| 1. |
- Tabassum, R, et al.
(author)
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Genetic architecture of human plasma lipidome and its link to cardiovascular disease
- 2019
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 4329-
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Journal article (peer-reviewed)abstract
- Understanding genetic architecture of plasma lipidome could provide better insights into lipid metabolism and its link to cardiovascular diseases (CVDs). Here, we perform genome-wide association analyses of 141 lipid species (n = 2,181 individuals), followed by phenome-wide scans with 25 CVD related phenotypes (n = 511,700 individuals). We identify 35 lipid-species-associated loci (P <5 ×10−8), 10 of which associate with CVD risk including five new loci-COL5A1, GLTPD2, SPTLC3, MBOAT7 and GALNT16 (false discovery rate<0.05). We identify loci for lipid species that are shown to predict CVD e.g., SPTLC3 for CER(d18:1/24:1). We show that lipoprotein lipase (LPL) may more efficiently hydrolyze medium length triacylglycerides (TAGs) than others. Polyunsaturated lipids have highest heritability and genetic correlations, suggesting considerable genetic regulation at fatty acids levels. We find low genetic correlations between traditional lipids and lipid species. Our results show that lipidomic profiles capture information beyond traditional lipids and identify genetic variants modifying lipid levels and risk of CVD.
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| 2. |
- Haycock, Philip C., et al.
(author)
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Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases A Mendelian Randomization Study
- 2017
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In: JAMA Oncology. - : American Medical Association. - 2374-2437 .- 2374-2445. ; 3:5, s. 636-651
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Journal article (peer-reviewed)abstract
- IMPORTANCE: The causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation. OBJECTIVE: To conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases. DATA SOURCES: Genomewide association studies (GWAS) published up to January 15, 2015. STUDY SELECTION: GWAS of noncommunicable diseases that assayed germline genetic variation and did not select cohort or control participants on the basis of preexisting diseases. Of 163 GWAS of noncommunicable diseases identified, summary data from 103 were available. DATA EXTRACTION AND SYNTHESIS: Summary association statistics for single nucleotide polymorphisms (SNPs) that are strongly associated with telomere length in the general population. MAIN OUTCOMES AND MEASURES: Odds ratios (ORs) and 95% confidence intervals (CIs) for disease per standard deviation (SD) higher telomere length due to germline genetic variation. RESULTS: Summary data were available for 35 cancers and 48 non-neoplastic diseases, corresponding to 420 081 cases (median cases, 2526 per disease) and 1 093 105 controls (median, 6789 per disease). Increased telomere length due to germline genetic variation was generally associated with increased risk for site-specific cancers. The strongest associations (ORs [ 95% CIs] per 1-SD change in genetically increased telomere length) were observed for glioma, 5.27 (3.15-8.81); serous low-malignant-potential ovarian cancer, 4.35 (2.39-7.94); lung adenocarcinoma, 3.19 (2.40-4.22); neuroblastoma, 2.98 (1.92-4.62); bladder cancer, 2.19 (1.32-3.66); melanoma, 1.87 (1.55-2.26); testicular cancer, 1.76 (1.02-3.04); kidney cancer, 1.55 (1.08-2.23); and endometrial cancer, 1.31 (1.07-1.61). Associations were stronger for rarer cancers and at tissue sites with lower rates of stem cell division. There was generally little evidence of association between genetically increased telomere length and risk of psychiatric, autoimmune, inflammatory, diabetic, and other non-neoplastic diseases, except for coronary heart disease (OR, 0.78 [ 95% CI, 0.67-0.90]), abdominal aortic aneurysm (OR, 0.63 [ 95% CI, 0.49-0.81]), celiac disease (OR, 0.42 [ 95% CI, 0.28-0.61]) and interstitial lung disease (OR, 0.09 [ 95% CI, 0.05-0.15]). CONCLUSIONS AND RELEVANCE: It is likely that longer telomeres increase risk for several cancers but reduce risk for some non-neoplastic diseases, including cardiovascular diseases.
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| 3. |
- Abraham, Mark James, et al.
(author)
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Sharing Data from Molecular Simulations
- 2019
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In: Journal of Chemical Information and Modeling. - : AMER CHEMICAL SOC. - 1549-9596 .- 1549-960X. ; 59:10, s. 4093-4099
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Journal article (peer-reviewed)abstract
- Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 (https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations.
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| 6. |
- Cousin, A., et al.
(author)
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Compositions of coarse and fine particles in martian soils at gale: A window into the production of soils
- 2015
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In: Icarus. - : Elsevier BV. - 0019-1035 .- 1090-2643. ; 249, s. 22-42
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Journal article (peer-reviewed)abstract
- The ChemCam instrument onboard the Curiosity rover provides for the first time an opportunity to study martian soils at a sub-millimeter resolution. In this work, we analyzed 24 soil targets probed by ChemCam during the first 250 sols on Mars. Using the depth profile capability of the ChemCam LIBS (Laser-Induced Breakdown Spectroscopy) technique, we found that 45% of the soils contained coarse grains (>500 μm). Three distinct clusters have been detected: Cluster 1 shows a low SiO2 content; Cluster 2 corresponds to coarse grains with a felsic composition, whereas Cluster 3 presents a typical basaltic composition. Coarse grains from Cluster 2 have been mostly observed exposed in the vicinity of the landing site, whereas coarse grains from Clusters 1 and 3 have been detected mostly buried, and were found all along the rover traverse. The possible origin of these coarse grains was investigated. Felsic (Cluster 2) coarse grains have the same origin as the felsic rocks encountered near the landing site, whereas the origin of the coarse grains from Clusters 1 and 3 seems to be more global. Fine-grained soils (particle size < laser beam diameter which is between 300 and 500 μm) show a homogeneous composition all along the traverse, different from the composition of the rocks encountered at Gale. Although they contain a certain amount of hydrated amorphous component depleted in SiO2, possibly present as a surface coating, their overall chemical homogeneity and their close-to-basaltic composition suggest limited, or isochemical alteration, and a limited interaction with liquid water. Fine particles and coarse grains from Cluster 1 have a similar composition, and the former could derive from weathering of the latter. Overall martian soils have a bulk composition between that of fine particles and coarse grains. This work shows that the ChemCam instrument provides a means to study the variability of soil composition at a scale not achievable by bulk chemical analyses.
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| 8. |
- Lasue, J., et al.
(author)
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Martian Eolian Dust Probed by ChemCam
- 2018
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In: Geophysical Research Letters. - : John Wiley & Sons. - 0094-8276 .- 1944-8007. ; 45:20, s. 10968-10977
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Journal article (peer-reviewed)abstract
- The ubiquitous eolian dust on Mars plays important roles in the current sedimentary and atmospheric processes of the planet. The ChemCam instrument retrieves a consistent eolian dust composition at the submillimeter scale from every first laser shot on Mars targets. Its composition presents significant differences with the Aeolis Palus soils and the Bagnold dunes as it contains lower CaO and higher SiO2. The dust FeO and TiO2contents are also higher, probably associated with nanophase oxide components. The dust spectra show the presence of volatile elements (S and Cl), and the hydrogen content is similar to Bagnold sands but lower than Aeolis Palus soils. Consequently, the dust may be a contributor to the amorphous component of soils, but differences in composition indicate that the two materials are not equivalent.
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| 10. |
- Stampoulidis, Leontios, et al.
(author)
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High-speed low-power and board-mountable optical transceivers for scalable & energy efficient advanced on-board digital processors
- 2018
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In: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 0277-786X .- 1996-756X. ; 11180
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Conference paper (peer-reviewed)abstract
- We present the development and verification testing of a high speed multimode, multicore transceiver technology for intra-satellite optical interconnects. We report the fabrication and functional testing of opto-parts including 25 Gb/s 850 nm VCSEL/PD as well as the verification testing of the VCSELs against radiation and lifetime performance. In addition we report the development and evaluation testing of a multi-core cable assembly that was fabricated and mated with MiniAVIM multi-core connectors to develop hi-rel multi-core optical patchcords for pigtailing the transceiver modules. The fiber optic, electronic and opto-parts were used to assemble the first ever fully packaged and pigtailed, six-core optical transceiver prototype module that operates at 25 Gb/s channel bit rate at an energy consumption of ∠4.5 mW/Gb/s.
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