| 1. |
- Weinstein, John N., et al.
(author)
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The cancer genome atlas pan-cancer analysis project
- 2013
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Research review (peer-reviewed)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 2. |
- Lindström, Michelle, et al.
(author)
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Lsm7 phase-separated condensates trigger stress granule formation
- 2022
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Journal article (peer-reviewed)abstract
- Stress granules are non-membranous organelles connected to stress responses and age-related disease. Here, the authors identify a conserved yeast protein, Lsm7, that facilitates stress granule formation through dynamic liquid-liquid phase separation condensates upon 2-deoxy-D-glucose-induced stress. Stress granules (SGs) are non-membranous organelles facilitating stress responses and linking the pathology of age-related diseases. In a genome-wide imaging-based phenomic screen, we identify Pab1 co-localizing proteins under 2-deoxy-D-glucose (2-DG) induced stress in Saccharomyces cerevisiae. We find that deletion of one of the Pab1 co-localizing proteins, Lsm7, leads to a significant decrease in SG formation. Under 2-DG stress, Lsm7 rapidly forms foci that assist in SG formation. The Lsm7 foci form via liquid-liquid phase separation, and the intrinsically disordered region and the hydrophobic clusters within the Lsm7 sequence are the internal driving forces in promoting Lsm7 phase separation. The dynamic Lsm7 phase-separated condensates appear to work as seeding scaffolds, promoting Pab1 demixing and subsequent SG initiation, seemingly mediated by RNA interactions. The SG initiation mechanism, via Lsm7 phase separation, identified in this work provides valuable clues for understanding the mechanisms underlying SG formation and SG-associated human diseases.
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| 3. |
- Wang, Fei, et al.
(author)
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Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level
- 2022
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 13:1
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Journal article (peer-reviewed)abstract
- Pigs are valuable large animal models for biomedical and genetic research, but insights into the tissue- and cell-type-specific transcriptome and heterogeneity remain limited. By leveraging single-cell RNA sequencing, we generate a multiple-organ single-cell transcriptomic map containing over 200,000 pig cells from 20 tissues/organs. We comprehensively characterize the heterogeneity of cells in tissues and identify 234 cell clusters, representing 58 major cell types. In-depth integrative analysis of endothelial cells reveals a high degree of heterogeneity. We identify several functionally distinct endothelial cell phenotypes, including an endothelial to mesenchymal transition subtype in adipose tissues. Intercellular communication analysis predicts tissue- and cell type-specific crosstalk between endothelial cells and other cell types through the VEGF, PDGF, TGF-beta, and BMP pathways. Regulon analysis of single-cell transcriptome of microglia in pig and 12 other species further identifies MEF2C as an evolutionally conserved regulon in the microglia. Our work describes the landscape of single-cell transcriptomes within diverse pig organs and identifies the heterogeneity of endothelial cells and evolutionally conserved regulon in microglia.
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| 4. |
- Dang, Junhua, et al.
(author)
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When the poor excel : Poverty facilitates procedural learning
- 2016
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In: Scandinavian Journal of Psychology. - : Wiley. - 0036-5564 .- 1467-9450. ; 57:4, s. 288-291
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Journal article (peer-reviewed)abstract
- Recent research has shown that poverty directly impeded cognitive functions because the poor could be easily distracted by monetary concerns. We argue that this effect may be limited to functions relying on working memory. For functions that rely on proceduralized processes however, monetary concerns elicited by reminding of financial demands would be conducive rather than harmful. Our results supported this hypothesis by showing that participants with lower income reached the learning criterion of the information-integration categorization task faster than their more affluent counterparts after reminding of financial demands.
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| 5. |
- de Vries, Paul S., et al.
(author)
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Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions
- 2019
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In: American Journal of Epidemiology. - : Oxford University Press. - 0002-9262 .- 1476-6256. ; 188:6, s. 1033-1054
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Journal article (peer-reviewed)abstract
- A person's lipid profile is influenced by genetic variants and alcohol consumption, but the contribution of interactions between these exposures has not been studied. We therefore incorporated gene-alcohol interactions into a multiancestry genome-wide association study of levels of high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. We included 45 studies in stage 1 (genome-wide discovery) and 66 studies in stage 2 (focused follow-up), for a total of 394,584 individuals from 5 ancestry groups. Analyses covered the period July 2014-November 2017. Genetic main effects and interaction effects were jointly assessed by means of a 2-degrees-of-freedom (df) test, and a 1-df test was used to assess the interaction effects alone. Variants at 495 loci were at least suggestively associated (P < 1 x 10(-6)) with lipid levels in stage 1 and were evaluated in stage 2, followed by combined analyses of stage 1 and stage 2. In the combined analysis of stages 1 and 2, a total of 147 independent loci were associated with lipid levels at P < 5 x 10(-8) using 2-df tests, of which 18 were novel. No genome-wide-significant associations were found testing the interaction effect alone. The novel loci included several genes (proprotein convertase subtilisin/kexin type 5 (PCSK5), vascular endothelial growth factor B (VEGFB), and apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1) complementation factor (A1CF)) that have a putative role in lipid metabolism on the basis of existing evidence from cellular and experimental models.
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| 6. |
- Ding, Yunmei, et al.
(author)
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Factors influencing kinesiophobia during the “blanking period” after radiofrequency catheter ablation in patients with atrial fibrillation by the fear-avoidance model
- 2022
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In: International Journal of Cardiology. - : Elsevier BV. - 0167-5273. ; 363, s. 49-55
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Journal article (peer-reviewed)abstract
- Background: The influencing factors of kinesiophobia (fear of movement) in patients with atrial fibrillation(AF)during the post-operative “Blanking Period” are not known. The aims were to investigate the status of kinesiophobia in patients with AF during the post-operative “Blanking Period”, then further describe the occurrence and analyze the influencing factors of patients' kinesiophobia by the Fear-Avoidance Model. Materials and methods: In total,400 patients diagnosed with atrial fibrillation, during the post-operative “Blanking Period” from the selected hospital were included in this study. The Tampa Scale for Kinesiophobia Heart (TSK-SV Heart), the Self-efficacy for Exercise (SEE) scale, and the Geriatric Locomotive Function Scale (GLFS) were used to assess kinesiophobia, exercise self-efficacy, and physical function. The study adopted a cross-sectional design. Results: The score of kinesiophobia during the “Blanking Period” after operation in patients with atrial fibrillation was (44.06 ± 10.77), and the rate of high kinesiophobia was 71.61%.Logistic regression results showed that age, education, household monthly income, resting heart rate, EHRA symptom classification, exercise self-efficacy, and physical function influenced the kinesiophobia of patients during the post-operative “Blanking Period”(p<0.05， p<0.01). Conclusions: Kinesiophobia is common in patients with atrial fibrillation during the postoperative “Blanking Period”, and the fear of movement is related to age, education, household monthly income, resting heart rate, EHRA symptom classification, exercise self-efficacy, and physical function. Clinical and nursing staff should pay close attention to the psychological problems in the post-operation “Blanking Period” of exercise rehabilitation in patients with atrial fibrillation, make timely interventions to reduce patients' fear of movement, and improve patients' compliance with exercise rehabilitation.
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| 7. |
- Dong, Yidan, et al.
(author)
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Study on the Associations of Individual and Work-Related Factors with Low Back Pain among Manufacturing Workers Based on Logistic Regression and Structural Equation Model
- 2021
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In: International Journal of Environmental Research and Public Health. - : MDPI. - 1661-7827 .- 1660-4601. ; 18:4
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Journal article (peer-reviewed)abstract
- Work-related musculoskeletal injuries are one of the major occupational health issues of the workers, especially low back pain (LBP). The aim of this study was to survey the prevalence of LBP among manufacturing workers and to identify associations of individual and work-related factors with LBP. A cross-sectional questionnaire study was performed with 1173 participating manufacturing workers. The questionnaire included individual factors, psychosocial and physical exposures, and musculoskeletal discomfort. It was analyzed by logistic regression and structural equation modeling (SEM). The 1-year prevalence of LBP among Chinese manufacturing workers was 33.6%. Logistic regression analysis showed that job tenure, awkward postures, vibration and job demand were positively-while social support and job control were negatively associated with LBP (p < 0.05). The SEM results indicated that, as shown in other studies, job types, job tenure, postural load, high job demand, low job control and vibration were directly associated with LBP, but also that job types, high job demand, low social support and vibration may have indirect effects on LBP-mediated by postural load.
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| 8. |
- Feitosa, Mary F., et al.
(author)
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Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries
- 2018
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In: PLOS ONE. - : Public library science. - 1932-6203. ; 13:6
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Journal article (peer-reviewed)abstract
- Heavy alcohol consumption is an established risk factor for hypertension; the mechanism by which alcohol consumption impact blood pressure (BP) regulation remains unknown. We hypothesized that a genome-wide association study accounting for gene-alcohol consumption interaction for BP might identify additional BP loci and contribute to the understanding of alcohol-related BP regulation. We conducted a large two-stage investigation incorporating joint testing of main genetic effects and single nucleotide variant (SNV)-alcohol consumption interactions. In Stage 1, genome-wide discovery meta-analyses in approximate to 131 K individuals across several ancestry groups yielded 3,514 SNVs (245 loci) with suggestive evidence of association (P <1.0 x 10(-5)). In Stage 2, these SNVs were tested for independent external replication in individuals across multiple ancestries. We identified and replicated (at Bonferroni correction threshold) five novel BP loci (380 SNVs in 21 genes) and 49 previously reported BP loci (2,159 SNVs in 109 genes) in European ancestry, and in multi-ancestry meta-analyses (P < 5.0 x 10(-8)). For African ancestry samples, we detected 18 potentially novel BP loci (P< 5.0 x 10(-8)) in Stage 1 that warrant further replication. Additionally, correlated meta-analysis identified eight novel BP loci (11 genes). Several genes in these loci (e.g., PINX1, GATA4, BLK, FTO and GABBR2 have been previously reported to be associated with alcohol consumption. These findings provide insights into the role of alcohol consumption in the genetic architecture of hypertension.
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| 9. |
- Feygenson, Mikhail, et al.
(author)
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Probing spin waves in Co3O4 nanoparticles for magnonics applications
- 2024
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In: Nanoscale. - : Royal Society of Chemistry. - 2040-3364 .- 2040-3372. ; 16:3, s. 1291-1303
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Journal article (peer-reviewed)abstract
- The magnetic properties of spinel nanoparticles can be controlled by synthesizing particles of a specific shape and size. The synthesized nanorods, nanodots and cubic nanoparticles have different crystal planes selectively exposed on the surface. The surface effects on the static magnetic properties are well documented, while their influence on spin waves dispersion is still being debated. Our ability to manipulate spin waves using surface and defect engineering in magnetic nanoparticles is the key to designing magnonic devices. We synthesized cubic and spherical nanoparticles of a classical antiferromagnetic material Co3O4 to study the shape and size effects on their static and dynamic magnetic proprieties. Using a combination of experimental methods, we probed the magnetic and crystal structures of our samples and directly measured spin wave dispersions using inelastic neutron scattering. We found a weak, but unquestionable, increase in exchange interactions for the cubic nanoparticles as compared to spherical nanoparticle and bulk powder reference samples. Interestingly, the exchange interactions in spherical nanoparticles have bulk-like properties, despite a ferromagnetic contribution from canted surface spins.
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| 10. |
- Gao, Lihua, et al.
(author)
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Interfacial phenomenon and Marangoni convection of Fe–C melt on coke substrate under in situ observation
- 2023
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1
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Journal article (peer-reviewed)abstract
- The interfacial phenomenon between liqiuid iron and coke is important for determining the melting efficiency in the blast furnace iron-making process. In this study, the interaction observed in the case of the iron-carbon (Fe–C) melt on coke substrate was investigated using a high-temperature vacuum wettability test equipment. The Fe–C melt did not wet and spread on the coke substrate with different graphitization degrees (r 0) at a high temperature of 1450 °C. The contact angles changed from 124.5° to 105.3°, and the r 0 increased from 9.30 to 50.00%, thus indicating a nonwetting state. The deepening of graphitization decreased the contact angle. Thereby, increasing the contact area between liquid iron and the carbonaceous material, which facilitated carbon dissolution. The irregular movements of Fe–C melt were observed in situ during the wetting process. The horizontal force of the droplet caused by interfacial tension and the contact angle; the Marangoni convection owing to the gradient of carbon concentration; and the impulse force caused by the generation, aggregation, and release of SiO bubbles at the interface were attributed to the driving force.
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