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  • 2019
  • Tidskriftsartikel (refereegranskat)
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6.
  • Klionsky, Daniel J., et al. (författare)
  • Guidelines for the use and interpretation of assays for monitoring autophagy
  • 2012
  • Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
  • Forskningsöversikt (refereegranskat)abstract
    • In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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7.
  • Ademuyiwa, Adesoji O., et al. (författare)
  • Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
  • 2016
  • Ingår i: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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8.
  • Catoire, MilSNe, et al. (författare)
  • Fatty acid-inducible ANGPTL4 governs lipid metabolic response to exercise
  • 2014
  • 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. ; 111:11, s. E1043-E1052
  • Tidskriftsartikel (refereegranskat)abstract
    • Physical activity increases energy metabolism in exercising muscle. Whether acute exercise elicits metabolic changes in nonexercising muscles remains unclear. We show that one of the few genes that is more highly induced in nonexercising muscle than in exercising human muscle during acute exercise encodes angiopoietin-like 4 (ANGPTL4), an inhibitor of lipoprotein lipase-mediated plasma triglyceride clearance. Using a combination of human, animal, and in vitro data, we show that induction of ANGPTL4 in nonexercising muscle is mediated by elevated plasma free fatty acids via peroxisome proliferator-activated receptor-delta, presumably leading to reduced local uptake of plasma triglyceride-derived fatty acids and their sparing for use by exercising muscle. In contrast, the induction of ANGPTL4 in exercising muscle likely is counteracted via AMP-activated protein kinase (AMPK)-mediated down-regulation, promoting the use of plasma triglycerides as fuel for active muscles. Our data suggest that nonexercising muscle and the local regulation of ANGPTL4 via AMPK and free fatty acids have key roles in governing lipid homeostasis during exercise.
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9.
  • Jones, Benedict C, et al. (författare)
  • To which world regions does the valence-dominance model of social perception apply?
  • 2021
  • Ingår i: Nature Human Behaviour. - : Springer Science and Business Media LLC. - 2397-3374. ; 5:1, s. 159-169
  • Tidskriftsartikel (refereegranskat)abstract
    • Over the past 10 years, Oosterhof and Todorov's valence-dominance model has emerged as the most prominent account of how people evaluate faces on social dimensions. In this model, two dimensions (valence and dominance) underpin social judgements of faces. Because this model has primarily been developed and tested in Western regions, it is unclear whether these findings apply to other regions. We addressed this question by replicating Oosterhof and Todorov's methodology across 11 world regions, 41 countries and 11,570 participants. When we used Oosterhof and Todorov's original analysis strategy, the valence-dominance model generalized across regions. When we used an alternative methodology to allow for correlated dimensions, we observed much less generalization. Collectively, these results suggest that, while the valence-dominance model generalizes very well across regions when dimensions are forced to be orthogonal, regional differences are revealed when we use different extraction methods and correlate and rotate the dimension reduction solution. PROTOCOL REGISTRATION: The stage 1 protocol for this Registered Report was accepted in principle on 5 November 2018. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.7611443.v1 .
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10.
  • Leebens-Mack, James H., et al. (författare)
  • One thousand plant transcriptomes and the phylogenomics of green plants
  • 2019
  • Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
  • Tidskriftsartikel (refereegranskat)abstract
    • Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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11.
  • Alexander, Stephen P. H., et al. (författare)
  • The Concise Guide to PHARMACOLOGY 2023/24: G protein-coupled receptors
  • 2023
  • Ingår i: BRITISH JOURNAL OF PHARMACOLOGY. - : British pharmacological society. - 0007-1188 .- 1476-5381. ; 180
  • Tidskriftsartikel (refereegranskat)abstract
    • The Concise Guide to PHARMACOLOGY 2023/24 is the sixth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of approximately 1800 drug targets, and about 6000 interactions with about 3900 ligands. There is an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes almost 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at . G protein-coupled receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2023, and supersedes data presented in the 2021/22, 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.
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13.
  • Backofen, Rolf, et al. (författare)
  • Requirements and specification of bioinformatics use cases
  • 2005
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • This deliverable specifies use cases based on bioinformatics research carried out by members ofA2. The use cases involve the use of rules to reason over ontologies and pathways (Dresden,Edinburgh, Paris, Linköping) and rules to specify workflows to integrate bioinformatics data (Lisbon, Skövde, Jena, Bucharest). The use cases are designed as a reference point to foster the take up of A2 use cases by I-work packages. Most notably, many of the use cases specify the need for querying and reactivity with languages like Xcerpt (I4), Erus (I5) and Prova (I5). The use cases range from basic research applications to fully deployed software with an international user base.
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  • Backofen, Rolf, et al. (författare)
  • Usage of bioinformatics tools and identification of information sources
  • 2005
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • Bioinformatics is an important application area for semantic web technologies as much of the data is online and accessible in XML format, as some sites already support web services, and as ontologies are widely used to annotate data. In this deliverable, we give a survey over 18 of the most important bioinformatics resources and discuss their availability and accessibility, which are two of the main criteria for these resources to act as bases for later demonstrators.
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17.
  • Calabrese, Claudia, et al. (författare)
  • Genomic basis for RNA alterations in cancer
  • 2020
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 129-136
  • Tidskriftsartikel (refereegranskat)abstract
    • Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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18.
  • Chen, Bi, et al. (författare)
  • Structure-Based Filtering for Ontology Alignment
  • 2006
  • Ingår i: Proceedings of the IEEE WETICE Workshop on Semantic Technologies in Collaborative Applications. - : Institute of Electrical and Electronics Engineers (IEEE). - 9780769526232 ; , s. 364-369
  • Konferensbidrag (refereegranskat)abstract
    • Ontologies are an important technology for the Semantic Web and many ontologies have already been developed. Many ontologies also contain overlapping information and to be able to use them together effectively, we need to align them. Some of the current alignment techniques use information about the structure of the ontologies, but they have not produced good results in evaluations. We propose an approach where, in contrast to the other approaches, structural information is used as a filtering method in the alignment process. We evaluate the approach in terms of quality and performance.
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19.
  • Christopoulos, Arthur, et al. (författare)
  • THE CONCISE GUIDE TO PHARMACOLOGY 2021/22: G protein-coupled receptors.
  • 2021
  • Ingår i: British journal of pharmacology. - : Wiley. - 1476-5381 .- 0007-1188. ; 178 Suppl 1
  • Forskningsöversikt (refereegranskat)abstract
    • The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes over 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/bph.15538. G protein-coupled receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2021, and supersedes data presented in the 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.
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20.
  • Duarte-Salles, Talita, et al. (författare)
  • Thirty-Day Outcomes of Children and Adolescents With COVID-19: An International Experience.
  • 2021
  • Ingår i: Pediatrics. - : American Academy of Pediatrics (AAP). - 1098-4275 .- 0031-4005. ; 148:3
  • Tidskriftsartikel (refereegranskat)abstract
    • To characterize the demographics, comorbidities, symptoms, in-hospital treatments, and health outcomes among children and adolescents diagnosed or hospitalized with coronavirus disease 2019 (COVID-19) and to compare them in secondary analyses with patients diagnosed with previous seasonal influenza in 2017-2018.International network cohort using real-world data from European primary care records (France, Germany, and Spain), South Korean claims and US claims, and hospital databases. We included children and adolescents diagnosed and/or hospitalized with COVID-19 at age <18 between January and June 2020. We described baseline demographics, comorbidities, symptoms, 30-day in-hospital treatments, and outcomes including hospitalization, pneumonia, acute respiratory distress syndrome, multisystem inflammatory syndrome in children, and death.A total of 242158 children and adolescents diagnosed and 9769 hospitalized with COVID-19 and 2084180 diagnosed with influenza were studied. Comorbidities including neurodevelopmental disorders, heart disease, and cancer were more common among those hospitalized with versus diagnosed with COVID-19. Dyspnea, bronchiolitis, anosmia, and gastrointestinal symptoms were more common in COVID-19 than influenza. In-hospital prevalent treatments for COVID-19 included repurposed medications (<10%) and adjunctive therapies: systemic corticosteroids (6.8%-7.6%), famotidine (9.0%-28.1%), and antithrombotics such as aspirin (2.0%-21.4%), heparin (2.2%-18.1%), and enoxaparin (2.8%-14.8%). Hospitalization was observed in 0.3% to 1.3% of the cohort diagnosed with COVID-19, with undetectable (n < 5 per database) 30-day fatality. Thirty-day outcomes including pneumonia and hypoxemia were more frequent in COVID-19 than influenza.Despite negligible fatality, complications including hospitalization, hypoxemia, and pneumonia were more frequent in children and adolescents with COVID-19 than with influenza. Dyspnea, anosmia, and gastrointestinal symptoms could help differentiate diagnoses. A wide range of medications was used for the inpatient management of pediatric COVID-19.
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21.
  • Falkmer, Marita, et al. (författare)
  • Local visual perception bias in children with high-functioning autism spectrum disorders: do we have the whole picture?
  • 2016
  • Ingår i: Developmental Neurorehabilitation. - : Informa UK Limited. - 1751-8423 .- 1751-8431. ; 19:2, s. 117-122
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective: While local bias in visual processing in children with autism spectrum disorders (ASD) has been reported to result in difficulties in recognizing faces and facially expressed emotions, but superior ability in disembedding figures, associations between these abilities within a group of children with and without ASD have not been explored.Methods: Possible associations in performance on the Visual Perception Skills Figure–Ground test, a face recognition test and an emotion recognition test were investigated within 25 8–12-years-old children with high-functioning autism/Asperger syndrome, and in comparison to 33 typically developing children.Results: Analyses indicated a weak positive correlation between accuracy in Figure–Ground recognition and emotion recognition. No other correlation estimates were significant.Conclusion: These findings challenge both the enhanced perceptual function hypothesis and the weak central coherence hypothesis, and accentuate the importance of further scrutinizing the existance and nature of local visual bias in ASD.
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22.
  • Fresard, Laure, et al. (författare)
  • Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
  • 2019
  • Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
  • Tidskriftsartikel (refereegranskat)abstract
    • It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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23.
  • Gao, Hong, et al. (författare)
  • The landscape of tolerated genetic variation in humans and primates
  • 2023
  • Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648
  • Tidskriftsartikel (refereegranskat)abstract
    • Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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24.
  • Golchin, Arash, et al. (författare)
  • Effect of shaft roughness and pressure on friction of polymer bearings in water
  • 2014
  • Ingår i: Proceedings of the Institution of mechanical engineers. Part J, journal of engineering tribology. - : SAGE Publications. - 1350-6501 .- 2041-305X. ; 228:4, s. 371-381
  • Tidskriftsartikel (refereegranskat)abstract
    • In this study, the frictional behavior of selected commercially available unfilled polymers, namely, polyether ether ketone, polytetrafluoroethylene, polyethylene terephthalate, and ultra-high molecular weight polyethylene against an Inconel shaft was investigated using a journal bearing test configuration in water-lubricated sliding contact. Dynamic friction curves were obtained for various shaft roughness values and polymer combinations. The results showed a significant influence of shaft surface roughness on running-in and steady state friction in water-lubricated conditions. Contact angle measurements revealed a significant increase in wettability of Inconel counterfaces. The X-ray photoelectron spectroscopy (XPS) analysis of the surfaces suggests formation of a reaction layer on worn Inconel surfaces when sliding against the polymers. The influences of counter surface roughness and load on frictional response of polymers were studied through intermittent tests by obtaining dynamic and breakaway friction maps for different polymer materials, shaft roughness values, and pressure combinations. In general, a trend of decreasing friction was obtained with increasing contact pressure; however, the materials' frictional responses to variations in counter surface roughness were different. These results indicate that although a reduced counter surface roughness may be beneficial for dynamic friction of polymers in all lubrication regimes, it can adversely affect the materials' breakaway friction response.
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25.
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26.
  • Ju, Young Seok, et al. (författare)
  • Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.
  • 2015
  • Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 25:6, s. 814-824
  • Tidskriftsartikel (refereegranskat)abstract
    • Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.
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27.
  • Kostka, Kristin, et al. (författare)
  • Unraveling COVID-19: A Large-Scale Characterization of 4.5 Million COVID-19 Cases Using CHARYBDIS.
  • 2022
  • Ingår i: Clinical epidemiology. - 1179-1349. ; 14, s. 369-384
  • Tidskriftsartikel (refereegranskat)abstract
    • Routinely collected real world data (RWD) have great utility in aiding the novel coronavirus disease (COVID-19) pandemic response. Here we present the international Observational Health Data Sciences and Informatics (OHDSI) Characterizing Health Associated Risks and Your Baseline Disease In SARS-COV-2 (CHARYBDIS) framework for standardisation and analysis of COVID-19 RWD.We conducted a descriptive retrospective database study using a federated network of data partners in the United States, Europe (the Netherlands, Spain, the UK, Germany, France and Italy) and Asia (South Korea and China). The study protocol and analytical package were released on 11th June 2020 and are iteratively updated via GitHub. We identified three non-mutually exclusive cohorts of 4,537,153 individuals with a clinical COVID-19 diagnosis or positive test, 886,193 hospitalized with COVID-19, and 113,627 hospitalized with COVID-19 requiring intensive services.We aggregated over 22,000 unique characteristics describing patients with COVID-19. All comorbidities, symptoms, medications, and outcomes are described by cohort in aggregate counts and are readily available online. Globally, we observed similarities in the USA and Europe: more women diagnosed than men but more men hospitalized than women, most diagnosed cases between 25 and 60 years of age versus most hospitalized cases between 60 and 80 years of age. South Korea differed with more women than men hospitalized. Common comorbidities included type 2 diabetes, hypertension, chronic kidney disease and heart disease. Common presenting symptoms were dyspnea, cough and fever. Symptom data availability was more common in hospitalized cohorts than diagnosed.We constructed a global, multi-centre view to describe trends in COVID-19 progression, management and evolution over time. By characterising baseline variability in patients and geography, our work provides critical context that may otherwise be misconstrued as data quality issues. This is important as we perform studies on adverse events of special interest in COVID-19 vaccine surveillance.
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28.
  • Kuderna, Lukas F. K., et al. (författare)
  • A global catalog of whole-genome diversity from 233 primate species
  • 2023
  • Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648, s. 906-913
  • Tidskriftsartikel (refereegranskat)abstract
    • The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage wholegenome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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29.
  • Kuderna, Lukas F. K., et al. (författare)
  • Identification of constrained sequence elements across 239 primate genomes
  • 2024
  • Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 625:7996, s. 735-742
  • Tidskriftsartikel (refereegranskat)abstract
    • Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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30.
  • Lahrouchi, Najim, et al. (författare)
  • Transethnic Genome-Wide Association Study Provides Insights in the Genetic Architecture and Heritability of Long QT Syndrome
  • 2020
  • Ingår i: Circulation. - : Lippincott Williams & Wilkins. - 0009-7322 .- 1524-4539. ; 142:4, s. 324-338
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Long QT syndrome (LQTS) is a rare genetic disorder and a major preventable cause of sudden cardiac death in the young. A causal rare genetic variant with large effect size is identified in up to 80% of probands (genotype positive) and cascade family screening shows incomplete penetrance of genetic variants. Furthermore, a proportion of cases meeting diagnostic criteria for LQTS remain genetically elusive despite genetic testing of established genes (genotype negative). These observations raise the possibility that common genetic variants with small effect size contribute to the clinical picture of LQTS. This study aimed to characterize and quantify the contribution of common genetic variation to LQTS disease susceptibility. Methods: We conducted genome-wide association studies followed by transethnic meta-analysis in 1656 unrelated patients with LQTS of European or Japanese ancestry and 9890 controls to identify susceptibility single nucleotide polymorphisms. We estimated the common variant heritability of LQTS and tested the genetic correlation between LQTS susceptibility and other cardiac traits. Furthermore, we tested the aggregate effect of the 68 single nucleotide polymorphisms previously associated with the QT-interval in the general population using a polygenic risk score. Results: Genome-wide association analysis identified 3 loci associated with LQTS at genome-wide statistical significance (P<5x10(-8)) nearNOS1AP,KCNQ1, andKLF12, and 1 missense variant inKCNE1(p.Asp85Asn) at the suggestive threshold (P<10(-6)). Heritability analyses showed that approximate to 15% of variance in overall LQTS susceptibility was attributable to common genetic variation (h2SNP0.148; standard error 0.019). LQTS susceptibility showed a strong genome-wide genetic correlation with the QT-interval in the general population (r(g)=0.40;P=3.2x10(-3)). The polygenic risk score comprising common variants previously associated with the QT-interval in the general population was greater in LQTS cases compared with controls (P<10-13), and it is notable that, among patients with LQTS, this polygenic risk score was greater in patients who were genotype negative compared with those who were genotype positive (P<0.005). Conclusions: This work establishes an important role for common genetic variation in susceptibility to LQTS. We demonstrate overlap between genetic control of the QT-interval in the general population and genetic factors contributing to LQTS susceptibility. Using polygenic risk score analyses aggregating common genetic variants that modulate the QT-interval in the general population, we provide evidence for a polygenic architecture in genotype negative LQTS.
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31.
  • Lambrix, Patrick, et al. (författare)
  • A Framework for Aligning Ontologies
  • 2005
  • Ingår i: PPSWR: International Workshop on Principles and Practice of Semantic Web Reasoning Principles and Practice of Semantic Web Reasoning Third International Workshop, PPSWR 2005, Dagstuhl Castle, Germany, September 11-16, 2005 Proceedings. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783540320289 ; , s. 17-31, s. 17-31
  • Konferensbidrag (refereegranskat)abstract
    • Ontologies are an important technology for the Semantic Web. In different areas ontologies have already been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies and thus the ontologies need to be aligned. Currently, there exist a number of systems that support users in aligning ontologies, but not many comparative evaluations have been performed. In this paper we present a general framework for aligning ontologies where different alignment strategies can be combined. Further, we exemplify the use of the framework by describing a system (SAMBO) that is developed according to this framework. Within this system we have implemented some already existing alignment algorithms as well as some new algorithms. We also show how the framework can be used to experiment with combinations of strategies. This is a first step towards defining a framework that can be used for comparative evaluations of alignment strategies. For our tests we used several well-known bio-ontologies.
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32.
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33.
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34.
  • Lambrix, Patrick, et al. (författare)
  • A system for repairing missing is-a structure in ontologies
  • 2009
  • Ingår i: Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, Amsterdam, The Netherlands, November 20, 2009.
  • Konferensbidrag (refereegranskat)abstract
    • Developing ontologies is not an easy task and often the resulting ontologies are not consistent or strucurally complete. Such ontologies, although often useful, also lead to problems when used in semantically-enabled applications. Wrong conclusions may be derived or valid conclusions may be missed. To deal with this problem we may want to repair the ontologies. In this demo we present a system that supports the repair of the is-a hierarchy in ontologies. We have developed a tool that, given missing is-a relations, generates and recommends relevant ways to repair the is-a structure of the ontology and that allows a domain expert to do the repair in a semi-automatic way.
  •  
35.
  •  
36.
  • Lambrix, Patrick, et al. (författare)
  • A Tool for Evaluating Ontology Alignment Strategies
  • 2007
  • Ingår i: Journal on Data Semantics. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 1861-2032. - 9783540706632 ; VIII, s. 182-202
  • Tidskriftsartikel (refereegranskat)abstract
    • Ontologies are an important technology for the Semantic Web. In different areas ontologies have already been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there exist a number of systems that support users in aligning ontologies, but not many comparative evaluations have been performed and there exists little support to perform such evaluations. However, the study of the properties, the evaluation and comparison of the alignment strategies and their combinations, would give us valuable insight in how the strategies could be used in the best way. In this paper we propose the KitAMO framework for comparative evaluation of ontology alignment strategies and their combinations and present our current implementation. We evaluate the implementation with respect to performance. We also illustrate how the system can be used to evaluate and compare alignment strategies and their combinations in terms of performance and quality of the proposed alignments. Further, we show how the results can be analyzed to obtain deeper insights into the properties of the strategies.
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37.
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38.
  • Lambrix, Patrick, et al. (författare)
  • Aligning Biomedical Ontologies
  • 2007
  • Ingår i: Integrative Bioinformatics Workshop,2007.
  • Konferensbidrag (refereegranskat)
  •  
39.
  • Lambrix, Patrick, et al. (författare)
  • Biological Ontologies
  • 2007
  • Ingår i: Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. - Boston, MA : Springer. - 0387484361 - 9780387484365 ; , s. 85-99
  • Bokkapitel (refereegranskat)abstract
    • Biological ontologies define the basic terms and relations in biological domains and are being used among others, as community reference, as the basis for interoperability between systems, and for search, integration, and exchange of biological data. In this chapter we present examples of biological ontologies and ontology-based knowledge, show how biological ontologies are used and discuss some important issues in ontology engineering.
  •  
40.
  • Lambrix, Patrick, et al. (författare)
  • Information integration in bioinformatics with ontologies and standards
  • 2009. - 1
  • Ingår i: Semantic Techniques for the Web. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783642045806 ; , s. 343-376
  • Bokkapitel (refereegranskat)abstract
    • New experimental methods allow researchers within molecular and systems biology to rapidly generate larger and larger amounts of data. This data is often made publicly available on the Internet and although this data is extremely useful, we are not using its full capacity. One important reason is that we still lack good ways to connect or integrate information from different resources. One kind of resource is the over 1000 data sources freely available on the Web. As most data sources are developed and maintained independently, they are highly heterogeneous. Information is also updated frequently. Other kinds of resources that are not so well-known or commonly used yet are the ontologies and the standards. Ontologies aim to define a common terminology for a domain of interest. Standards provide a way to exchange data between data sources and tools, even if the internal representations of the data in the resources and tools are different. In this chapter we argue that ontological knowledge and standards should be used for integration of data. We describe properties of the different types of data sources, ontological knowledge and standards that are available on the Web and discuss how this knowledge can be used to support integrated access to multiple biological data sources. Further, we present an integration approach that combines the identified ontological knowledge and standards with traditional information integration techniques. Current integration approaches only cover parts of the suggested approach. We also discuss the components in the model on which much recent work has been done in more detail: ontology-based data source integration, ontology alignment and integration using standards. Although many of our discussions in this chapter are general we exemplify mainly using work done within the REWERSE working group on Adding Semantics to the Bioinformatics Web.
  •  
41.
  • Lambrix, Patrick, et al. (författare)
  • Literature-based alignment of ontologies
  • 2008
  • Ingår i: Proceedings of the 3rd International Workshop on Ontology Matching (OM-2008). ; , s. 219-223
  • Konferensbidrag (refereegranskat)abstract
    • In this paper we propose and evaluate new strategies for aligning ontologies based on text categorization of literature using support vector machines-based text classifiers, and compare them with existing literature-based strategies. We also compare and combine these strategies with linguistic strategies.
  •  
42.
  •  
43.
  • Lambrix, Patrick, et al. (författare)
  • Merging DAML+OIL bio-ontologies
  • 2003
  • Ingår i: Proceedings of the 2003 International Workshop on Description Logics (DL2003), Rome, Italy, September 5-7, 2003.
  • Konferensbidrag (refereegranskat)abstract
    • Ontologies are being used nowadays in many areas. Within the bioinformatics area there are a number of bio-ontologies that cover different aspects in molecular biology. Many of these ontologies contain overlapping information. In applications using multiple ontologies it is therefore of interest to be able to merge these ontologies. In this paper we describe a prototype implementation of an ontology merging tool for DAML+OIL ontologies. The tool generates suggestions for merging roles and concepts and for is-a relationships between concepts. We also evaluate the quality of the suggestions using well-known bio-ontologies
  •  
44.
  • Lambrix, Patrick, et al. (författare)
  • Merging DAML+OIL bio-ontologies
  • 2003
  • Ingår i: International workshop on description logics.
  • Konferensbidrag (refereegranskat)
  •  
45.
  • Lambrix, Patrick, et al. (författare)
  • Merging DAML+OIL Ontologies
  • 2005
  • Ingår i: Databases and Information Systems (Selected Papers from the Sixth International Baltic Conference DB&amp;IS'2004). - Amsterdam : IOS Press. - 1586034855 ; , s. 249-258
  • Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
    • Ontologies arebeing used nowadays in many areas. Within eacharea there are a number of ontologies, each with their own focus,that containoverlapping information. In applications using multiple ontologiesit istherefore of interest to be able to merge these ontologies. In thispaper wedescribe a prototype implementation of SAMBO, an ontology mergetool forDAML+OIL ontologies. The tool generates suggestions for mergingconceptsand relations and for creating is-a relationships between concepts.Weevaluate different strategies for the generation of suggestions. Wealsocompare our tool with the ontology merge tools Protégé-2000 withPROMPTand Chimaera in terms of the quality of suggestions and the time ittakes tomerge ontologies using these tools.
  •  
46.
  • Lambrix, Patrick, et al. (författare)
  • Merging DAML+OIL Ontologies
  • 2004
  • Ingår i: International Baltic Conference on Databases and Information Systems,2004. ; , s. 425-
  • Konferensbidrag (refereegranskat)
  •  
47.
  • Lambrix, Patrick, et al. (författare)
  • Merging DAML plus OIL Ontologies
  • 2005
  • Ingår i: Databases and Information Systems. - : IOS Press. - 1586034855 - 9781586034856 ; , s. 249-258
  • Bokkapitel (refereegranskat)abstract
    • Modern databases and information systems essentially differ from their predecessors. Ontology-based and knowledge-based approaches to system development, UML based IS development methodologies, XML databases and heterogeneous information models have come to the fore. All these fundamental aspects are discussed in this book. This publication contains a collection of 22 high quality papers written by 44 authors. These articles present original results in modern database technologies, database applications, data warehousing, data mining, ontologies, and modern information systems. Special emphasis is put on multimedia database systems, heterogeneous data integration methods, view optimizations, ontology engineering tools, modeling and model transformations (MDA). Theoretical aspects as well as technical development issues are considered. The intended audience for this book is researchers, advanced students and practitioners who are interested in advanced topics on databases and information systems
  •  
48.
  • Lambrix, Patrick, et al. (författare)
  • Ontology alignment and merging
  • 2008
  • Ingår i: Anatomy Ontologies for Bioinformatics: Principles and Practice. - London : Springer Publishing Company. - 9781846288845 ; , s. 133-150
  • Bokkapitel (refereegranskat)abstract
    • In recent years many biomedical ontologies, including anatomy ontologies, have been developed. Many of these ontologies contain overlapping information and often we would want to be able to use multiple ontologies. This requires finding the relationships between terms in the different ontologies, i.e. we need to align them. Sometimes we also want to merge ontologies into a new one. In this chapter we give an overview of current ontology alignment and merging systems. We focus on systems that compute similarities between terms in the different ontologies. We present a general framework for these kind of systems and discuss the existing strategies. We also present such a system (SAMBO) and discuss its use using anatomy ontologies. Further, we take a first step in dealing with the problem of using the best alignment algorithms for the ontologies we want to align. We present and illustrate the use of a framework and a tool (KitAMO) for comparative evaluation of ontology alignment strategies and their combinations.
  •  
49.
  • Lambrix, Patrick, et al. (författare)
  • Repairing the missing is-a structure of ontologies
  • 2009
  • Ingår i: The semantic web. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783642108709 ; , s. 76-90
  • Konferensbidrag (refereegranskat)abstract
    • Developing ontologies is not an easy task and often the resulting ontologies are not consistent or complete. Such ontologies, although often useful, also lead to problems when used insemantically-enabled applications. Wrong conclusions may be derived or valid conclusions may be missed. To deal with this problem we may want to repair the ontologies. Up to date most work has been performed on finding and repairing the semantic defects such as unsatisfiable concepts and inconsistent ontologies. In this paper we tackle the problem of repairing modeling defects and in particular, the repairing of structural relations (is-a hierarchy) in the ontologies. We study the case where missing is-arelations are given. We define the notion of a structural repair and develop algorithms to compute repairing actions that would allow deriving the missing is-a relations in the repaired ontology. Further, we define preferences between repairs. We also look at how we can use external knowledge to recommend repairing actions to a domain expert. Further, we discuss an implemented prototype and its use as well as an experiment using the ontologies of the Anatomy track of the Ontology Alignment Evaluation Initiative.
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50.
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