| 1. |
- Hatos, Andras, et al.
(författare)
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DisProt : intrinsic protein disorder annotation in 2020
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:D1, s. D269-D276
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Tidskriftsartikel (refereegranskat)abstract
- The Database of Protein Disorder (DisProt, URL:https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome.
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| 2. |
- Hultkvist, Henrik, et al.
(författare)
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Evaluation of left ventricular diastolic function in patients operated for aortic stenosis
- 2022
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 17:2
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Tidskriftsartikel (refereegranskat)abstract
- Background Left ventricular diastolic dysfunction is common in patients with aortic valve stenosis (AS) and reportedly affects prognosis after surgical aortic valve replacement (SAVR). Here we investigated whether and how diastolic function (assessed following the most recent guidelines) was affected by SAVR, and whether preoperative diastolic function affected postoperative outcome. We also examined whether long-term mortality was associated with preoperative NT-proBNP and postoperative heart failure (PHF). Methods We performed a prospective observational study of 273 patients with AS who underwent AVR with or without concomitant coronary artery bypass surgery. Of these patients, 247 were eligible for assessment of left ventricular (LV) filling pressure. Preoperatively and at the 6-month postoperative follow-up, we measured N-terminal pro-B type natriuretic peptide (NT-proBNP) in serum and assessed diastolic function with Doppler echocardiography. PHF was diagnosed using prespecified criteria. Multivariable logistic regression was performed to explore variables associated with high LV filling pressure. Cox regression was performed to explore variables associated with mortality, accounting for timeto-event. Results At the time of surgery, 22% (n = 54) of patients had diastolic dysfunction expressed as high LV filling pressure. Of these 54 patients, 27 (50%) showed postoperative diastolic function improvement. Among the 193 patients with preoperative low LV filling pressure, 24 (12%) showed postoperative diastolic function deterioration. Increased long-term mortality was associated with PHF and high preoperative NT-proBNP, but not with preoperative or postoperative diastolic dysfunction. Cox regression revealed the following independent risk factors for long-term mortality: diabetes, renal dysfunction, preoperative NT-proBNP>960 ng/L, age, and male gender. Conclusions Surgery for aortic stenosis improved diastolic function in patients with high LV filling pressure in 50% of the patients. Our results could not confirm the previously suggested role of diastolic dysfunction as a marker for poor long-term survival after SAVR. Our findings showed that both PHF and high preoperative NT-proBNP were associated with long-term mortality.
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| 3. |
- Baloch, Ramen Munir, et al.
(författare)
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Indoor air pollution, physical and comfort parameters related to schoolchildren's health : Data from the European SINPHONIE study
- 2020
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Ingår i: Science of the Total Environment. - : ELSEVIER. - 0048-9697 .- 1879-1026. ; 739
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Tidskriftsartikel (refereegranskat)abstract
- Substantial knowledge is available on the association of the indoor school environment and its effect among schoolchildren. In the same context, the SINPHONIE (School indoor pollution and health: Observatory network in Europe) conducted a study to collect data and determine the distribution of several indoor air pollutants (IAPs), physical and thermal parameters and their association with eye, skin, upper-, lower respiratory and systemic disorder symptoms during the previous three months. Finally, data from 115 schools in 54 European cities from 23 countries were collected and included 5175 schoolchildren using a harmonized and standardized protocol. The association between exposures and the health outcomes were examined using logistic regression models on the environmental stressors assessed in classroom while adjusting for several confounding factors; a VOC (volatile organic compound) score defined as the sum of the number of pollutants to which the children were highly exposed (concentration > median of the distribution) in classroom was also introduced to evaluate the mul tiexposu re - outcome association. Schoolchildren while adjusting for several confounding factors. Schoolchildren exposed to above or equal median concentration of PM2.5, benzene, limonene, ozone and radon were at significantly higher odds of suffering from upper, lower airways, eye and systemic disorders. Increased odds were also observed for any symptom (sick school syndrome) among schoolchildren exposed to concentrations of limonene and ozone above median values. Furthermore, the risks for upper and lower airways and systemic disorders significantly increased with the VOCs score. Results also showed that increased ventilation rate was significantly associated with decreased odds of suffering from eye and skin disorders whereas similar association was observed between temperature and upper airways symptoms. The present study provides evidence that exposure to IAPs in schools is associated with various health problems in children. Further investigations are needed to confirm our findings. (C) 2020 Elsevier B.V. All rights reserved.
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| 4. |
- Holmberg, Erica, et al.
(författare)
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Right ventricular function in severe aortic stenosis assessed by echocardiography and MRI
- 2023
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Ingår i: Clinical Physiology and Functional Imaging. - : WILEY. - 1475-0961 .- 1475-097X.
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Tidskriftsartikel (refereegranskat)abstract
- Background: The prevalence of aortic valve stenosis (AS) is increasing due to an ageing population. Despite that right ventricular function has prognostic value for postoperative outcome, the right ventricle (RV) is not extensively studied and often not routinely assessed in AS. Our aim was to explore the relation between severe AS and RV function in a surgical aortic valve replacement (SAVR) cohort, comparing two imaging modalities for RV evaluation.Methods: Patients with severe AS, underwent cardiovascular magnetic resonance imaging (CMR) and transthoracic echocardiography (TTE) before SAVR. RV dysfunction was defined as one or more of the following: tricuspid annular plane systolic excursion (TAPSE) < 17 mm, RV free wall strain (RVFWS) > -20% by TTE and RV ejection fraction (RVEF) <50% by CMR.Results: Sixteen (33%) patients were found to have RV dysfunction. Patients with RV dysfunction showed significantly lower indexed aortic valve area, left ventricular (LV) ejection fraction as well as RV and LV stroke volumes compared to patients with maintained RV function. All patients with reduced RVEF also had changes in TAPSE or RVFWS and a larger number of patients had a reduced longitudinal RV function despite a normal RVEF.Conclusion: In a SAVR cohort one-third of the patients had RV dysfunction, defined by RVEF, TAPSE or RVFW strain. Echocardiography detected subtle changes in RV function before RVEF was reduced. It is likely that the more pronounced the AS, the more frequent the occurrence of RV dysfunction.
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| 5. |
- Quaglia, Federica, et al.
(författare)
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DisProt in 2022 : improved quality and accessibility of protein intrinsic disorder annotation
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:D1, s. D480-D487
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Tidskriftsartikel (refereegranskat)abstract
- The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.
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| 6. |
- Cinege, Gyöngyi, et al.
(författare)
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Broad Ultrastructural and Transcriptomic Changes Underlie the Multinucleated Giant Hemocyte Mediated Innate Immune Response against Parasitoids
- 2022
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Ingår i: Journal of Innate Immunity. - : S. Karger. - 1662-811X .- 1662-8128. ; 14:4, s. 335-354
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Tidskriftsartikel (refereegranskat)abstract
- Multinucleated giant hemocytes (MGHs) represent a novel type of blood cell in insects that participate in a highly efficient immune response against parasitoid wasps involving isolation and killing of the parasite. Previously, we showed that circulating MGHs have high motility and the interaction with the parasitoid rapidly triggers encapsulation. However, structural and molecular mechanisms behind these processes remained elusive. Here, we used detailed ultrastructural analysis and live cell imaging of MGHs to study encapsulation in Drosophila ananassae after parasitoid wasp infection. We found dynamic structural changes, mainly driven by the formation of diverse vesicular systems and newly developed complex intracytoplasmic membrane structures, and abundant generation of giant cell exosomes in MGHs. In addition, we used RNA sequencing to study the transcriptomic profile of MGHs and activated plasmatocytes 72 h after infection, as well as the uninduced blood cells. This revealed that differentiation of MGHs was accompanied by broad changes in gene expression. Consistent with the observed structural changes, transcripts related to vesicular function, cytoskeletal organization, and adhesion were enriched in MGHs. In addition, several orphan genes encoding for hemolysin-like proteins, pore-forming toxins of prokaryotic origin, were expressed at high level, which may be important for parasitoid elimination. Our results reveal coordinated molecular and structural changes in the course of MGH differentiation and parasitoid encapsulation, providing a mechanistic model for a powerful innate immune response.
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| 7. |
- Linkner, Tamás Richárd, et al.
(författare)
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Cellular proteo-transcriptomic changes in the immediate early-phase of lentiviral transduction
- 2021
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Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:11
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Tidskriftsartikel (refereegranskat)abstract
- Lentivirus-based vectors derived from human immunodeficiency viruses type 1 and 2 (HIV-1 and 2) are widely used tools in research and may also be utilized in clinical settings. Like their parental virions, they are known to depend on the cellular machinery for successful gene delivery and integration. While most of the studies on cellular proteomic and transcriptomic changes have focused on the late phase of the transduction, studies of those changes in early time-points, especially in the case of HIV-2 based vectors, are widely lacking. Using second generation HIV-1 and 2 vesicular stomatitis virus G protein (VSV-G) pseudotyped lentiviral vectors, we transduced HEK-293T human embryonic kidney cells and carried out transcriptomic profiling at 0 and 2 h time points, with accompanying proteomic analysis at 2 h following transduction. Significant variations were observed in gene expression profile between HIV-1 and HIV-2 transduced samples. Thrombospondin 1 (THBS1), collagens (COL1A2, COL3A1), and eukaryotic translation factors (EIF3CL) in addition to various genes coding for long non-coding RNA (lncRNA) were significantly upregulated 2 h after HIV-2 transduction compared to HIV-1. Label-free quantification mass spectrometry (MS) indicated that seven proteins involved in RNA binding, mRNA transport, and chaperoning were significantly downregulated. The identification of cellular protein targets of lentiviral vectors and their effect on the cellular transcriptome will undoubtedly shed more light on their complex life cycle and may be utilized against infection by their parental lentiviruses. Furthermore, characterizing the early phase of HIV-2 infection may aid in the understanding of its pathomechanism and long incubation period.
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| 8. |
- Linkner, Tamás Richárd, et al.
(författare)
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Comparative Analysis of Differential Cellular Transcriptome and Proteome Regulation by HIV-1 and HIV-2 Pseudovirions in the Early Phase of Infection
- 2024
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Ingår i: International Journal of Molecular Sciences. - 1661-6596. ; 25:1
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Tidskriftsartikel (refereegranskat)abstract
- In spite of the similar structural and genomic organization of human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2), striking differences exist between them in terms of replication dynamics and clinical manifestation of infection. Although the pathomechanism of HIV-1 infection is well characterized, relatively few data are available regarding HIV-2 viral replication and its interaction with host–cell proteins during the early phase of infection. We utilized proteo-transcriptomic analyses to determine differential genome expression and proteomic changes induced by transduction with HIV-1/2 pseudovirions during 8, 12 and 26 h time-points in HEK-293T cells. We show that alteration in the cellular milieu was indeed different between the two pseudovirions. The significantly higher number of genes altered by HIV-2 in the first two time-points suggests a more diverse yet subtle effect on the host cell, preparing the infected cell for integration and latency. On the other hand, GO analysis showed that, while HIV-1 induced cellular oxidative stress and had a greater effect on cellular metabolism, HIV-2 mostly affected genes involved in cell adhesion, extracellular matrix organization or cellular differentiation. Proteomics analysis revealed that HIV-2 significantly downregulated the expression of proteins involved in mRNA processing and translation. Meanwhile, HIV-1 influenced the cellular level of translation initiation factors and chaperones. Our study provides insight into the understudied replication cycle of HIV-2 and enriches our knowledge about the use of HIV-based lentiviral vectors in general.
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| 9. |
- Matthews, Bethany E., et al.
(författare)
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Micro- and Nanoscale Surface Analysis of Late Iron Age Glass from Broborg, a Vitrified Swedish Hillfort
- 2023
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Ingår i: Microscopy and Microanalysis. - : Oxford University Press. - 1431-9276 .- 1435-8115. ; 29:1, s. 50-68
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Tidskriftsartikel (refereegranskat)abstract
- Archaeological glasses with prolonged exposure to biogeochemical processes in the environment can be used to understand glass alteration, which is important for the safe disposal of vitrified nuclear waste. Samples of mafic and felsic glasses with different chemistries, formed from melting amphibolitic and granitoid rocks, were obtained from Broborg, a Swedish Iron Age hillfort. Glasses were excavated from the top of the hillfort wall and from the wall interior. A detailed microscopic, spectroscopic, and diffraction study of surficial textures and chemistries were conducted on these glasses. Felsic glass chemistry was uniform, with a smooth surface showing limited chemical alteration (<150 nm), irrespective of the position in the wall. Mafic glass was heterogeneous, with pyroxene, spinel, feldspar, and quartz crystals in the glassy matrix. Mafic glass surfaces in contact with topsoil were rougher than those within the wall and had carbon-rich material consistent with microbial colonization. Limited evidence for chemical or physical alteration of mafic glass was found; the thin melt film that coated all exposed surfaces remained intact, despite exposure to hydraulically unsaturated conditions, topsoil, and associated microbiome for over 1,500 years. This supports the assumption that aluminosilicate nuclear waste glasses will have a high chemical durability in near-surface disposal facilities.
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| 10. |
- Ohlsson, Linus, et al.
(författare)
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Echocardiographic haemodynamic monitoring in the context of HeartMate 3™ therapy: a systematic review
- 2024
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Ingår i: ESC Heart Failure. - : WILEY PERIODICALS, INC. - 2055-5822.
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Tidskriftsartikel (refereegranskat)abstract
- AimsWhile echocardiography remains essential within haemodynamic monitoring of durable mechanical circulatory support, previous echocardiographic guidelines are missing scientific evidence for the novel HeartMate 3 (TM) (HM3) system. Accordingly, this review aims to summarize available echocardiographic evidence including HM3.Methods and resultsThis systematic review adhered to the PRISMA 2020 guidelines. Searches were conducted during August 2023 across PubMed, Embase, and Google Scholar using specific echocardiographic terms combined with system identifiers. Study quality was assessed using the Newcastle-Ottawa Scale (NOS) for cohort studies and Critical Appraisal Instrument (PCAI) for cross-sectional studies. Nine studies met the inclusion criteria, of which eight cohort studies and one cross-sectional study. Aortic regurgitation (AR) prevalence at approximately 12 months of support exhibited heterogenicity (33.5% (Delta 33%)) in a limited number of studies (n = 3). Several studies (n = 5) demonstrated an increasing prevalence and severity of AR during HM3 support, generating moderate to high level of evidence. One AR study showed a higher cumulative incidence of death and heart failure (HF) readmission compared with those without significant AR, hazard ratio 3.42 (95% CI 1.48-8.76). A second study showed that a worsening AR group had significantly lower survival-free from HF readmission (59% vs. 89%, P = 0.023) with a hazard ratio of 5.18 (95% CI 1.07-25.0), while a third study did not reveal any differences in cardiac-related hospitalizations in the 12 months follow-up or non-cardiac-related hospitalization. Mitral regurgitation (MR) prevalence at approximately 12 months of support exhibited good consistency 15.0% (Delta 0.8%) in both included studies, which did not reveal any significant pattern of changing prevalence over time. Tricuspid regurgitation (TR) prevalence at approximately 12 months of support exhibited fair consistency 28.5% (Delta 8.3%) in a limited number of studies (n = 2); both studies showed a statistically un-confirmed trend of increased TR prevalence over time. The evidence of general prevalence of right ventricular dysfunction (RVD) was insufficient due to lack of studies.ConclusionsThere are few methodologically consistent studies with focus on long-term haemodynamic effects. Aortic regurgitation still seems to be a prevalent and potentially significant finding. The available evidence concerning right heart function is limited despite clinical relevance and potential prognostic value. Potential interventricular and haemodynamic interplay are identified as a white field for future research.
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