) were tested in a meta-analysis including five publicly available independent lung cancer cohorts (n = 860).Results: The meta-analysis revealed 14 genes that were significantly associated with survival (P < 0.001) with a false discovery rate < 1%. The prognostic impact of one of these genes, the cell adhesion molecule 1 (CADM1), was confirmed by use of immunohistochemistry on tissue microarrays from 2 independent NSCLC cohorts, altogether including 617 NSCLC samples. Low CADM1 protein expression was significantly associated with shorter survival, with particular influence in the adenocarcinoma patient subgroup.Conclusions: Using a novel NSCLC cohort together with a meta-analysis validation approach, we have identified a set of single genes with independent prognostic impact. One of these genes, CADM1, was further established as an immunohistochemical marker with a potential application in clinical diagnostics. Clin Cancer Res; 19(1); 194-204. (c) 2012 AACR.
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| 3. |
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| 4. |
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| 5. |
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| 6. |
- Lindblad-Toh, Kerstin, et al.
(författare)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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| 7. |
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| 8. |
- Mattsson, Johanna Sofia Margareta, 1985-, et al.
(författare)
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Inconsistent results in the analysis of ALK rearrangements in non-small cell lung cancer
- 2016
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Ingår i: BMC Cancer. - London, United Kingdom : Springer Science and Business Media LLC. - 1471-2407. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- Background: Identification of targetable EML4-ALK fusion proteins has revolutionized the treatment of a minor subgroup of non-small cell lung cancer (NSCLC) patients. Although fluorescence in situ hybridization (FISH) is regarded as the gold standard for detection of ALK rearrangements, ALK immunohistochemistry (IHC) is often used as screening tool in clinical practice. In order to unbiasedly analyze the diagnostic impact of such a screening strategy, we compared ALK IHC with ALK FISH in three large representative Swedish NSCLC cohorts incorporating clinical parameters and gene expression data.Methods: ALK rearrangements were detected using FISH on tissue microarrays (TMAs), including tissue from 851 NSCLC patients. In parallel, ALK protein expression was detected using IHC, applying the antibody clone D5F3 with two different protocols (the FDA approved Ventana CDx assay and our in house Dako IHC protocol). Gene expression microarray data (Affymetrix) was available for 194 patients.Results: ALK rearrangements were detected in 1.7% in the complete cohort and 2.0% in the non-squamous cell carcinoma subgroup. ALK protein expression was observed in 1.9% and 1.5% when applying the Ventana assay or the in house Dako protocol, respectively. The specificity and accuracy of IHC was high (>99%), while the sensitivity was between 69% (Ventana) and 62% (in house Dako protocol). Furthermore, only 67% of the ALK IHC positive cases were positive in both IHC assays. Gene expression analysis revealed that 6/194 (3%) tumors showed high ALK gene expression (≥6AU) and of them only three were positive by either FISH or IHC.Conclusion: The overall frequency of ALK rearrangements based on FISH was lower than previously reported. The sensitivity of both IHC assays was low, and the concordance between the FISH and the IHC assays poor, questioning current strategies to screen with IHC prior to FISH or completely replace FISH by IHC.
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| 9. |
- Mattsson, Johanna Sofia Margareta, 1985-, et al.
(författare)
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Prognostic impact of COX-2 in non-small cell lung cancer : a comprehensive compartment-specific evaluation of tumor and stromal cell expression
- 2015
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Ingår i: Cancer Letters. - : Elsevier BV. - 0304-3835 .- 1872-7980. ; 356:2, s. 837-845
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Tidskriftsartikel (refereegranskat)abstract
- Cyclooxygenase-2 (COX-2) is an enzyme that has been extensively investigated as a prognostic marker in cancer. In non-small cell lung cancer (NSCLC) previous results regarding the prognostic impact of COX-2 expression are inconsistent. Therefore we evaluated the association between transcript levels and overall survival in nine publicly available gene expression data sets (total n = 1337) and determined in situ compartment-specific tumor and stromal cell protein expression in two independent cohorts (n = 616). Gene expression did not show any correlation with clinical parameters or with overall survival. Protein expression in tumor and stromal cells did not correlate with any clinical parameter or with overall survival in one of the analyzed cohorts, while a significant association of high stromal expression with longer survival was observed in both univariate and multivariate analysis in the other cohort. Stromal expression of COX-2 has not been separately evaluated in NSCLC previously and may be a subject of further investigation, whereas the presented findings from this comprehensive compartment specific evaluation clearly reject the hypothesis of COX-2 tumor cell expression having a prognostic value in NSCLC. (C) 2014 Elsevier Ireland Ltd. All rights reserved.
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| 10. |
- Sarhan, Dhifaf, et al.
(författare)
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Antibody targeting of tumor associated macrophages in lung cancer remodel the tumor microenvironment and revives immune targeting of tumor cells
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Immunotherapy for cancer has revolutionized clinical practice and enabled cures for previously lethal cancers. However, the clinical responses are variable and highly influenced by immune regulatory compartments in the tumor microenvironment. This is especially true for immune-excluded tumors, where clinical trials aiming to recover T cell anti-tumor activity have been disappointing. Thus, in NSCLC and other cancers there is a clinical need for additional and combinatory treatments. We have previously shown that antibodies targeting scavenger receptors expressed on tumor-associated macrophages (TAMs), reduces tumor growth and impair metastasis in murine cancer models. Here we investigated targeting of the scavenger receptor MARCO on human TAMs in NSCLC. We found that expression of this receptor in the tumor correlated with immune-exclusion phenotype. Also, we found that lung cancer cell lines converted healthy myeloid cells towards TAM like cells with high expression of MARCO. These human MARCO+ myeloid cells stopped cytotoxic T cells and natural killer (NK) cells from killing tumors and inhibited their overall activity. We then generated anti-human MARCO antibodies and found that these could repolarize TAMs leading to augmented cytolytic ability of NK cells and T cells to kill tumor cells and recovered their proliferation and IFNγ production capacity. Overall, our data demonstrate that it is feasible to use antibodies to alter human TAM immune suppression of NK and T cell anti-tumor activities.
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| 11. |
- Smith, Jennifer A, et al.
(författare)
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Genome-wide association study identifies 74 loci associated with educational attainment
- 2016
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Ingår i: Nature (London). - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 533:7604, s. 539-542
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Tidskriftsartikel (refereegranskat)abstract
- Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 genome-wide significant loci associated with the number of years of schooling completed. Single-nucleotide polymorphisms associated with educational attainment are disproportionately found in genomic regions regulating gene expression in the fetal brain. Candidate genes are preferentially expressed in neural tissue, especially during the prenatal period, and enriched for biological pathways involved in neural development. Our findings demonstrate that, even for a behavioural phenotype that is mostly environmentally determined, a well-powered GWAS identifies replicable associated genetic variants that suggest biologically relevant pathways. Because educational attainment is measured in large numbers of individuals, it will continue to be useful as a proxy phenotype in efforts to characterize the genetic influences of related phenotypes, including cognition and neuropsychiatric diseases.
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| 12. |
- Adams Lyngbäck, Liz, 1966-
(författare)
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Experiences, networks and uncertainty : parenting a child who uses a cochlear implant
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this dissertation project is to describe the ways people experience parenting a deaf child who uses a cochlear implant. Within a framework of social science studies of disability this is done by combining approaches using ethnographic and netnographic methods of participant observation with an interview study. Interpretations are based on the first-person perspective of 19 parents against the background of their related networks of social encounters of everyday life. The netnographic study is presented in composite conversations building on exchanges in 10 social media groups, which investigates the parents’ meaning-making in interaction with other parents with similar living conditions. Ideas about language, technology, deafness, disability, and activism are explored. Lived parenting refers to the analysis of accounts of orientation and what 'gets done' in respect to these ideas in situations where people utilize the senses differently. In the results, dilemmas surrounding language, communication and cochlear implantation are identified and explored. The dilemmas extend from if and when to implant, to decisions about communication modes, intervention approaches, and schools. An important finding concerns the parents’ orientations within the dilemmas, where most parents come up against antagonistic conflicts. There are also examples found of a development process in parenting based on lived, in-depth experiences of disability and uncertainty which enables parents to transcend the conflictive atmosphere. This process is analyzed in terms of a social literacy of dis/ability.
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| 13. |
- Ahnesjö, Jonas, 1969-, et al.
(författare)
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Benefits of outdoor exercise and recovery outdoors in elderly
- 2019
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Ingår i: HEPA Europe, Odense, Denmark, August 28-30, 2019. ; , s. 38-38
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Konferensbidrag (refereegranskat)abstract
- Purpose: The purpose of this study was to test the hypothesis that the ”outdoors” has an added health effect on top of that of physical activity. This hypothesis is based on the fairly extensive volume of evidens suggesting that the outdoor environment is beneficial for overall health. We, however, consider most previous studies insufficiently designed in order to draw causal relationship between spending time outdoors and examined health parameters. In this study we state that our experimental design allows us to do just that. Methods:In this randomized cross-over experimental design, 49 healthy subjects (+65 years, 27 female) performed a standardized submaximal bike ergometer test in three different environments (indoors, simulated outdoors and outdoors). The test consisted of 20 minutes cycling and subjects were instructed to stay between 11-13 at the Borg RPE scale (i.e. moderate intensity). Each test was followed by two hours of passive recovery. We measured power output, heart rate, lactate and counts of five fractions (lymphocytes, monocytes, neutrophiles, basophiles and eosinophiles) of white blood cells (leukocytes) in circulation. Results:Our results revealed that the outdoor treatment resulted in higher levels of lactate, higher heart rate and higher power output despite that there were no differences in Borg RPE-rating between the treatments. The white blood cell analysis showed an increase of circulating leukocytes in almost all fractions immediately post exercise in all treatments. Numbers decreased rapidly post exercise and the lymphocyte numbers stayed well under baseline for more than one hour during recovery. This is referred to as an “open window” where the immune function is temporarily suppressed and there is an elevated risk of infection of primarily URTI. Conclusions:Our results not only suggest that exercise is more efficient out of doors such that more exercise/effort is obtained but also that recovery outdoors may be a way to decrease the risk of infections due to exercise induced immune suppression. The risk of getting an infection is known to be generally lower out of doors. Taken together, our results support the notion that exercising and spending time outdoors indeed is beneficial for health in senior citizens.
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| 14. |
- Ahnesjö, Jonas, 1969-, et al.
(författare)
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The effect of exercising in different environments on heart rate and power output among older adults–a randomized crossover study
- 2022
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 17:11
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundA growing body of evidence suggests that exposure to nature is beneficial for human health. However, the observed health effect of nature may be mediated by physical activity and that humans are physically active at a higher intensity outdoors compared to when they are physical active indoors.ObjectiveThis study examines the variation of heart rate and power output for a fixed rating of perceived exertion in a group of healthy older adults in three different environments representing three levels of exposure to nature.MethodsTo this randomized, 3-by-3 crossover design study, healthy older adults (≥65 years) were recruited from local gyms. All participants participated in three experimental conditions; indoors, simulated outdoors and outdoor environments, in a randomized order. The participants exercised for 20 minutes at an intensity equivalent to a rating of 11–13 on the Borg scale for perceived exertion (RPE). Measurements of heart rate, power output (Watt) and ratings of perceived exertion were taken at minutes 1 to 6 and at minute 20. To examine the effect of the environment on heart rate and power, linear mixed models were used.ResultsIn all, 48 participants (56% females) were included in the analysis. No significant main effects on the outcomes were observed for power output (p = 0.073, η2 = 0.04) or heart rate (p = 0.067, η2 = 0.04)ConclusionNo significant effect on the outcomes was observed. However, borderline significant outcomes for power output or heart rate outdoors in nature, along with previous studies in the field, indicates that such an effect cannot be completely ruled out, but any effect is likely to be small. Future research examining health benefits of the independent exposure to nature are encouraged to adjust for the dose of physical activity.
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| 15. |
- Allamani, Allaman, et al.
(författare)
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Contextual Determinants of Alcohol Consumption Changes and Preventive Alcohol Policies : A 12-Country European Study in Progress 2011
- 2011
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Ingår i: Substance Use & Misuse. - : Informa UK Limited. - 1082-6084 .- 1532-2491. ; 46:10, s. 1288-1303
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Tidskriftsartikel (refereegranskat)abstract
- Beginning with France in the 1950s, alcohol consumption has decreased in Southern European countries with few or no preventive alcohol policy measures being implemented, while alcohol consumption has been increasing in Northern European countries where historically more restrictive alcohol control policies were in place, even though more recently they were loosened. At the same time, Central and Eastern Europe have shown an intermediate behavior. We propose that country-specific changes in alcohol consumption between 1960 and 2008 are explained by a combination of a number of factors: (1) preventive alcohol policies and (2) social, cultural, economic, and demographic determinants. This article describes the methodology of a research study designed to understand the complex interactions that have occurred throughout Europe over the past five decades. These include changes in alcohol consumption, drinking patterns and alcohol-related harm, and the actual determinants of such changes
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| 16. |
- Almstedt, Åsa, 1977-, et al.
(författare)
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Beyond Post-productivism : From Rural Policy Discource to Rural Diversity
- 2014
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Ingår i: European Countryside. - Berlin : Walter de Gruyter GmbH. - 1803-8417. ; 6:4, s. 297-306
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Tidskriftsartikel (refereegranskat)abstract
- There has been a strong discourse in public policy aimed at transforming rural places from venues of primary production into truly diverse socioeconomic landscapes. Yet conceptualisations of the rural as envisioned in the policy and politics of the ‘new economy’ often prove to be elusive on the ground. However, post-productive activity in rural areas has become a major focus for rural studies scholars. This paper investigates the ideas of post-productivism in the existing literature, and argues for a holistic understanding of post-productivism as an idea and political ambition rather than an imperative and irreversible change of rural economic activity. The purpose of the study is to make clear the division between post-productivism and the related concepts of post-production and post-productive activities in order to better understand processes of rural change in relation to different geographical contexts. It is argued that post-productivism as a concept stands apart from de facto post-production and alternative concepts such as multifunctionality and should be regarded as part of broader regional development discourses. The paper outlines several important fields in which post-productivism is a necessary component for rural transformation and development. While it is not always easily captured in indicators or empirical studies in rural locations, post- productivism exists at the level of discourse and planning and thus has real effects on the ground. The paper concludes by offering suggestions on how to apply the concepts of post-productivism, post-production and multifunctionality in future studies.
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| 17. |
- Andersson, Evelyn, et al.
(författare)
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Genetics of response to cognitive behavior therapy in adults with major depression : a preliminary report
- 2019
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Ingår i: Molecular Psychiatry. - : Nature Publishing Group. - 1359-4184 .- 1476-5578. ; 24:4, s. 484-490
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Tidskriftsartikel (refereegranskat)abstract
- Major depressive disorder is heritable and a leading cause of disability. Cognitive behavior therapy is an effective treatment for major depression. By quantifying genetic risk scores based on common genetic variants, the aim of this report was to explore the utility of psychiatric and cognitive trait genetic risk scores, for predicting the response of 894 adults with major depressive disorder to cognitive behavior therapy. The participants were recruited in a psychiatric setting, and the primary outcome score was measured using the Montgomery Asberg Depression Rating Scale-Self Rated. Single-nucleotide polymorphism genotyping arrays were used to calculate the genomic risk scores based on large genetic studies of six phenotypes: major depressive disorder, bipolar disorder, attention-deficit/hyperactivity disorder, autism spectrum disorder, intelligence, and educational attainment. Linear mixed-effect models were used to test the relationships between the six genetic risk scores and cognitive behavior therapy outcome. Our analyses yielded one significant interaction effect (B = 0.09, p < 0.001): the autism spectrum disorder genetic risk score correlated with Montgomery Asberg Depression Rating Scale-Self Rated changes during treatment, and the higher the autism spectrum disorder genetic load, the less the depressive symptoms decreased over time. The genetic risk scores for the other psychiatric and cognitive traits were not related to depressive symptom severity or change over time. Our preliminary results indicated, as expected, that the genomics of the response of patients with major depression to cognitive behavior therapy were complex and that future efforts should aim to maximize sample size and limit subject heterogeneity in order to gain a better understanding of the use of genetic risk factors to predict treatment outcome.
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| 18. |
- Ara, Kazi Zubaida Gulshan, et al.
(författare)
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Engineering CGTase to improve synthesis of alkyl glycosides
- 2021
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 1460-2423. ; 31:5, s. 603-612
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Tidskriftsartikel (refereegranskat)abstract
- Alkyl glycoside surfactants with elongated carbohydrate chains are useful in different applications due to their improved biocompatibility. Cyclodextrin glucanotransferases can catalyse the elongation process through the coupling reaction. However, due to the presence of a hydrophobic tail, the interaction between an alkyl glycoside acceptor and the active site residues is weaker than the interaction with maltooligosaccharides at the corresponding site. Here we report the mutations of F197, G263 and E266 near the acceptor subsites in the CGTase CspCGT13 from Carboxydocella sp. The results showed that substitutions of both F197 and G263 were important for the binding of acceptor substrate dodecyl maltoside during coupling reaction. The double mutant F197Y/G263A showed enhanced coupling activity and displayed a 2-fold increase of the primary coupling product using γ-cyclodextrin as donor when compared to wildtype CspCGT13. Disproportionation activity was also reduced, which was also the case for another double mutant (F197Y/E266A) that however not showed the corresponding increase in coupling. A triple mutant F197Y/G263A/E266A maintained the increase in primary coupling product (1.8-fold increase) using dodecyl maltoside as acceptor, but disproportionation was approximately at the same level as in the double mutants. In addition, hydrolysis of starch was slightly increased by the F197Y and G263A substitutions, indicating that interactions at both positions influenced the selectivity between glycosyl and alkyl moieties.
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| 19. |
- Baccarini, Andrea, et al.
(författare)
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Frequent new particle formation over the high Arctic pack ice by enhanced iodine emissions
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- In the central Arctic Ocean the formation of clouds and their properties are sensitive to the availability of cloud condensation nuclei (CCN). The vapors responsible for new particle formation (NPF), potentially leading to CCN, have remained unidentified since the first aerosol measurements in 1991. Here, we report that all the observed NPF events from the Arctic Ocean 2018 expedition are driven by iodic acid with little contribution from sulfuric acid. Iodic acid largely explains the growth of ultrafine particles (UFP) in most events. The iodic acid concentration increases significantly from summer towards autumn, possibly linked to the ocean freeze-up and a seasonal rise in ozone. This leads to a one order of magnitude higher UFP concentration in autumn. Measurements of cloud residuals suggest that particles smaller than 30nm in diameter can activate as CCN. Therefore, iodine NPF has the potential to influence cloud properties over the Arctic Ocean. Which vapors are responsible for new particle formation in the Arctic is largely unknown. Here, the authors show that the formation of new particles at the central Arctic Ocean is mainly driven by iodic acid and that particles smaller than 30nm in diameter can activate as cloud condensation nuclei.
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| 20. |
- Bastiat, Guillaume, et al.
(författare)
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Development of Non-Phospholipid Liposomes Containing a High Cholesterol Concentration
- 2007
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 23:14, s. 7695-7699
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Tidskriftsartikel (refereegranskat)abstract
- We present a novel formulation of non-phospholipid liposomes formed from cholesterol and palmitic acid. Despite the fact that these two lipidic species do not form individually fluid bilayers, we show that once mixed together, fluid bilayers can be obtained and, moreover, these can be extruded using classical extrusion processes to form liposomes. The chem. anal. indicates that these liposomes contain 70 mol % cholesterol, a content that is considerably higher that the satn. limit generally reported for phospholipid bilayers. These cholesterol-rich liposomes, formed with mols. that have low toxicity in vivo, display an improved impermeability relative to that of traditional phospholipid liposomes. In addn., because of the presence of palmitic acid, the stability of the liposomes is pH-dependent, and it is possible to trigger the release of encapsulated materials by pH stimuli.
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| 21. |
- Becker, Joel, et al.
(författare)
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Resource profile and user guide of the Polygenic Index Repository
- 2021
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Ingår i: Nature Human Behaviour. - : Nature Research (part of Springer Nature). - 2397-3374. ; 51:6, s. 694-695
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Tidskriftsartikel (refereegranskat)abstract
- Polygenic indexes (PGIs) are DNA-based predictors. Their value for research in many scientific disciplines is growing rapidly. As a resource for researchers, we used a consistent methodology to construct PGIs for 47 phenotypes in 11 datasets. To maximize the PGIs’ prediction accuracies, we constructed them using genome-wide association studies—some not previously published—from multiple data sources, including 23andMe and UK Biobank. We present a theoretical framework to help interpret analyses involving PGIs. A key insight is that a PGI can be understood as an unbiased but noisy measure of a latent variable we call the ‘additive SNP factor’. Regressions in which the true regressor is this factor but the PGI is used as its proxy therefore suffer from errors-in-variables bias. We derive an estimator that corrects for the bias, illustrate the correction, and make a Python tool for implementing it publicly available. © 2021, The Author(s), under exclusive licence to Springer Nature Limited.
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| 22. |
- Berger, Karin, et al.
(författare)
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Cereal Byproducts Have Prebiotic Potential in Mice Fed a High-Fat Diet
- 2014
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Ingår i: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 62:32, s. 8169-8178
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Tidskriftsartikel (refereegranskat)abstract
- Barley husks, rye bran, and a fiber residue from oat milk production were processed by heat pretreatment, various separation steps, and treatment with an endoxylanase in order to improve the prebiotic potential of these cereal byproducts. Metabolic functions were intended to improve along with improved microbial activity. The products obtained were included in a high-fat mouse diet so that all diets contained 5% dietary fiber. In addition, high-fat and low-fat controls as well as partially hydrolyzed guar gum were included in the study. The soluble fiber product obtained from rye bran caused a significant increase in the bifidobacteria (log copies of 16S rRNA genes; median (25−75 percentile): 6.38 (6.04−6.66) and 7.47 (7.30−7.74), respectively; p < 0.001) in parallel with a tendency of increased production of propionic acid and indications of improved metabolic function compared with high-fat fed control mice. The oat-derived product caused an increase in the pool of cecal propionic (from 0.62 ± 0.12 to 0.94 ± 0.08) and butyric acid (from 0.38 ± 0.04 to 0.60 ± 0.04) compared with the high-fat control, and it caused a significant increase in lactobacilli (log copies of 16S rRNA genes; median (25−75 percentile): 6.83 (6.65−7.53) and 8.04 (7.86−8.33), respectively; p < 0.01) in the cecal mucosa. However, no changes in measured metabolic parameters were observed by either oat or barley products.
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| 23. |
- Berger, Karin, et al.
(författare)
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Xylooligosaccharides Increase Bifidobacteria and Lachnospiraceae in Mice on a High-Fat Diet, with a Concomitant Increase in Short-Chain Fatty Acids, Especially Butyric Acid
- 2021
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Ingår i: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 69:12, s. 3617-3625
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Tidskriftsartikel (refereegranskat)abstract
- Effects of xylooligosaccharides (XOSs) as well as a mixture of XOS, inulin, oligofructose, and partially hydrolyzed guar gum (MIX) in mice fed a high-fat diet (HFD) were studied. Control groups were fed an HFD or a low-fat diet. Special attention was paid to the cecal composition of the gut microbiota and formation of short-chain fatty acids, but metabolic parameters were also documented. The XOS group had significantly higher cecum levels of acetic, propionic, and butyric acids than the HFD group, and the butyric acid content was higher in the XOS than in the MIX group. The cecum microbiota of the XOS group contained more Bifidobacteria, Lachnospiraceae, and S24-7 bacteria than the HFD group. A tendency of lower body weight gain was observed on comparing the XOS and HFD groups. In conclusion, the XOS was shown to be a promising prebiotic candidate. The fiber diversity in the MIX diet did not provide any advantages compared to the XOS diet.
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| 24. |
- Bhattacharya, Abhishek, et al.
(författare)
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Enzyme synergy for the production of arabinoxylo-oligosaccharides from highly substituted arabinoxylan and evaluation of their prebiotic potential
- 2020
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Ingår i: Lebensmittel-Wissenschaft + Technologie. - : Elsevier BV. - 0023-6438 .- 1096-1127. ; 131
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Tidskriftsartikel (refereegranskat)abstract
- Wheat bran arabinoxylan can be converted by enzymatic hydrolysis into short arabinoxylo-oligosaccharides (AXOS) with prebiotic potential. Alkali extraction of arabinoxylan from wheat-bran offers advantages in terms of yield and results in arabinoxylan with highly-substituted regions which has been a challenge to hydrolyse using endoxylanases. We show that this hurdle can be overcome by selecting an arabinoxylanase that attacks these regions. The yield of AXOS can be increased by enzyme synergy, involving the hydrolysis of some arabinoxylan side groups. Thus, arabinoxylanase (CtXyl5At) from Clostridium thermocellum, belonging to subfamily 34 of glycoside hydrolase (GH) family 5 was investigated pertaining to its specificity for highly-substituted regions in the arabinoxylan-backbone. CtXyl5At preferentially hydrolysed the water-soluble fraction of alkali-extracted arabinoxylan. AXOS with DP 2-4 were determined as major products from CtXyl5At catalyzed hydrolysis. Increase in AXOS yield was observed with enzyme synergy, involving an initial treatment of soluble arabinoxylan with a GH43 alpha-L-arabinofuranosidase from Bifidobacterium adolescentis termed BaAXHd3 (30 degrees C, 6h), followed by hydrolysis with CtXyl5At (50 degrees C, 24h). The prebiotic potential of AXOS was shown by growth analysis using the human gut bacteria Bifidobacterium adolescentis ATCC 15703 and Roseburia hominis DSM 6839. Importantly, AXOS were utilized by the bacteria and short-chain fatty acids were produced.
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| 25. |
- Bize, Ariane, et al.
(författare)
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A unique virus release mechanism in the Archaea
- 2009
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 106:27, s. 11306-11311
-
Tidskriftsartikel (refereegranskat)abstract
- Little is known about the infection cycles of viruses infecting cells from Archaea, the third domain of life. Here, we demonstrate that the virions of the archaeal Sulfolobus islandicus rod-shaped virus 2 (SIRV2) are released from the host cell through a mechanism, involving the formation of specific cellular structures. Large pyramidal virus-induced protrusions transect the cell envelope at several positions, rupturing the S-layer; they eventually open out, thus creating large apertures through which virions escape the cell. We also demonstrate that massive degradation of the host chromosomes occurs because of virus infection, and that virion assembly occurs in the cytoplasm. Furthermore, intracellular viral DNA is visualized by flow cytometry. The results show that SIRV2 is a lytic virus, and that the host cell dies as a consequence of elaborated mechanisms orchestrated by the virus. The generation of specific cellular structures for a distinct step of virus life cycle is known in eukaryal virus-host systems but is unprecedented in cells from other domains.
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| 26. |
- Blomberg, Sara, et al.
(författare)
-
Bridging the Pressure Gap in CO Oxidation
- 2021
-
Ingår i: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 11:15, s. 9128-9135
-
Tidskriftsartikel (refereegranskat)abstract
- Performing fundamental operando catalysis studies under realistic conditions is a key to further develop and increase the efficiency of industrial catalysts. Operando X-ray photoelectron spectroscopy (XPS) experiments have been limited to pressures, and the relevance for industrial applications has been questioned. Herein, we report on the CO oxidation experiment on Pd(100) performed at a total pressure of 1 bar using XPS. We investigate the light-off regime and the surface chemical composition at the atomistic level in the highly active phase. Furthermore, the observed gas-phase photoemission peaks of CO2, CO, and O2 indicate that the kinetics of the reaction during the light-off regime can be followed operando, and by studying the reaction rate of the reaction, the activation energy is calculated. The reaction was preceded by an in situ oxidation study in 7% O2 in He and a total pressure of 70 mbar to confirm the surface sensitivity and assignment of the oxygen-induced photoemission peaks. However, oxygen-induced photoemission peaks were not observed during the reaction studies, but instead, a metallic Pd phase is present in the highly active regime under the conditions applied. The novel XPS setup utilizes hard X-rays to enable high-pressure studies, combined with a grazing incident angle to increase the surface sensitivity of the measurement. Our findings demonstrate the possibilities of achieving chemical information of the catalyst, operando, on an atomistic level, under industrially relevant conditions.
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| 27. |
- Brouder, Patrick, et al.
(författare)
-
Hyper-production : a new metric of multifinctionality
- 2015
-
Ingår i: European Countryside. - : Walter de Gruyter. - 1803-8417. ; 7:3, s. 134-143
-
Tidskriftsartikel (refereegranskat)abstract
- Multifunctionality has emerged as the dominant framework for understanding rural socioeconomic landscapes. The central claim of multifunctionality – that rural regions need to be understood as being made up of more than just traditional uses – has led to the incorporation of new rural activities into regional development plans, e.g., tourism. In some places, such post-productive activity is perceived to be slowly replacing productive uses of the land, e.g., agriculture/forestry. However, there is limited empirical evidence to support such claims. Drawing on previous research and data from the Swedish countryside this paper shows that, even as the number of persons employed within traditional activities decreases, the economic output per areal unit and per labour hour is increasing over time and traditional uses still occupy the majority of rural space. Hyper-production is introduced as a new metric for understanding multifunctional regions going forward. The complementary union of economic mainstays, such as agriculture, and newer activities with more quality-of-life benefits, such as tourism, is highlighted in terms of economic diversification, job creation and local social capital development, while the conflict-prone intersection of these two modes is also acknowledged. Understanding hyper-production as a key metric of multifunctionality is thus argued as integral to planning and developing resilient rural regions now and for the future.
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| 28. |
- Christmas, Matthew, et al.
(författare)
-
Evolutionary constraint and innovation across hundreds of placental mammals
- 2023
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6643
-
Tidskriftsartikel (refereegranskat)abstract
- Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (similar to 10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.
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| 29. |
- Colleoni, Marco, et al.
(författare)
-
Extended adjuvant intermittent letrozole versus continuous letrozole in postmenopausal women with breast cancer (SOLE): a multicentre, open-label, randomised, phase 3 trial.
- 2018
-
Ingår i: The Lancet. Oncology. - : Elsevier. - 1474-5488 .- 1470-2045. ; 19:1, s. 127-138
-
Tidskriftsartikel (refereegranskat)abstract
- In animal models of breast cancer, resistance to continuous use of letrozole can be reversed by withdrawal and reintroduction of letrozole. We therefore hypothesised that extended intermittent use of adjuvant letrozole would improve breast cancer outcome compared with continuous use of letrozole in postmenopausal women.We did the multicentre, open-label, randomised, parallel, phase 3 SOLE trial in 240 centres (academic, primary, secondary, and tertiary care centres) in 22 countries. We enrolled postmenopausal women of any age with hormone receptor-positive, lymph node-positive, and operable breast cancer for which they had undergone local treatment (surgery with or without radiotherapy) and had completed 4-6 years of adjuvant endocrine therapy. They had to be clinically free of breast cancer at enrolment and without evidence of recurrent disease at any time before randomisation. We randomly assigned women (1:1) to treatment groups of either continuous use of letrozole (2·5 mg/day orally for 5 years) or intermittent use of letrozole (2·5 mg/day orally for 9 months followed by a 3-month break in years 1-4 and then 2·5 mg/day during all 12 months of year 5). Randomisation was done by principal investigators or designee at respective centres through the internet-based system of the International Breast Cancer Study Group, was stratified by type of previous endocrine therapy (aromatase inhibitors only vs selective oestrogen receptor modulators only vs both therapies), and used permuted block sizes of four and institutional balancing. No one was masked to treatment assignment. The primary endpoint was disease-free survival, analysed by the intention-to-treat principle using a stratified log-rank test. All patients in the intention-to-treat population who initiated protocol treatment during their period of trial participation were included in the safety analyses. This study is registered with ClinicalTrials.gov, number NCT00553410, and EudraCT, number 2007-001370-88; and long-term follow-up of patients is ongoing.Between Dec 5, 2007, and Oct 8, 2012, 4884 women were enrolled and randomised after exclusion of patients at a non-adherent centre, found to have inadequate documentation of informed consent, immediately withdrew consent, or randomly assigned to intervention groups in error. 4851 women comprised the intention-to-treat population that compared extended intermittent letrozole use (n=2425) with continuous letrozole use (n=2426). After a median follow-up of 60 months (IQR 53-72), disease-free survival was 85·8% (95% CI 84·2-87·2) in the intermittent letrozole group compared with 87·5% (86·0-88·8) in the continuous letrozole group (hazard ratio 1·08, 95% CI 0·93-1·26; p=0·31). Adverse events were reported as expected and were similar between the two groups. The most common grade 3-5 adverse events were hypertension (584 [24%] of 2417 in the intermittent letrozole group vs 517 [21%] of 2411 in the continuous letrozole group) and arthralgia (136 [6%] vs 151 [6%]). 54 patients (24 [1%] in the intermittent letrozole group and 30 [1%] in the continuous letrozole group) had grade 3-5 CNS cerebrovascular ischaemia, 16 (nine [<1%] vs seven [<1%]) had grade 3-5 CNS haemorrhage, and 40 (19 [1%] vs 21 [1%]) had grade 3-5 cardiac ischaemia. In total, 23 (<1%) of 4851 patients died while on trial treatment (13 [<1%] of 2417 patients in the intermittent letrozole group vs ten [<1%] of 2411 in the continuous letrozole group).In postmenopausal women with hormone receptor-positive breast cancer, extended use of intermittent letrozole did not improve disease-free survival compared with continuous use of letrozole. An alternative schedule of extended adjuvant endocrine therapy with letrozole, including intermittent administration, might be feasible and the results of the SOLE trial support the safety of temporary treatment breaks in selected patients who might require them.Novartis and the International Breast Cancer Study Group.
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| 30. |
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| 31. |
- Cristea, Alexander, et al.
(författare)
-
Effects of aging and gender on the spatial organization of nuclei in single human skeletal muscle cells
- 2010
-
Ingår i: Aging Cell. - : Wiley. - 1474-9718 .- 1474-9726. ; 9:5, s. 685-697
-
Tidskriftsartikel (refereegranskat)abstract
- The skeletal muscle fibre is a syncitium where each myonucleus regulates the gene products in a finite volume of the cytoplasm, i.e., the myonuclear domain (MND). We analysed aging- and gender-related effects on myonuclei organization and the MND size in single muscle fibres from six young (21–31 years) and nine old men (72–96 years), and from six young (24–32 years) and nine old women (65–96 years), using a novel image analysis algorithm applied to confocal images. Muscle fibres were classified according to myosin heavy chain (MyHC) isoform expression. Our image analysis algorithm was effective in determining the spatial organization of myonuclei and the distribution of individual MNDs along the single fibre segments. Significant linear relations were observed between MND size and fibre size, irrespective age, gender and MyHC isoform expression. The spatial organization of individual myonuclei, calculated as the distribution of nearest neighbour distances in 3D, and MND size were affected in old age, but changes were dependent on MyHC isoform expression. In type I muscle fibres, average NN-values were lower and showed an increased variability in old age, reflecting an aggregation of myonuclei in old age. Average MND size did not change in old age, but there was an increased MND size variability. In type IIa fibres, average NN-values and MND sizes were lower in old age, reflecting the smaller size of these muscle fibres in old age. It is suggested that these changes have a significant impact on protein synthesis and degradation during the aging process.
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| 32. |
- David, Jennifer, 1987-, et al.
(författare)
-
Design and Development of a Hexacopter for the Search and Rescue of a Lost Drone
- 2019
-
Konferensbidrag (refereegranskat)abstract
- Search and rescue with an autonomous robot is an attractive and challenging task within the research community. This paper presents the development of an autonomous hexacopter that is designed for retrieving a lost object, like a drone, from a vast-open space, like a desert area. Navigating its path with a proposed coverage path planning strategy, the hexacopter can efficiently search for a lost target and locate it using an image-based object detection algorithm. Moreover, after the target is located, our hexacopter can grasp it with a customised gripper and transport it back to a destined location. It is also capable of avoiding static obstacles and dynamic objects. The proposed system was realised in simulations before implementing it in a real hardware setup, i.e. assembly of the drone, crafting of the gripper, software implementation and testing under real-world scenarios. The designed hexacopter won the best UAV design award at the CPS-VO 2018 Competition held in Arizona, USA.
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| 33. |
- Degerman, Johan, et al.
(författare)
-
Modeling stem cell migration by Hidden Markov
- 2004
-
Ingår i: Proceedings of the Swedish Symposium on Image Analysis, SSBA 2004. ; , s. 122-125
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 34. |
- Doherty, Patrick, 1957-, et al.
(författare)
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(TAL) temporal action logics : Language specification and tutorial.
- 1998
-
Ingår i: Electronic Transactions on Artifical Intelligence. - : Linköping University Electronic Press. - 1403-3534 .- 1403-3526. ; 2:3-4, s. 273-306
-
Tidskriftsartikel (refereegranskat)abstract
- The purpose of this article is to provide a uniform, lightweight language specication and tutorial for a class of temporal logics for reasoning about action and change that has been developed by our group during the period 1994-1998. The class of logics are collected under the name TAL, an acronym for Temporal Action Logics. TAL has its origins and inspiration in the work with Features and Fluents (FF) by Sandewall, but has diverged from the methodology and approach through the years. We first discuss distinctions and compatibility with FF, move on to the lightweight language specication, and then present a tutorial in terms of an excursion through the different parts of a relatively complex narrative defined using TAL. We conclude with an annotated list of published work from our group. The article tries to strike a reasonable balance between detail and readability, making a number of simplications regarding narrative syntax and translation to a base logical language. Full details are available in numerous technical reports and articles which are listed in the final section of this article.
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| 35. |
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| 36. |
- Dyrager, Christine, et al.
(författare)
-
Design, Synthesis and Biological Evaluation of Chromone-based p38 MAP Kinase Inhibitors
- 2011
-
Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 54:20, s. 7427-7431
-
Tidskriftsartikel (refereegranskat)abstract
- A series of 3-(4-fluorophenyl)-2-(4-pyridyl)-chromone derivs. were synthesized and evaluated as p38 MAP kinase inhibitors. Introduction of an amino group in the 2-position of the pyridyl moiety gave p38 inhibitors with IC50 values in the low nanomolar range (e.g. 8a; IC50 = 17 nm). Addnl., the inhibitors (8a and 8e) demonstrate an excellent selectivity profile towards the p38 kinase among other kinases, as well as inhibition (8e) of p38 signaling in human breast cancer cells. [on SciFinder(R)]
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| 37. |
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| 38. |
- Engström, Maria, et al.
(författare)
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Working Memory in 8 Kleine-Levin Syndrome Patients : An fMRI Study
- 2009
-
Ingår i: SLEEP. - 0161-8105. ; 32:5, s. 681-688
-
Tidskriftsartikel (refereegranskat)abstract
- Study Objectives: The objectives of this study were to investigate possible neuropathology behind the Kleine-Levin Syndrome (KLS), a severe form of hypersomnia with onset during adolescence.Design: Functional magnetic resonance imaging (fMRI) applying a verbal working memory task was used in conjunction with a paper-and-pencil version of the task. Participants: Eight patients with KLS and 12 healthy volunteers participated in the study.Results: The results revealed a pattern of increased thalamic activity and reduced frontal activity (involving the anterior cingulate and adjacent prefrontal cortex) while performing a reading span task.Discussion: This finding may explain the clinical symptoms observed in KLS, in that the thalamus is known to be involved in the control of sleep. Given the increasing access to fMRI, this investigation may aid clinicians in the diagnosis of patients suffering from severe forms of hypersomnia.
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| 39. |
- Escaned, Javier, et al.
(författare)
-
Safety of the Deferral of Coronary Revascularization on the Basis of Instantaneous Wave-Free Ratio and Fractional Flow Reserve Measurements in Stable Coronary Artery Disease and Acute Coronary Syndromes
- 2018
-
Ingår i: JACC. - : Elsevier. - 1936-8798 .- 1876-7605. ; 11:15, s. 1437-1449
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES The aim of this study was to investigate the clinical outcomes of patients deferred from coronary revascularization on the basis of instantaneous wave-free ratio (iFR) or fractional flow reserve (FFR) measurements in stable angina pectoris (SAP) and acute coronary syndromes (ACS). BACKGROUND Assessment of coronary stenosis severity with pressure guidewires is recommended to determine the need for myocardial revascularization. METHODS The safety of deferral of coronary revascularization in the pooled per-protocol population (n = 4,486) of the DEFINE-FLAIR (Functional Lesion Assessment of Intermediate Stenosis to Guide Revascularisation) and iFR-SWEDEHEART (Instantaneous Wave-Free Ratio Versus Fractional Flow Reserve in Patients With Stable Angina Pectoris or Acute Coronary Syndrome) randomized clinical trials was investigated. Patients were stratified according to revascularization decision making on the basis of iFR or FFR and to clinical presentation (SAP or ACS). The primary endpoint was major adverse cardiac events (MACE), defined as the composite of all-cause death, nonfatal myocardial infarction, or unplanned revascularization at 1 year. RESULTS Coronary revascularization was deferred in 2,130 patients. Deferral was performed in 1,117 patients (50%) in the iFR group and 1,013 patients (45%) in the FFR group (p < 0.01). At 1 year, the MACE rate in the deferred population was similar between the iFR and FFR groups (4.12% vs. 4.05%; fully adjusted hazard ratio: 1.13; 95% confidence interval: 0.72 to 1.79; p = 0.60). A clinical presentation with ACS was associated with a higher MACE rate compared with SAP in deferred patients (5.91% vs. 3.64% in ACS and SAP, respectively; fully adjusted hazard ratio: 0.61 in favor of SAP; 95% confidence interval: 0.38 to 0.99; p = 0.04). CONCLUSIONS Overall, deferral of revascularization is equally safe with both iFR and FFR, with a low MACE rate of about 4%. Lesions were more frequently deferred when iFR was used to assess physiological significance. In deferred patients presenting with ACS, the event rate was significantly increased compared with SAP at 1 year. (C) 2018 The Authors. Published by Elsevier on behalf of the American College of Cardiology Foundation.
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| 40. |
- Estrada, Karol, et al.
(författare)
-
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
- 2012
-
Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 44:5, s. 491-501
-
Tidskriftsartikel (refereegranskat)abstract
- Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We identified 56 loci (32 new) associated with BMD at genome-wide significance (P < 5 × 10(-8)). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways. However, we also discovered loci that were localized to genes not known to have a role in bone biology. Fourteen BMD-associated loci were also associated with fracture risk (P < 5 × 10(-4), Bonferroni corrected), of which six reached P < 5 × 10(-8), including at 18p11.21 (FAM210A), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility.
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| 41. |
- Falck, Peter, et al.
(författare)
-
Arabinoxylanase from glycoside hydrolase family 5 is a selective enzyme for production of specific arabinoxylooligosaccharides
- 2018
-
Ingår i: Food Chemistry. - : Elsevier BV. - 0308-8146. ; 242, s. 579-584
-
Tidskriftsartikel (refereegranskat)abstract
- An arabinose specific xylanase from glycoside hydrolase family 5 (GH5) was used to hydrolyse wheat and rye arabinoxylan, and the product profile showed that it produced arabinose substituted oligosaccharides (AXOS) having 2-10 xylose residues in the main chain but no unsubstituted xylooligosaccharides (XOS). Molecular modelling showed that the active site has an open structure and that the hydroxyl groups of all xylose residues in the active site are solvent exposed, indicating that arabinose substituents can be accommodated in the glycone as well as the aglycone subsites. The arabinoxylan hydrolysates obtained with the GH5 enzyme stimulated growth of Bifidobacterium adolescentis but not of Lactobacillus brevis. This arabinoxylanase is thus a good tool for the production of selective prebiotics.
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| 42. |
- Falck, Peter, et al.
(författare)
-
Characterization of a family 43 β-xylosidase from the xylooligosaccharide utilizing putative probiotic Weissella sp. strain 92.
- 2015
-
Ingår i: Glycobiology. - : Oxford University Press (OUP). - 1460-2423 .- 0959-6658. ; 26:2, s. 193-202
-
Tidskriftsartikel (refereegranskat)abstract
- In this work we present the first XOS degrading glycoside hydrolase from Weissella, WXyn43, a two-domain enzyme from GH43. The gene was amplified from genomic DNA of the XOS utilizing Weissella strain 92, classified under the species pair Weissella cibaria/W.confusa, and expressed in Escherichia coli. The enzyme is lacking a putative signal peptide and is, from a homology model, shown to be composed of an N-terminal 5-fold ß-propeller catalytic domain and a C-terminal ß-sandwich domain of unknown function. WXyn43 hydrolysed short (1-4)-β-D-xylooligosaccharides, with similar kcat/KM for Xylobiose (X2) and xylotriose (X3) and clearly lower efficiency in xylotetraose (X4) conversion. WXyn43 displays the highest reported kcat for conversion of X3 (900 s(-1) at 37°C) and X4 (770 s(-1)), and kcat for hydrolysis of X2 (907 s(-1)) is comparable to or greater than the highest previously reported. The purified enzyme adopted a homotetrameric state in solution, while a truncated form with isolated N-terminal catalytic domain adopted a mixture of oligomeric states and lacked detectable activity. The homology model shows that residues from both domains are involved in monomer-monomer hydrogen bonds, while the bonds creating dimer-dimer interactions only involved residues from the N-terminal domain. Docking of X2 and X3 in the active site show interactions corresponding to sub-sites -1 and +1, while presence of a third subsite is unclear, but interactions between a loop and the reducing-end xylose of X3 may be present.
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| 43. |
- Falck, Peter, et al.
(författare)
-
Production of arabinoxylan-oligosaccharide mixtures of varying composition from rye bran by combination of process conditions and type of xylanase.
- 2014
-
Ingår i: Bioresource Technology. - : Elsevier BV. - 1873-2976 .- 0960-8524. ; 174, s. 118-125
-
Tidskriftsartikel (refereegranskat)abstract
- The aim was to study arabinoxylan-oligosaccharide production from rye bran using heat pretreatment and enzymatic hydrolysis. Due to the potential application in foods, the purity of arabinoxylan was also assessed. Rye bran was heat pretreated to improve xylanase-catalyzed hydrolysis of arabinoxylan into arabinoxylan-oligosaccharides. Enzymatic removal of starch and proteins before or after heat pretreatment increased the purity, although at lower yield. The most attractive process resulted in 62% (w/w) arabinoxylan content after ethanol precipitation. Using xylanases from two glycoside hydrolase families (RmXyn10A from GH10 and Pentopan Mono BG from GH11), different mixtures of unsubstituted and arabinose-substituted xylooligosaccharides were produced. GH10 gave a higher yield of short oligosaccharides (60% w/w) with xylobiose as the main product; xylobiose and xylotriose were the main products with GH11 (40% w/w). Thus, heat pretreatment combined with enzymatic hydrolysis can be used to produce arabinoxylan-oligosaccharides from rye bran that are potentially useful in functional foods.
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| 44. |
- Falck, Peter, et al.
(författare)
-
Xylooligosaccharides from Hardwood and Cereal Xylans Produced by a Thermostable Xylanase as Carbon Sources for Lactobacillus brevis and Bifidobacterium adolescentis.
- 2013
-
Ingår i: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 61:30, s. 7333-7340
-
Tidskriftsartikel (refereegranskat)abstract
- To compare xylans from forestry with agricultural origins, hardwood xylan (birch) and cereal arabinoxylan (rye) were hydrolyzed using two variants of the xylanase RmXyn10A, full-length enzyme and catalytic module only, from Rhodothermus marinus . Cultivations of four selected bacterial species, using the xylooligosaccharide (XOS) containing hydrolysates as carbon source, showed selective growth of Lactobacillus brevis DSMZ 1264 and Bifidobacterium adolescentis ATCC 15703. Both strains were confirmed to utilize the XOS fraction (DP 2-5), whereas putative arabinoxylooligosaccharides from the rye arabinoxylan hydrolysate were utilized by only B. adolescentis. Escherichia coli did not grow, despite its capability to grow on the monosaccharides arabinose and xylose. It was also shown that Pediococcus parvulus strain 2.6 utilized neither xylose nor XOS for growth. In summary, RmXyn10A or its catalytic module proved suitable for high-temperature hydrolysis of hardwood xylan and cereal arabinoxylan, producing XOS that could qualify as prebiotics for use in functional food products.
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| 45. |
- Feng, Zhaozhong, et al.
(författare)
-
A unifying explanation for variation in ozone sensitivity among woody plants
- 2018
-
Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 24:1, s. 78-84
-
Tidskriftsartikel (refereegranskat)abstract
- Tropospheric ozone is considered the most detrimental air pollutant for vegetation at the global scale, with negative consequences for both provisioning and climate regulating ecosystem services. In spite of recent developments in ozone exposure metrics, from a concentration-based to a more physiologically relevant stomatal flux-based index, large-scale ozone risk assessment is still complicated by a large and unexplained variation in ozone sensitivity among tree species. Here, we explored whether the variation in ozone sensitivity among woody species can be linked to interspecific variation in leaf morphology. We found that ozone tolerance at the leaf level was closely linked to leaf dry mass per unit leaf area (LMA) and that whole-tree biomass reductions were more strongly related to stomatal flux per unit leaf mass (r 2 =0.56) than to stomatal flux per unit leaf area (r 2 =0.42). Furthermore, the interspecific variation in slopes of ozone flux–response relationships was considerably lower when expressed on a leaf mass basis (coefficient of variation, CV=36%) than when expressed on a leaf area basis (CV=66%), and relationships for broadleaf and needle-leaf species converged when using the mass-based index. These results show that much of the variation in ozone sensitivity among woody plants can be explained by interspecific variation in LMA and that large-scale ozone impact assessment could be greatly improved by considering this well-known and easily measured leaf trait.
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| 46. |
- Freire, Sergio Miranda, et al.
(författare)
-
Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data
- 2016
-
Ingår i: PLOS ONE. - : Public Library Science. - 1932-6203. ; 11:3
-
Tidskriftsartikel (refereegranskat)abstract
- This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest.
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| 47. |
- Freire, Sergio Miranda, et al.
(författare)
-
Performance of XML Databases for Epidemiological Queries in Archetype-Based EHRs
- 2012
-
Ingår i: Proceedings Scandinavian Conference on Health Informatics 2012. - Linköping : Linköping University Electronic Press. - 9789175197586 ; , s. 51-57
-
Konferensbidrag (refereegranskat)abstract
- There are very few published studies regarding the performance of persistence mechanisms for systems that use the openEHR multi level modelling approach. This paper addresses the performance and size of XML databases that store openEHR compliant documents. Database size and response times to epidemiological queries are described. An anonymized relational epidemiology database and associated epidemiological queries were used to generate openEHR XML documents that were stored and queried in four opensource XML databases. The XML databases were considerably slower and required much more space than the relational database. For population-wide epidemiological queries the response times scaled in order of magnitude at the same rate as the number of records (total database size) but were orders of magnitude slower than the original relational database. For individual focused clinical queries where patient ID was specified the response times were acceptable. This study suggests that the tested XML database configurations without further optimizations are not suitable as persistence mechanisms for openEHR-based systems in production if population-wide ad hoc querying is needed.
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| 48. |
- Gauffin, Helena, et al.
(författare)
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Similar Profile and Magnitude of Cognitive Impairments in Focal and Generalized Epilepsy : A Pilot Study
- 2022
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Ingår i: Frontiers in Neurology. - Lausanne, Switzerland : Frontiers Media S.A.. - 1664-2295. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Cognitive impairments in epilepsy are not well-understood. In addition, long-term emotional, interpersonal, and social consequences of the underlying disturbances are important to evaluate.Purpose: To compare cognitive function including language in young adults with focal or generalized epilepsy. In addition, quality of life and self-esteem were investigated.Patients and Methods: Young adults with no primary intellectual disability, 17 with focal epilepsy and 11 with generalized epilepsy participated and were compared to 28 healthy controls. Groups were matched on age (mean = 26 years), sex, and education. Participants were administered a battery of neuropsychological tasks and carried out self-ratings of quality of life, self-esteem, and psychological problems.Results: Similar impairments regarding cognitive function were noted in focal and generalized epilepsy. The cognitive domains tested were episodic long-term memory, executive functions, attention, working memory, visuospatial functions, and language. Both epilepsy groups had lower results compared to controls (effect sizes 0.24-1.07). The total number of convulsive seizures was predictive of episodic long-term memory function. Participants with focal epilepsy reported lower quality of life than participants with generalized epilepsy. Lowered self-esteem values were seen in both epilepsy groups and particularly in those with focal epilepsy. Along with measures of cognitive speed and depression, the total number of seizures explained more than 50% of variation in quality of life.Conclusion: Interestingly, similarities rather than differences characterized the widespread cognitive deficits that were seen in focal and generalized epilepsy, ranging from mild to moderate. These similarities were modified by quality of life and self-esteem. This study confirms the notion that epilepsy is a network disorder.
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| 49. |
- Grundberg, Elin, et al.
(författare)
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Population genomics in a disease targeted primary cell model
- 2009
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 19:11, s. 1942-1952
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Tidskriftsartikel (refereegranskat)abstract
- The common genetic variants associated with complex traits typically lie in noncoding DNA and may alter gene regulation in a cell type-specific manner. Consequently, the choice of tissue or cell model in the dissection of disease associations is important. We carried out an expression quantitative trait loci (eQTL) study of primary human osteoblasts (HOb) derived from 95 unrelated donors of Swedish origin, each represented by two independently derived primary lines to provide biological replication. We combined our data with publicly available information from a genome-wide association study (GWAS) of bone mineral density (BMD). The top 2000 BMD-associated SNPs (P < approximately 10(-3)) were tested for cis-association of gene expression in HObs and in lymphoblastoid cell lines (LCLs) using publicly available data and showed that HObs have a significantly greater enrichment (threefold) of converging cis-eQTLs as compared to LCLs. The top 10 BMD loci with SNPs showing strong cis-effects on gene expression in HObs (P = 6 x 10(-10) - 7 x 10(-16)) were selected for further validation using a staged design in two cohorts of Caucasian male subjects. All 10 variants were tested in the Swedish MrOS Cohort (n = 3014), providing evidence for two novel BMD loci (SRR and MSH3). These variants were then tested in the Rotterdam Study (n = 2090), yielding converging evidence for BMD association at the 17p13.3 SRR locus (P(combined) = 5.6 x 10(-5)). The cis-regulatory effect was further fine-mapped to the proximal promoter of the SRR gene (rs3744270, r(2) = 0.5, P = 2.6 x 10(-15)). Our results suggest that primary cells relevant to disease phenotypes complement traditional approaches for prioritization and validation of GWAS hits for follow-up studies.
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| 50. |
- Gräber, Martin, et al.
(författare)
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A novel direct screening method for alkyl glucoside production by glucosidases expressed in E. coli in 96-well plates.
- 2010
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Ingår i: Journal of Biotechnology. - : Elsevier BV. - 1873-4863 .- 0168-1656. ; 145, s. 186-192
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Tidskriftsartikel (refereegranskat)abstract
- The present work describes the development of a novel direct screening method, assayed in 96-well format, for evaluation of enzymatic alkyl glycoside production in a hexanol water two-phase system. Alkyl glycosides are surfactants with a range of applications and with good biodegradability and low toxicity. Enzymatic synthesis makes it possible to prepare beta-D-glucopyranosides with high purity. In the developed screening assay, hexyl-ss-D-glucopyranoside was chosen as a model product to be synthesised by reversed hydrolysis in a water-hexanol two-phase system. In a first step the model product is produced by glucosidases expressed in E. coli cells in 96 deep well plates. After phase separation, the hexyl-ss-D-glucopyranoside in the organic phase is degraded enzymatically and the released glucose detected spectrophotometrically at 405nm utilizing peroxidase/glucose oxidase, and the reagent 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS). The aqueous phase is used to monitor hydrolysis of p-NPG at 405nm, allowing use of a ratio of the two assays to compensate for expression differences. The complete method was used for comparison of two different ss-glucosidases, classified under glycoside hydrolase family 1 and 3, respectively, showing a significant difference in their ability to synthesise hexyl-ss-D-glucopyranoside by reversed hydrolysis.
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