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- Ramilowski, JA, et al.
(författare)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Tidskriftsartikel (refereegranskat)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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| 4. |
- Zhou, D, et al.
(författare)
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Low copy numbers of complement C4 and C4A deficiency are risk factors for myositis, its subgroups and autoantibodies
- 2023
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Ingår i: Annals of the rheumatic diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 82:2, s. 235-245
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Tidskriftsartikel (refereegranskat)abstract
- Idiopathic inflammatory myopathies (IIM) are a group of autoimmune diseases characterised by myositis-related autoantibodies plus infiltration of leucocytes into muscles and/or the skin, leading to the destruction of blood vessels and muscle fibres, chronic weakness and fatigue. While complement-mediated destruction of capillary endothelia is implicated in paediatric and adult dermatomyositis, the complex diversity of complementC4in IIM pathology was unknown.MethodsWe elucidated the gene copy number (GCN) variations of totalC4,C4AandC4B, longandshort genesin 1644 Caucasian patients with IIM, plus 3526 matched healthy controls using real-time PCR or Southern blot analyses. Plasma complement levels were determined by single radial immunodiffusion.ResultsThe large study populations helped establish the distribution patterns of variousC4GCN groups. Low GCNs ofC4T(C4T=2+3) andC4Adeficiency (C4A=0+1) were strongly correlated with increased risk of IIM with OR equalled to 2.58 (2.28–2.91), p=5.0×10−53forC4T, and 2.82 (2.48–3.21), p=7.0×10−57forC4Adeficiency. Contingency and regression analyses showed that among patients withC4Adeficiency, the presence ofHLA-DR3became insignificant as a risk factor in IIM except for inclusion body myositis (IBM), by which 98.2% hadHLA-DR3with an OR of 11.02 (1.44–84.4). Intragroup analyses of patients with IIM for C4 protein levels and IIM-related autoantibodies showed that those with anti-Jo-1 or with anti-PM/Scl had significantly lower C4 plasma concentrations than those without these autoantibodies.ConclusionsC4Adeficiency is relevant in dermatomyositis,HLA-DRB1*03is important in IBM and bothC4Adeficiency andHLA-DRB1*03contribute interactively to risk of polymyositis.
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| 7. |
- Ergeneman, O., et al.
(författare)
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Morphology, structure and magnetic properties of cobalt-nickel films obtained from acidic electrolytes containing glycine
- 2011
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Ingår i: Electrochimica Acta. - : Elsevier BV. - 0013-4686 .- 1873-3859. ; 56:3, s. 1399-1408
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Tidskriftsartikel (refereegranskat)abstract
- This paper focuses on the development and optimization of electroplated cobalt-nickel (CoNi) alloys for use in biomedical microdevices. CoNi films were electrodeposited from glycine-containing electrolyte solutions at acidic pH. The influence of pH (2.5-5), temperature (55 and 80 degrees C). current density (from -5 to -40 mA cm(-2)), glycine concentration (0.5 and 1 mol dm(-3)) and the nature of the metal salts (chlorides or sulphates) on the composition and the magnetic properties of the films were systematically analyzed. The cobalt content varied between 50 and 83 wt% depending on the applied conditions. As a result, deposits showed variable morphologies, different structures (either hexagonal close-packed (hcp) or mixed hcp and face-centered cubic phases) and tunable magnetic properties, ranging from semi-hard (18.51 kA m(-1). i.e. 233 Oe) to very soft (1.43 kA m(-1), i.e. 18 Oe). To understand the role of glycine in this system, a comparison of the electrochemical processes, and the structural and magnetic properties is made for samples produced in glycine-containing and glycine-free baths. (C) 2010 Elsevier Ltd. All rights reserved.
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| 8. |
- Maguire, Casey A., et al.
(författare)
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Microvesicle-associated AAV Vector as a Novel Gene Delivery System
- 2012
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Ingår i: Molecular Therapy. - New York : Nature Publishing Group. - 1525-0016 .- 1525-0024. ; 20:5, s. 960-971
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Tidskriftsartikel (refereegranskat)abstract
- Adeno-associated virus (AAV) vectors have shown remarkable efficiency for gene delivery to cultured cells and in animal models of human disease. However, limitations to AAV vectored gene transfer exist after intravenous transfer, including off-target gene delivery (e.g., liver) and low transduction of target tissue. Here, we show that during production, a fraction of AAV vectors are associated with microvesicles/exosomes, termed vexosomes (vector-exosomes). AAV capsids associated with the surface and in the interior of microvesicles were visualized using electron microscopy. In cultured cells, vexosomes outperformed conventionally purified AAV vectors in transduction efficiency. We found that purified vexosomes were more resistant to a neutralizing anti-AAV antibody compared to conventionally purified AAV. Finally, we show that vexosomes bound to magnetic beads can be attracted to a magnetized area in cultured cells. Vexosomes represent a unique entity which offers a promising strategy to improve gene delivery.
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| 11. |
- Ali, Nadeem, et al.
(författare)
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Semi-Volatile Organic Compounds in Car Dust : A Pilot Study in Jeddah, Saudi Arabia
- 2021
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Ingår i: International Journal of Environmental Research and Public Health. - : MDPI AG. - 1661-7827 .- 1660-4601. ; 18:9
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Tidskriftsartikel (refereegranskat)abstract
- People may spend a significant amount of their daily time in cars and thus be exposed to chemicals present in car dust. Various chemicals are emitted from during car use, contaminating the car dust. In this study, we compiled published and unpublished data on the occurrence of phthalates, flame retardants (FRs), polycyclic aromatic hydrocarbons (PAHs), and polychlorinated biphenyls (PCBs) in Saudi car dust. Phthalates, a class of chemical commonly used as plasticizers in different car parts, were the major pollutants found in car dust, with a median value of n-ary sumation phthalates 1,279,000 ng/g. Among other chemicals, organophosphate flame retardants (OPFRs) were found to be between 1500-90,500 ng/g, which indicates their use as alternative FRs in the car industry. The daily exposure to Saudi drivers (regular and taxi drivers) was below the respective reference dose (RfD) values of the individual chemicals. However, the estimated incremental lifetime cancer risk (ILCR) values due to chronic exposure to these chemicals was >1 x 10(-5) for taxi drivers for phthalates and PAHs, indicating that the long-term exposure to these chemicals is a cause of concern for drivers who spend considerable time in cars. The study has some limitations, due to the small number of samples, lack of updated RfD values, and missing cancer slope factors for many studied chemicals. Despite these limitations, this study indicates the possible range of exposure to drivers from chemicals in car dust and warrants further extensive studies to confirm these patterns.
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| 12. |
- de Souza, Fabio A. L., et al.
(författare)
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Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/h-BN nanopore
- 2020
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 12:35, s. 18289-18295
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Tidskriftsartikel (refereegranskat)abstract
- The feasibility of synthesizing unnatural DNA/RNA has recently been demonstrated, giving rise to new perspectives and challenges in the emerging field of synthetic biology, DNA data storage, and even the search for extraterrestrial life in the universe. In line with this outstanding potential, solid-state nanopores have been extensively explored as promising candidates to pave the way for the next generation of label-free, fast, and low-cost DNA sequencing. In this work, we explore the sensitivity and selectivity of a graphene/h-BN based nanopore architecture towards detection and distinction of synthetic Hachimoji nucleobases. The study is based on a combination of density functional theory and the non-equilibrium Green's function formalism. Our findings show that the artificial nucleobases are weakly binding to the device, indicating a short residence time in the nanopore during translocation. Significant changes in the electron transmission properties of the device are noted depending on which artificial nucleobase resides in the nanopore, leading to a sensitivity in distinction of up to 80%. Our results thus indicate that the proposed nanopore device setup can qualitatively discriminate synthetic nucleobases, thereby opening up the feasibility of sequencing even unnatural DNA/RNA.
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| 13. |
- Sivaraman, Ganesh, et al.
(författare)
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Electronic Transport along Hybrid MoS2 Monolayers
- 2016
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 120:41, s. 23389-23396
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Tidskriftsartikel (refereegranskat)abstract
- Molybdenum disulfide (MoS2) is a two-dimensional material in which a semiconducting and a metallic phase can coexist. In this work, we investigate the electronic and transport properties of a hybrid MoS2 monolayer composed of a metallic strip embedded in the semiconducting MoS2 phase. Using quantum mechanical calculations within the density functional theory scheme together with the non-equilibrium Greens functions approach, we study in detail the structural and electronic properties of this hybrid material and its metal semiconductor interface. A single point-defect analysis is performed in order to assess the stability of the hybrid system. Focus is given to the electronic transport properties of the hybrid MoS2 monolayer extracted from the electronic transmission spectra. These are linked to the local current across the monolayer. A clear asymmetry of the current flowing across the hybrid monolayer was found and was attributed to the atomistic characteristics of the material's interfaces. The results suggest strong potential for the application of hybrid MoS2 in the next generation biosensing devices.
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