123 research outputs found

    Origin and diversification of polycyclic triterpene and carotenoid metabolisms in the Tree of Life

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    Programa de Doctorado en Biotecnología, Ingeniería y Tecnología QuímicaLínea de Investigación: Biotecnología en la Agricultura, el Medioambiente, la Industria y la AlimentaciónClave Programa: DBICódigo Línea: 109Cell membranes are key components of life, delimiting the cells, performing essential physiological functions and having important roles in environmental adaptations. Membranes have therefore, a crucial influence in the Tree of Life and resolving their evolution is a fundamental issue in Biology. Membranes have evolved heterogeneously between Bacteria, Archaea and Eukaryotes due to the prevalence of specific metabolisms that produce diverse components. Understanding the origin and evolution of membrane components could shed light into the ancestral relationship between the three domains of life as well as the mode of diversification of metabolisms. In this work, we analyzed the origin and evolution of two kind of isoprenoid derivatives (terpenoids) that form different components of the membranes: polycyclic triterpenes and carotenoids. Polycyclic triterpenes are derived from the cyclization of the squalene precursor, a terpene backbone with 30 carbon atoms (C30), including molecules such as hopanoids that are mostly found in Bacteria and are associated to environmental adaptations, or sterols, whose biosynthesis is almost omnipresent in Eukaryotes, and thus, represents a key component of the process of eukaryogenesis. Carotenoids in contrast, are mostly linear terpenoids, mostly classified in C30, C40 and C50 backbones, whose biosynthetic pathways show a more restricted distribution in the Tree of Life as they are mostly associated to photosynthetic organisms. So carotenoids could be one of the many components that contributed to the photosynthesis metabolism. On the other hand, carotenoids are also present in non-photosynthetic organisms (mostly prokaryotes and fungi) in which in addition to the antioxidant and light absorbency properties, carotenoids are also involved in environmental adaptations modulating membrane properties, similarly to hopanoids. Therefore, both kind of molecules have similar functions at the level of membranes. Another important feature of polycyclic triterpenes and carotenoids is their capacity to fossilize through diagenetic process, which is perfect to use them as biomarkers in the fossil record. Biomarkers are remains of biological compounds that are stable over geological timescales and thus, terpene fossils provide a window to understand the lifestyles through the Earth's history. The homologies between the enzymes that form the biosynthetic pathways of carotenoids and polycyclic triterpenes demonstrate that the biosynthesis of both is evolutionarily related. Although their evolution have been previously addressed independently, their specific relationships remain less understood. Elucidating the origin and evolution of the polycyclic triterpene and carotenoid biosynthetic pathways is important to understand the role of these compounds in the tree of life as well as their geobiological value as biomarkers in the fossil record. In this study we address two main question regarding these molecules: first, how did eukaryotes obtained the sterol synthesis genes, and second, what are the biosynthetic and evolutionary relationships between polycyclic triterpenes and carotenoids. While the first questions resolves questions about eukaryogenesis, the second resolves the evolutionary relationship between polycyclic triterpenes and carotenoids. Through phylogenetic and syntenic analyses, and using more than 20,000 prokaryotic and 36 representative eukaryotic genomes, we reconstructed the evolutionary history of the squalene (HpnCDE or Sqs), hopanoid and sterol (through Shc and Osc respectively) and the diverse C30, C40 or C50 (through CrtI-CrtD, CrtN-CrtP, CrtI-50) biosynthetic pathways. Squalene is biosynthesized by two distantly related pathways, HpnCDE and Sqs. The HpnCDE is mostly found bacteria and it is closely related to carotenoid enzymes. This pathway seems to have assembled relatively early in bacteria evolution as the phylogeny of the three enzymes shows a common evolutionary history of the monophyletic groups and form a conserved operon between distant organisms. Sqs in contrast, is the most divergent subfamily of its protein family that also includes HpnC, HpnD or carotenoid synthases like CrtB or CrtM. Sqs is present in the three domains of life, although the taxonomic distribution combined with the phylogeny suggest that Sqs had a bacterial origin and was later transferred to eukaryotes and archaea independently. Another relevant fact, is that when we combined the evolution of HpnCDE and Sqs, we observed that Sqs has been more prone to LGT and in some cases, has displaced the function of HpnCDE through gene loss, which could be in agreement with the fact that it is easier and more efficient to conserved one gene rather than three. The evolution of hopanoids biosynthesis through Shc, shows a most likely vertical evolution in the Gracilicutes bacterial supergroup, but we suspected that it has been transferred through LGT to different Terrabacteria clades. Thus, hopanoid biosynthesis seems to be ancestral but with a heterogenous evolution in the Bacteria domain. Sterol biosynthesis in bacteria shows a limited distribution although number of bacteria bearing sterol genes seem to increase as more amount of genomic information we have. Phylogenetic reconstructions of sterol enzymes, Osc and Sqmo, shows that few bacteria have obtained the sterol genes from eukaryotes, while other bacteria have sterol genes that are possibly unrelated to eukaryotic sources. Bacterial Osc and Sqmo have similar evolutionary histories because they are usually contiguously in the genomes and therefore, are transferred together. Indeed, the osc gene is also associated to other sterol-related genes in the genomes, showing that bacteria have developed gene clusters for sterol metabolism. Another important fact from these results is that we did not found any triterpene cyclase in Archaea, invoking a potential scenario in which eukaryotic genes for sterol biosynthesis assembled from ancestral bacterial contributions in early eukaryotic lineages. One of the major bacterial contributions during the eukaryogenesis was the mitochondria. Due to the scarcity of sterol genes in Alphaproteobacteria, it is unlikely that sterol genes have mitochondrial origin. However, according to recent discoveries placing the origin of mitochondria outside Alphaprotebacteria, it is uncertain whether sterol genes assembled from mitochondrial contributions. On the other hand, due to the existence of a specific sterol pathway in bacteria, and the fact that sterol can be also essential for some bacteria, like for the Plactomycete Gemmata obscuriglobus, we also consider, and indeed favor, the possibility that sterol genes originated in bacteria independently of the eukaryotes. We then combined the evolution of squalene with the one of polycyclic triterpenes. HpnCDE-Shc have more similar evolutionary patterns than Sqs-SHC, which suggests that HpnCDE could have been the primitive pathway for hopanoids. On the other hand, our result also argues against a concurrent origin of Sqs and Osc/Sqmo. In cases like Deltaprotebacteria or Planctomycetes, the production of polycyclic triterpenes could be independent of squalene precursors, as could be the case of Firmicutes and their biosynthesis of sporulenol (a very specific polycyclic triterpene). Another important observation was the lack of carotenoid synthases (CrtB or CrtM) in bacteria that are known to produce carotenoids, such as the Planctomycetes. Taking into account that by genetic engineer it has been demonstrated that squalene is a potential precursor for C30 carotenoids, we suspected that Planctomycetes make use of this route to produce carotenoids. This prompted us to understand the evolution of carotenoid biosynthesis mainly focusing on the C30 pathway, which could represent an interesting connection between hopanoids and carotenoids evolution. The evolution of the carotenoid pathways (C30, C40 and C50) shows more scattered distributions than the one of hopanoids. There are two C40 pathways, one typically from Proteobacteria and the other from Cyanobacteria, and both have common origin but probably emerged sepparately. In contrast, we observed evidence of direct evolution between C40 and C30 pathways, which could be explained by the duplication and neofunctionalization of a entire operon containing the respective C30 or C40 genes. Focusing on the C30 pathway, we observe that its evolution is heterogenous because it has been transferred through LGT multiple times between bacteria. In addition, C30 carotenoid pathway is associated with CrtM only in Firmicutes (the canonical pathway) while in other organisms like in Planctomycetes, it is usually associated to the squalene pathways, either to HpnCDE or Sqs, showing that the potential source of precursor have changed between bacteria, and supporting the idea that C30 carotenoids are synthesized from squalene. We then demonstrated experimentally the natural production of carotenoids through squalene in Planctomycetes (work by Elena Rivas-Marin, Valentina Henriques and Damaso Hornero). Through random transposon insertion in the Planctomycete Planctopirus limnophila, heterologous expression in Escherichia coli, and high performance liquid chromatography analyses (HPLC), we confirm the production of C30 carotenoids via squalene in Planctomycetes being the first description of such pathway in nature. Finally, we integrated the evolutionary history of polycyclic triterpenes and carotenoids to try to determine how the biosynthesis of both originated. Which metabolism is more ancestral? Did ancestral organisms share the same precursor of carotenoid and polycyclic triterpene (squalene) and through the time the metabolic pathways separated and diversified (into C40 pathways for example)? Or did C30 carotenoids and hopanoids originate independently, and coincided just by metabolic compatibility? According to our results, it is difficult to infer a consecutive evolution of carotenoids and polycyclic triterpenes and instead, they could have originated independently. In addition, hopanoids display a more ancestral and/or conserved evolution than carotenoids, which could argue against the classical view of carotenoids as more ancestral than polycyclic triterpenes. In conclusion this is the first work that integrate the evolution of polycyclic triterpenes and carotenoids in the context of the Tree of Life, and altogether, provides novel insights into the evolution cell membranes through the history of life.Universidad Pablo de Olavide de Sevilla. Departamento de Biología Molecular e Ingeniería Bioquímic

    Comparative Genomics of Peroxisome Biogenesis Proteins:Making Sense of the PEX Proteins

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    PEX genes encode proteins involved in peroxisome biogenesis and proliferation. Using a comparative genomics approach, we clarify the evolutionary relationships between the 37 known PEX proteins in a representative set of eukaryotes, including all common model organisms, pathogenic unicellular eukaryotes and human. A large number of previously unknown PEX orthologs were identified. We analyzed all PEX proteins, their conservation and domain architecture and defined the core set of PEX proteins that is required to make a peroxisome. The molecular processes in peroxisome biogenesis in different organisms were put into context, showing that peroxisomes are not static organelles in eukaryotic evolution. Organisms that lack peroxisomes still contain a few PEX proteins, which probably play a role in alternative processes. Finally, the relationships between PEX proteins of two large families, the Pex11 and Pex23 families, were analyzed, thereby contributing to the understanding of their complicated and sometimes incorrect nomenclature. We provide an exhaustive overview of this important eukaryotic organelle

    The role of Cis-Regulatory elements in morphological adaptation to cave environment in Astyanax mexicanus

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    Trabajo presentado en EMBO Workshop Enhanceropathies: Understanding enhancer function to understand human disease, celebrado en Santander (Espa√Īa) del 06 al 09 de octubre de 2021

    Genome evolution in morphological adaptation to cave environment in Astyanax mexicanus

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    Trabajo presentado en el EMBO Workshop The evolution of animal genomes, celebrado en modalidad virtual del 13 al 17 de septiembre de 2021

    Estudios de marcado y recaptura de especies marinas

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    Los resultados obtenidos del marcado y posterior recaptura de los ejemplares son una herramienta muy valiosa para contribuir a mejorar el conocimiento de la biolog√≠a y ecolog√≠a de una especie, examinando ciertos aspectos como son: el crecimiento, los movimientos o migraciones, la mortalidad o supervivencia, la abundancia y distribuci√≥n de la especie, el h√°bitat y diferenciaci√≥n de poblaciones o stocks. Actualmente la t√©cnica de marcado se aplica a muchas especies, tanto terrestres como marinas, pertenecientes a diversos grupos zool√≥gicos: peces, crust√°ceos, reptiles, moluscos y mam√≠feros. Este libro repasa algunos ejemplos de marcado de especies marinas de inter√©s comercial. No todas las especies pueden ser marcadas, porque es necesario cumplir una serie de requisitos para poder llevar a cabo con √©xito un experimento de marcado. En uno de los apartados de esta gu√≠a, se describen los distintos aspectos a tener en cuenta para obtener buenos resultados. Se describen los principales proyectos de marcado actualmente en ejecuci√≥n o en marcha llevados a cabo por el Instituto Espa√Īol de Oceanograf√≠a (IEO). En primer lugar, se describe brevemente la especie, su distribuci√≥n, crecimiento, reproducci√≥n, alimentaci√≥n, etc. A continuaci√≥n, se presenta la informaci√≥n del marcado, es decir, campa√Īas realizadas, n√ļmero de ejemplares marcados y algunos de los resultados obtenidos hasta la fecha a partir de las recapturas disponibles. En algunas especies, los programas de marcado se llevan realizando desde hace m√°s de 20 a√Īos, como es el caso del at√ļn rojo, por lo que la informaci√≥n disponible es bastante amplia. En otros casos por el contrario como la merluza, los proyectos son relativamente recientes, no obstante los resultados son bastante interesantes y prometedores.Nowadays many different marine animals are being tagged. This book summarizes recent tagging programs carried out by the Spanish Institute of Oceanography (IEO). Although the objectives of these various studies mainly depend on the species and each project in particular, the general aim is to better understand the biology and ecology of these animals the structure and dynamics of their populations and their capacity to respond to human activities. This book provides an overview of different aspects of this technique such as a brief history of tagging, the types of tags currently used, including both conventional and electronic tags, where and how to put them on the marine animals, some recommendations regarding how to perform a tagging survey and where to go or what to do if anyone recovers a tagged fish or marine animal. The book then summarizes the main species tagged by the IEO, making a short description of their biology followed by some of the results obtained from tagging studies undertaken until now. Other applications are to know the spatial distribution (spawning or feeding areas), estimate growth parameters, mortality and survival rates, longevity, the size of the population or identifying stocks. Nowadays the advances in electronics have also open new fields such us the possibility of tracking an animal and knowing its habitat preferences and behaviour. Besides some of these tags have the capacity of recording this information during long periods and sending the data from long distances even without the need to recover the animal. Tagging activities constitute a very useful tool to improve the knowledge of many species and contribute to their management and conservation. For that reason this methodology is included in many IEO projects in which other activities like the monitoring of the fishery (landings, fishing effort, fleet characteristics, fishing areas, biological sampling, etc.) are carried out. Some projects are related with coastal pelagic fisheries including anchovy, sardine and mackerel or oceanic pelagic fisheries like tuna and billfish species and pelagic sharks. Others are focused on benthic and demersal species such as hake, black spot seabream, anglerfish, flatfish, etc. Nevertheless not all species can be tagged, as they have to survive being caught and handled before being release. For this reason, tagging techniques may not easily be applied to some species

    Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

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    Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio

    Design and baseline characteristics of the finerenone in reducing cardiovascular mortality and morbidity in diabetic kidney disease trial

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    Background: Among people with diabetes, those with kidney disease have exceptionally high rates of cardiovascular (CV) morbidity and mortality and progression of their underlying kidney disease. Finerenone is a novel, nonsteroidal, selective mineralocorticoid receptor antagonist that has shown to reduce albuminuria in type 2 diabetes (T2D) patients with chronic kidney disease (CKD) while revealing only a low risk of hyperkalemia. However, the effect of finerenone on CV and renal outcomes has not yet been investigated in long-term trials. Patients and Methods: The Finerenone in Reducing CV Mortality and Morbidity in Diabetic Kidney Disease (FIGARO-DKD) trial aims to assess the efficacy and safety of finerenone compared to placebo at reducing clinically important CV and renal outcomes in T2D patients with CKD. FIGARO-DKD is a randomized, double-blind, placebo-controlled, parallel-group, event-driven trial running in 47 countries with an expected duration of approximately 6 years. FIGARO-DKD randomized 7,437 patients with an estimated glomerular filtration rate >= 25 mL/min/1.73 m(2) and albuminuria (urinary albumin-to-creatinine ratio >= 30 to <= 5,000 mg/g). The study has at least 90% power to detect a 20% reduction in the risk of the primary outcome (overall two-sided significance level alpha = 0.05), the composite of time to first occurrence of CV death, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for heart failure. Conclusions: FIGARO-DKD will determine whether an optimally treated cohort of T2D patients with CKD at high risk of CV and renal events will experience cardiorenal benefits with the addition of finerenone to their treatment regimen. Trial Registration: EudraCT number: 2015-000950-39; ClinicalTrials.gov identifier: NCT02545049

    Estudios de marcado y recaptura de especies marinas

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    Los resultados obtenidos del marcado y posterior recaptura de los ejemplares son una herramienta muy valiosa para contribuir a mejorar el conocimiento de la biolog√≠a y ecolog√≠a de una especie, examinando ciertos aspectos como son: el crecimiento, los movimientos o migraciones, la mortalidad o supervivencia, la abundancia y distribuci√≥n de la especie, el h√°bitat y diferenciaci√≥n de poblaciones o stocks. Actualmente la t√©cnica de marcado se aplica a muchas especies, tanto terrestres como marinas, pertenecientes a diversos grupos zool√≥gicos: peces, crust√°ceos, reptiles, moluscos y mam√≠feros. Este libro repasa algunos ejemplos de marcado de especies marinas de inter√©s comercial. No todas las especies pueden ser marcadas, porque es necesario cumplir una serie de requisitos para poder llevar a cabo con √©xito un experimento de marcado. En uno de los apartados de esta gu√≠a, se describen los distintos aspectos a tener en cuenta para obtener buenos resultados. Se describen los principales proyectos de marcado actualmente en ejecuci√≥n o en marcha llevados a cabo por el Instituto Espa√Īol de Oceanograf√≠a (IEO). En primer lugar, se describe brevemente la especie, su distribuci√≥n, crecimiento, reproducci√≥n, alimentaci√≥n, etc. A continuaci√≥n, se presenta la informaci√≥n del marcado, es decir, campa√Īas realizadas, n√ļmero de ejemplares marcados y algunos de los resultados obtenidos hasta la fecha a partir de las recapturas disponibles. En algunas especies, los programas de marcado se llevan realizando desde hace m√°s de 20 a√Īos, como es el caso del at√ļn rojo, por lo que la informaci√≥n disponible es bastante amplia. En otros casos por el contrario como la merluza, los proyectos son relativamente recientes, no obstante los resultados son bastante interesantes y prometedores.Nowadays many different marine animals are being tagged. This book summarizes recent tagging programs carried out by the Spanish Institute of Oceanography (IEO). Although the objectives of these various studies mainly depend on the species and each project in particular, the general aim is to better understand the biology and ecology of these animals the structure and dynamics of their populations and their capacity to respond to human activities. This book provides an overview of different aspects of this technique such as a brief history of tagging, the types of tags currently used, including both conventional and electronic tags, where and how to put them on the marine animals, some recommendations regarding how to perform a tagging survey and where to go or what to do if anyone recovers a tagged fish or marine animal. The book then summarizes the main species tagged by the IEO, making a short description of their biology followed by some of the results obtained from tagging studies undertaken until now. Other applications are to know the spatial distribution (spawning or feeding areas), estimate growth parameters, mortality and survival rates, longevity, the size of the population or identifying stocks. Nowadays the advances in electronics have also open new fields such us the possibility of tracking an animal and knowing its habitat preferences and behaviour. Besides some of these tags have the capacity of recording this information during long periods and sending the data from long distances even without the need to recover the animal. Tagging activities constitute a very useful tool to improve the knowledge of many species and contribute to their management and conservation. For that reason this methodology is included in many IEO projects in which other activities like the monitoring of the fishery (landings, fishing effort, fleet characteristics, fishing areas, biological sampling, etc.) are carried out. Some projects are related with coastal pelagic fisheries including anchovy, sardine and mackerel or oceanic pelagic fisheries like tuna and billfish species and pelagic sharks. Others are focused on benthic and demersal species such as hake, black spot seabream, anglerfish, flatfish, etc. Nevertheless not all species can be tagged, as they have to survive being caught and handled before being release. For this reason, tagging techniques may not easily be applied to some species.Versi√≥n del edito

    The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

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    Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase&nbsp;1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation&nbsp;disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age&nbsp; 6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score&nbsp; 652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc&nbsp;= 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N&nbsp;= 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in&nbsp;Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in&nbsp;Asia&nbsp;and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701
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