| 11. |
- Deans, Andrew R, et al.
(författare)
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Finding Our Way through Phenotypes.
- 2015
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Ingår i: PLoS Biology. - : Public Library of Science (PLoS). - 1545-7885. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
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| 12. |
- Delle, M., et al.
(författare)
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Celiac trunk coverage in endovascular aneurysm repair
- 2010
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Ingår i: Scandinavian Journal of Surgery. - : SAGE Publications. - 1457-4969. ; 99:4, s. 226-229
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND AND AIMS: This retrospective study was undertaken to examine the risks associated with obstruction of the coeliac trunk in the process of treating aneurysms with endografting. MATERIAL AND METHODS: 120 patients were treated by endografting for aneurysmal disease. Of these, a subgroup of 9 patients had their celiac trunk covered. If possible, a preoperative angiography was performed to evaluate collateral flow from the superior mesenteric artery. This was considered to predict the risk for ischemia. RESULTS: None of the patients had any severe clinical event of the celiac trunk occlusion or clinical signs of intestinal ischemia. Three patients had transient increase of liver enzymes. CONCLUSIONS: In cases where the distal landing zone of the descending thoracic aorta is to short for endografting, covering of the celiac trunk may be an option if no other surgical alter-native is apparent. Preoperative angiography to visualise the presence of collateral vessels from the superior mesenteric artery is recommended.
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| 13. |
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| 14. |
- Frey, H U, et al.
(författare)
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Freja and ground-based analysis of inverted-V events
- 1998
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Ingår i: JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS. - 0148-0227. ; 103:A3, s. 4303-4314
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Tidskriftsartikel (refereegranskat)abstract
- During two campaigns, ground-based auroral observations were performed in coordination with Freja. The high temporal and spatial resolution of the satellite instruments as well as the real-time recording with a stereoscopic camera system from the ground enabled detailed comparison of small- and large-scale optical phenomena with particle and field data measured by the satellite. Three passes of the satellite over inverted-V auroral arcs and over precipitation regions with strong field-aligned electron spectra are investigated. Brightness modulations within auroral arcs coincide with modulations of primary electron fluxes. The dynamics of small-scale structures within arcs as well as the proper motion of arcs are analyzed and compared with electric fields measured by the satellite and with BARS radar measurements. Energy fluxes independently determined from the ground and from the satellite are used to calculate the field-aligned conductance. The results agree with predictions of the kinetic theory of the mirror force, if we allow for variations of the density and thermal energy of the electrons in the source region of the magnetosphere. Detailed comparison of electron spectra and electric and magnetic field perturbations provide evidence of different acceleration mechanisms for the electrons, electrostatic acceleration inside inverted-V's, and wave acceleration in transient regions.
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| 15. |
- Hendriks, Kasper P., et al.
(författare)
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Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
- 2023
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Ingår i: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 33:19, s. 4052-4068
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Tidskriftsartikel (refereegranskat)abstract
- The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Bras-sicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To eval-uate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moder-ate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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| 16. |
- Kurek, Magdalena, et al.
(författare)
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Spermatogonia Loss Correlates with LAMA 1 Expression in Human Prepubertal Testes Stored for Fertility Preservation
- 2021
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Ingår i: Cells. - : MDPI AG. - 2073-4409. ; 10:2
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Tidskriftsartikel (refereegranskat)abstract
- Fertility preservation for male childhood cancer survivors not yet capable of producing mature spermatozoa, relies on experimental approaches such as testicular explant culture. Although the first steps in somatic maturation can be observed in human testicular explant cultures, germ cell depletion is a common obstacle. Hence, understanding the spermatogonial stem cell (SSC) niche environment and in particular, specific components such as the seminiferous basement membrane (BM) will allow progression of testicular explant cultures. Here, we revealed that the seminiferous BM is established from 6 weeks post conception with the expression of laminin alpha 1 (LAMA 1) and type IV collagen, which persist as key components throughout development. With prepubertal testicular explant culture we found that seminiferous LAMA 1 expression is disrupted and depleted with culture time correlating with germ cell loss. These findings highlight the importance of LAMA 1 for the human SSC niche and its sensitivity to culture conditions.
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| 17. |
- Marouli, Eirini, et al.
(författare)
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Rare and low-frequency coding variants alter human adult height
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 542:7640, s. 186-190
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Tidskriftsartikel (refereegranskat)abstract
- Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2 centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height increasing alleles of STC2 (giving an increase of 1-2 centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.
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| 18. |
- Nyberg Åkerström, Wolmar, et al.
(författare)
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Developing and implementing the semantic interoperability recommendations of the EOSC Interoperability Framework
- 2024
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This document expands on and provides nuance to some of the concepts defined in the EOSC Interoperability Framework report from the EOSC Executive Board Working Groups (WG) FAIR and Architecture published in 2021 and the conceptualisation of an EOSC Interoperability Framework that it embodies (EOSC-IF). It accounts for a deep-dive into the landscape of semantic interoperability implementations and a wide range of interoperability scenarios focused around the Semantic Interoperability Specification, some subtypes of Semantic Business Objects, as well as the Semantic Artefact Catalogue and Mapping Repository. A small set of new concepts of relevance to this work and to EOSC at large have also been added.The introduction provides context to the creation of this report, the basic concepts section provides and overview of the related components of the EOSC-IF, and the following four sections summarise explorations that frame the concluding set of recommendations to the EOSC community at large.The explorations that frame the recommendations are titled as follows:The Semantic Interoperability Specification: Implementation profiles for communitiesThe Semantic Artefact Catalogue: Twelve maturity dimensionsThe Mapping Repository: Making a case for FAIR mappings and crosswalksImplementation examples: Common use cases and real-world case studiesThe recommendations themselves are organised under the following five broad categories:Align emerging adaptations and implementations to the Semantic View of the EOSC-IF (pp. 39–42) reference architecture.Identify and consolidate different approaches to representing and exchanging (meta)data with the FAIR Digital Objects model described in the EOSC-IF (pp. 29–34).Extend the EOSC-IF to include a research process perspective that can support convergence on solutions for common use cases.Extend the set of Semantic Business Objects described in the EOSC-IF (pp. 40–41) to include artefacts such as mappings and crosswalks.Recognise Semantic Artefact Catalogue component described in the EOSC-IF (p. 42) as a critical part of the long-term viability of any research data infrastructure.
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| 19. |
- Orlando, Ludovic, et al.
(författare)
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Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 499:7456, s. 74-
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Tidskriftsartikel (refereegranskat)abstract
- The rich fossil record of equids has made them a model for evolutionary processes(1). Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP)(2,3). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. prze-walskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus(4,5). We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population(6). We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.
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| 20. |
- Peng, Guotao, et al.
(författare)
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Nitric oxide-dependent biodegradation of graphene oxide reduces inflammation in the gastrointestinal tract
- 2020
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 12:32, s. 16730-16737
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the biological fate of graphene-based materials such as graphene oxide (GO) is crucial to assess adverse effects following intentional or inadvertent exposure. Here we provide first evidence of biodegradation of GO in the gastrointestinal tract using zebrafish as a model. Raman mapping was deployed to assess biodegradation. The degradation was blocked upon knockdown ofnos2aencoding the inducible nitric oxide synthase (iNOS) or by pharmacological inhibition of NOS usingl-NAME, demonstrating that the process was nitric oxide (NO)-dependent. NO-dependent degradation of GO was further confirmedin vitroby combining a superoxide-generating system, xanthine/xanthine oxidase (X/XO), with an NO donor (PAPA NONOate), or by simultaneously producing superoxide and NO by decomposition of SIN-1. Finally, by using the transgenic strainTg(mpx:eGFP) to visualize the movement of neutrophils, we could show that inhibition of the degradation of GO resulted in increased neutrophil infiltration into the gastrointestinal tract, indicative of inflammation.
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