| 1. |
- Montoliu-Gaya, Laia, et al.
(författare)
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Optimal blood tau species for the detection of Alzheimer's disease neuropathology: an immunoprecipitation mass spectrometry and autopsy study.
- 2024
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Ingår i: Acta neuropathologica. - 1432-0533. ; 147:1
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Tidskriftsartikel (refereegranskat)abstract
- Plasma-to-autopsy studies are essential for validation of blood biomarkers and understanding their relation to Alzheimer's disease (AD) pathology. Few such studies have been done on phosphorylated tau (p-tau) and those that exist have made limited or no comparison of the different p-tau variants. This study is the first to use immunoprecipitation mass spectrometry (IP-MS) to compare the accuracy of eight different plasma tau species in predicting autopsy-confirmed AD. The sample included 123 participants (AD=69, non-AD=54) from the Boston University Alzheimer's disease Research Center who had an available ante-mortem plasma sample and donated their brain. Plasma samples proximate to death were analyzed by targeted IP-MS for six different tryptic phosphorylated (p-tau-181, 199, 202, 205, 217, 231), and two non-phosphorylated tau (195-205, 212-221) peptides. NIA-Reagan Institute criteria were used for the neuropathological diagnosis of AD. Binary logistic regressions tested the association between each plasma peptide and autopsy-confirmed AD status. Area under the receiver operating curve (AUC) statistics were generated using predicted probabilities from the logistic regression models. Odds Ratio (OR) was used to study associations between the different plasma tau species and CERAD and Braak classifications. All tau species were increased in AD compared to non-AD, but p-tau217, p-tau205 and p-tau231 showed the highest fold-changes. Plasma p-tau217 (AUC=89.8), p-tau231 (AUC=83.4), and p-tau205 (AUC=81.3) all had excellent accuracy in discriminating AD from non-AD brain donors, even among those with CDR<1). Furthermore, p-tau217, p-tau205 and p-tau231 showed the highest ORs with both CERAD (ORp-tau217=15.29, ORp-tau205=5.05 and ORp-tau231=3.86) and Braak staging (ORp-tau217=14.29, ORp-tau205=5.27 and ORp-tau231=4.02) but presented increased levels at different amyloid and tau stages determined by neuropathological examination. Our findings support plasma p-tau217 as the most promising p-tau species for detecting AD brain pathology. Plasma p-tau231 and p-tau205 may additionally function as markers for different stages of the disease.
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| 2. |
- Alseekh, Saleh, et al.
(författare)
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Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices
- 2021
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 18:7, s. 747-756
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Forskningsöversikt (refereegranskat)abstract
- This Perspective, from a large group of metabolomics experts, provides best practices and simplified reporting guidelines for practitioners of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics. Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.
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| 3. |
- Cox, Michael, et al.
(författare)
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How academic podcasting can change academia and its relationship with society : A conversation and guide
- 2023
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Ingår i: Frontiers in Communication. - 2297-900X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we explore the potential of academic podcasting to e ect positive change within academia and between academia and society. Building on the concept of epistemic living spaces, we consider how podcasting can change how we evaluate what is legitimate knowledge and methods for knowledge production, who has access to what privileges and power, the nature of our connections within academia and with other partners, and how we experience the constraints and opportunities of space and time. We conclude by o ering a guide for others who are looking to develop their own academic podcasting projects and discuss the potential for podcasting to be formalized as amainstream academic output. To listen to an abridged and annotated version of this paper, visit: https://soundcloud.com/conservechange/podcastinginacademia.
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| 4. |
- Cox, Michael, et al.
(författare)
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How academic podcasting can change academia and its relationship with society: A conversation and guide
- 2023
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Ingår i: Frontiers in Communication. - 2297-900X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we explore the potential of academic podcasting to effect positive change within academia and between academia and society. Building on the concept of “epistemic living spaces,” we consider how podcasting can change how we evaluate what is legitimate knowledge and methods for knowledge production, who has access to what privileges and power, the nature of our connections within academia and with other partners, and how we experience the constraints and opportunities of space and time. We conclude by offering a guide for others who are looking to develop their own academic podcasting projects and discuss the potential for podcasting to be formalized as a mainstream academic output. To listen to an abridged and annotated version of this paper, visit: https://soundcloud.com/conservechange/podcastinginacademia.
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| 5. |
- Gericke, Martin, et al.
(författare)
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The European Polysaccharide Network of Excellence (EPNOE) research roadmap 2040: Advanced strategies for exploiting the vast potential of polysaccharides as renewable bioresources
- 2024
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Ingår i: Carbohydrate Polymers. - : Elsevier BV. - 0144-8617 .- 1879-1344. ; 326
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Tidskriftsartikel (refereegranskat)abstract
- Polysaccharides are among the most abundant bioresources on earth and consequently need to play a pivotal role when addressing existential scientific challenges like climate change and the shift from fossil-based to sustainable biobased materials. The Research Roadmap 2040 of the European Polysaccharide Network of Excellence (EPNOE) provides an expert's view on how future research and development strategies need to evolve to fully exploit the vast potential of polysaccharides as renewable bioresources. It is addressed to academic researchers, companies, as well as policymakers and covers five strategic areas that are of great importance in the context of polysaccharide related research: (I) Materials & Engineering, (II) Food & Nutrition, (III) Biomedical Applications, (IV) Chemistry, Biology & Physics, and (V) Skills & Education. Each section summarizes the state of research, identifies challenges that are currently faced, project achievements and developments that are expected in the upcoming 20 years, and finally provides outlines on how future research activities need to evolve.
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| 6. |
- Geuens, Sam, et al.
(författare)
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Testing a Home Solution for Preparing Young Children for an Awake MRI : A Promising Smartphone Application
- 2023
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Ingår i: Children. - : Multidisciplinary Digital Publishing Institute (MDPI). - 2227-9067. ; 10:12
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Tidskriftsartikel (refereegranskat)abstract
- Thanks to its non-invasive nature and high-resolution imaging capabilities, magnetic resonance imaging (MRI) is a valuable diagnostic tool for pediatric patients. However, the fear and anxiety experienced by young children during MRI scans often result in suboptimal image quality and the need for sedation/anesthesia. This study aimed to evaluate the effect of a smartphone application called COSMO@home to prepare children for MRI scans to reduce the need for sedation or general anesthesia. The COSMO@home app was developed incorporating mini-games and an engaging storyline to prepare children for learning goals related to the MRI procedure. A multicenter study was conducted involving four hospitals in Belgium. Eligible children aged 4–10 years were prepared with the COSMO@home app at home. Baseline, pre-scan, and post-scan questionnaires measured anxiety evolution in two age groups (4–6 years and 7–10 years). Eighty-two children participated in the study, with 95% obtaining high-quality MRI images. The app was well-received by children and parents, with minimal technical difficulties reported. In the 4–6-year-old group (N = 33), there was a significant difference between baseline and pre-scan parent-reported anxiety scores, indicating an increase in anxiety levels prior to the scan. In the 7–10-year-old group (N = 49), no significant differences were observed between baseline and pre-scan parent-reported anxiety scores. Overall, the COSMO@home app proved to be useful in preparing children for MRI scans, with high satisfaction rates and successful image outcomes across different hospitals. The app, combined with minimal face-to-face guidance on the day of the scan, showed the potential to replace or assist traditional face-to-face training methods. This innovative approach has the potential to reduce the need for sedation or general anesthesia during pediatric MRI scans and its associated risks and improve patient experience.
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| 7. |
- Ginesy, Mireille
(författare)
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Production of L-arginine by Escherichia coli : Impact of genetic modifications, carbon and nitrogen sources
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In the recent years, the demand for environmental friendly produced L-arginine has risen with the increasing number of applications for this amino acid in pharmaceuticals, nutraceuticals, cosmetics, animal feed and fertilizers.Microbial production of L-arginine usually relies on Corynebacterium glutam-icum and Corynebacterium crenatum strains. However, Escherichia coli presents the advantage of being able to utilize a wider range of substrates, including pentose sugars found in lignocellulosic feedstocks.The present thesis illustrates the first steps in the development of a sustain-able process to produce L-arginine using E. coli. It starts with the construction of an L-arginine overproducing strain, followed by an investigation into adequate nitrogen and carbon sources for cell growth and L-arginine production.The first part of this thesis aimed at engineering an E. coli strain able to produce high level of L-arginine. Mutations on key genes of the L-arginine biosynthesis pathway were stepwisely done. The mutants obtained at each step were tested in bioreactor fermentations to assess the effect of each genetic modification. The final strain was able to produce almost 12 g/L during fer-mentation, at a productivity of 0.24 g/L/h. In comparison, the starting strain, E. coli K12 C600, was not able to excrete any L-arginine. Besides, one mutant from each step was further examined in a metabolomic study in order to gain deeper insight into the effects of the various genetic modifications performed.To minimize nitrogen waste and optimize the L-arginine production the impact of different nitrogen sources and concentrations were then investigated. Ammonium phosphate dibasic, ammonium sulfate and ammonia solution were the best nitrogen sources for L-arginine production. In minimal medium, the optimum carbon to nitrogen ratio was 6, yielding about 4 g/L L-arginine from 30 g/L glucose. At this ratio, both glucose and the nitrogen source were com-pletely utilized during fermentation.Finaly various carbon courses commonly found in lignocellulosic feedstocks were tested. D-glucose and D-xylose were the most suitable carbon sources followed by L-arabinose. D-galactose and D-mannose resulted in significantly less arginie formation. However, a mixture of all five sugars yielded a higher production than any individual sugar.
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| 8. |
- Hansen, Sabine, et al.
(författare)
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A Novel Growth-Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator PrfA in Listeria monocytogenes
- 2020
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Ingår i: Journal of Bacteriology. - : American Society for Microbiology. - 0021-9193 .- 1098-5530. ; 202:11
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Tidskriftsartikel (refereegranskat)abstract
- Listeria monocytogenes is a Gram-positive pathogen able to cause severe human infections. Its major virulence regulator is the transcriptional activator PrfA, a member of the Crp/Fnr family of transcriptional regulators. To establish a successful L. monocytogenes infection, the PrfA protein needs to be in an active conformation, either by binding the cognate inducer glutathione (GSH) or by possessing amino acid substitutions rendering the protein constitutively active (PrfA*). By a yet unknown mechanism, phosphotransferase system (PTS) sugars repress the activity of PrfA. We therefore took a transposon-based approach to identify the mechanism by which PTS sugars repress PrfA activity. For this, we screened a transposon mutant bank to identify clones able to grow in the presence of glucose-6-phosphate as the sole carbon source. Surprisingly, most of the isolated transposon mutants also carried amino acid substitutions in PrfA. In transposon-free strains, the PrfA amino acid substitution mutants displayed growth, virulence factor expression, infectivity, and DNA binding, agreeing with previously identified PrIA* mutants. Hence, the initial growth phenotype observed in the isolated clone was due to the amino acid substitution in PrfA and unrelated to the loci inactivated by the transposon mutant. Finally, we provide structural evidence for the existence of an intermediately activated PrfA state, which gives new insights into PrfA protein activation. IMPORTANCE The Gram-positive bacterium Listeria monocytogenes is a human pathogen affecting mainly the elderly, immunocompromised people, and pregnant women. It can lead to meningoencephalitis, septicemia, and abortion. The major virulence regulator in L. monocytogenes is the PrfA protein, a transcriptional activator. Using a growth-based selection strategy, we identified mutations in the PrfA protein leading to constitutively active virulence factor expression. We provide structural evidence for the existence of an intermediately activated PrfA state, which gives new insights into PrfA protein activation.
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| 9. |
- Iakovleva, Irina, et al.
(författare)
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Structural basis for transthyretin amyloid formation in vitreous body of the eye
- 2021
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Amyloid transthyretin (ATTR) amyloidosis is characterized by the abnormal accumulation of ATTR fibrils in multiple organs. However, the structure of ATTR fibrils from the eye is poorly understood. Here, we used cryo-EM to structurally characterize vitreous body ATTR fibrils. These structures were distinct from previously characterized heart fibrils, even though both have the same mutation and type A pathology. Differences were observed at several structural levels: in both the number and arrangement of protofilaments, and the conformation of the protein fibril in each layer of protofilaments. Thus, our results show that ATTR protein structure and its assembly into protofilaments in the type A fibrils can vary between patients carrying the same mutation. By analyzing and matching the interfaces between the amino acids in the ATTR fibril with those in the natively folded TTR, we are able to propose a mechanism for the structural conversion of TTR into a fibrillar form.
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| 10. |
- Koscielniak, Ewa, et al.
(författare)
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Extraskeletal Ewing sarcoma in children, adolescents, and young adults. An analysis of three prospective studies of the Cooperative Weichteilsarkomstudiengruppe (CWS)
- 2021
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Ingår i: Pediatric Blood & Cancer. - : John Wiley & Sons. - 1545-5009 .- 1545-5017. ; 68:10
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Tidskriftsartikel (refereegranskat)abstract
- Background We have analyzed the outcome of patients with localized extraskeletal Ewing sarcoma (EES) treated in three consecutive Cooperative Weichteilsarkomstudiengruppe (CWS) soft tissue sarcoma (STS) studies: CWS-91, CWS-96, and CWS-2002P. Methods Patients were treated in CWS-91 with four- (vincristine, dactinomycin, doxorubicin, and ifosfamide [VAIA] or cyclophosphamide [VACA II]) or five-drug (+etoposide [EVAIA]) cycles, in CWS-96 they were randomly assigned to receive VAIA or CEVAIE (+carboplatin and etoposide), and in CWS-2002P with VAIA III plus optional maintenance therapy (MT) with cyclophosphamide and vinblastine. Local therapy consisted of resection and/or radiotherapy (RT). Results Two hundred forty-three patients fulfilled the eligibility criteria. The 5-year event-free survival (EFS) and overall survival (OS) were 63% (95% confidence interval [CI] 57-69) and 73% (95% CI 67-79), respectively. The 5-year EFS by study was 64% (95% CI 54-74) in CWS-91, 57% (95% CI 48-66) in CWS-96, and 79% (95% CI 67-91) in CWS-2002P (n.s.). The 5-year OS was 72% (95% CI 62-82) in CWS-91, 70% (95% CI 61-79) in CWS-96, and 86% (95% CI 76-96) in CWS-2002P (n.s.). In CWS-96, 5-year EFS and OS in the VAIA arm versus the CEVAIE were 65% (95% CI 52-81) versus 55% (95% CI 39-76) log-rank p = .13, and 85% (95% CI 75-96) versus 61% (95% CI 45-82), log-rank p = .09. Conclusion Our analysis provides interesting information on the treatment and specificities of EES, which can be useful for a better understanding of this rare entity and should be considered in the development of future clinical trials for Ewing sarcoma defined as FET-ETS fusion positive tumors.
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