| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Chen, Yicheng, et al.
(författare)
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Computational fluid-structure interaction analysis of flapping uvula on aerodynamics and pharyngeal vibration in a pediatric airway
- 2023
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 13:1, s. 2013-
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Tidskriftsartikel (refereegranskat)abstract
- The uvula flapping is one of the most distinctive features of snoring and is critical in affecting airway aerodynamics and vibrations. This study aimed to elucidate the mechanism of pharyngeal vibration and pressure fluctuation due to uvula flapping employing fluid-structure interaction simulations. The followings are the methodology part: we constructed an anatomically accurate pediatric pharynx model and put attention on the oropharynx region where the greatest level of upper airway compliance was reported to occur. The uvula was assumed to be a rigid body with specific flapping frequencies to guarantee proper boundary conditions with as little complexity as possible. The airway tissue was considered to have a uniform thickness. It was found that the flapping frequency had a more significant effect on the airway vibration than the flapping amplitude, as the flapping uvula influenced the pharyngeal aerodynamics by altering the jet flow from the mouth. Breathing only through the mouth could amplify the effect of flapping uvula on aerodynamic changes and result in more significant oropharynx vibration.
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| 3. |
- Chen, Yicheng, et al.
(författare)
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Evaluation of computational fluid dynamics models for predicting pediatric upper airway airflow characteristics
- 2023
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Ingår i: Medical and Biological Engineering and Computing. - : Springer. - 0140-0118 .- 1741-0444. ; 61:1, s. 259-270
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Tidskriftsartikel (refereegranskat)abstract
- Computational fluid dynamics (CFD) has the potential for use as a clinical tool to predict the aerodynamics and respiratory function in the upper airway (UA) of children; however, careful selection of validated computational models is necessary. This study constructed a 3D model of the pediatric UA based on cone beam computed tomography (CBCT) imaging. The pediatric UA was 3D printed for pressure and velocity experiments, which were used as reference standards to validate the CFD simulation models. Static wall pressure and velocity distribution inside of the UA under inhale airflow rates from 0 to 266.67 mL/s were studied by CFD simulations based on the large eddy simulation (LES) model and four Reynolds-averaged Navier-Stokes (RANS) models. Our results showed that the LES performed best for pressure prediction; however, it was much more time-consuming than the four RANS models. Among the RANS models, the Low Reynolds number (LRN) SST k-ω model had the best overall performance at a series of airflow rates. Central flow velocity determined by particle image velocimetry was 3.617 m/s, while velocities predicted by the LES, LRN SST k-ω, and k-ω models were 3.681, 3.532, and 3.439 m/s, respectively. All models predicted jet flow in the oropharynx. These results suggest that the above CFD models have acceptable accuracy for predicting pediatric UA aerodynamics and that the LRN SST k-ω model has the most potential for clinical application in pediatric respiratory studies.
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| 4. |
- Chen, Yicheng, et al.
(författare)
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Impact of sleep posture and breathing pattern on soft palate flutter and pharynx vibration in a pediatric airway using fluid-structure interaction
- 2023
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Ingår i: Journal of Biomechanics. - : Elsevier. - 0021-9290 .- 1873-2380. ; 152
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Tidskriftsartikel (refereegranskat)abstract
- Snoring is a common condition in the general population, and the management of snoring requires a better understanding of its mechanism through a fluid-structure interaction (FSI) perspective. Despite the recent popularity of numerical FSI techniques, outstanding challenges are accurately predicting airway deformation and its vibration during snoring due to complex airway morphology. In addition, there still needs to be more un-derstanding of snoring inhibition when lying on the side, and the possible effect of airflow rates, as well as nose or mouth-nose breathing, on snoring remains to be investigated. In this study, an FSI method verified against in vitro models was introduced to predict upper airway deformation and vibration. The technique was applied to predict airway aerodynamics, soft palate flutter, and airway vibration in four sleep postures (supine, left/right lying, and sitting positions) and four breathing patterns (mouth-nose, nose, mouth, and unilateral nose breathing). It was found that, at given elastic properties of soft tissues, the evaluated flutter frequency of 19.8 Hz in inspiration was in good agreement with the reported frequency of snoring sound in literature. Reduction in flutter and vibrations due to the mouth-nose airflow proportion changes were also noticed when having side-lying and sitting positions. Breathing through the mouth results in larger airway deformation than breathing through the nose or mouth-nose. These results collectively demonstrate the potential of FSI for studying the physics of airway vibration and clarify to some degree the reason for snoring inhibition during sleep postures and breathing patterns.
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| 5. |
- Hudson, Thomas J., et al.
(författare)
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International network of cancer genome projects
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7291, s. 993-998
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Tidskriftsartikel (refereegranskat)abstract
- The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
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| 6. |
- Kozhevnikov, Evgeny, et al.
(författare)
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A dual-transduction-integrated biosensing system to examine the 3D cell-culture for bone regeneration
- 2019
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Ingår i: Biosensors & bioelectronics. - : ELSEVIER ADVANCED TECHNOLOGY. - 0956-5663 .- 1873-4235. ; 141
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional (3D) cell cultures developed with living cells and scaffolds have demonstrated outstanding potential for tissue engineering and regenerative medicine applications. However, no suitable tools are available to monitor dynamically variable cell behavior in such a complex microenvironment. In particular, simultaneously assessing cell behavior, cell secretion, and the general state of a 3D culture system is of a really challenging task. This paper presents our development of a dual-transduction-integrated biosensing system that assesses electrical impedance in conjunction with imaging techniques to simultaneously investigate the 3D cell-culture for bone regeneration. First, we created models to mimic the dynamic deposition of the extracellular matrix (ECM) in 3D culture, which underwent osteogenesis by incorporating different amounts of bone-ECM components (collagen, hydroxyapatite [HAp], and hyaluronic acid [HA]) into alginate-based hydrogels. The formed models were investigated by means of electrical impedance spectroscopy (EIS), with the results showing that the impedances increased linearly with collagen and hyaluronan, but changed in a more complex manner with HAp. Thereafter, we created two models that consisted of primary osteoblast cells (OBs), which expressed the enhanced green fluorescent protein (EGFP), and 4T1 cells, which secreted the EGFP-HA, in the alginate hydrogel. We found the capacitance (associated with impedance and measured by EIS) increased with the increases in initial embedded OBs, and also confirmed the cell proliferation over 3 days with the EGFP signal as monitored by the fluorescent imaging component in our system. Interestingly, the change in capacitance is found to be associated with OB migration following stimulation. Also, we show higher capacitance in 4T1 cells that secret HA when compared to control 4T1 cells after a 3-day culture. Taken together, we demonstrate that our biosensing system is able to investigate the dynamic process of 3D culture in a non-invasive and real-time manner.
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| 7. |
- Li, Ruiyun, et al.
(författare)
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Operando Formation of Van der Waals Heterostructures for Achieving Macroscale Superlubricity on Engineering Rough and Worn Surfaces
- 2022
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Ingår i: Advanced Functional Materials. - : John Wiley & Sons. - 1616-301X .- 1616-3028. ; 32:18
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Tidskriftsartikel (refereegranskat)abstract
- Macroscale superlubricity breakdown of lubricating materials caused by substrate surface roughening and mechanochemical modification poses great challenges for their practical tribological applications. Here, a facile way is reported to access robust macroscale superlubricity in a vacuum environment, via the operando formation of graphene/transition-metal dichalcogenide (TMDC) heterostructures at wear-induced rough surfaces. By trapping active amorphous carbon (a-C) wear products between TMDC flakes, the sandwich structures readily transform into graphene/TMDC heterostructures during running-in stage, based on shear-induced confinement and load-driven graphitization effects. Then they assemble into multipoint flake-like tribofilms to achieve macroscale superlubricity at steady stage by reducing contact area, eliminating strong cross-interface carbon–carbon interactions and polishing a-C rough nascent surface. Atomistic simulations reveal the preferential formation of graphene/TMDC heterostructures during running-in stage and demonstrate the superlubric sliding of TMDCs on the graphene. The findings are of importance to achieve robust superlubricity and provide a good strategy for the synthesis of other van der Waals heterostructures.
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| 8. |
- Liang, Xiubo, et al.
(författare)
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Menstrual Monster : A Tangible Interactive Co-educational Game Designed for Teenagers
- 2022
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Ingår i: CHI EA '22. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450391566
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Konferensbidrag (refereegranskat)abstract
- Learning menstruation in early adolescence could reduce teenagers’ misunderstanding of it and help them treat menstruation in a proper way. This paper explored a tangible game for teenagers of different genders learning menstruation through collaborative playing. The game included five levels where users play together and learn the cause, products, symptoms of menstruation as well as try to judge some scenarios and listen to audios about menstruation. In our user study, we invited three groups of teenagers ages 11 to 16. Each group contained at least one male and one female, and we let them play the game freely. Teenagers were successfully able to play the game collaboratively, learn menstruation-related knowledge. The results revealed motivation differences related to gender, and after the game, teenagers demonstrated the observable change of the attitude towards menstruation.
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| 9. |
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| 10. |
- Man, Weizhen, et al.
(författare)
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Synthesis of novel CuO@Graphene nanocomposites for lubrication application via a convenient and economical method
- 2022
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Ingår i: Wear. - : Elsevier. - 0043-1648 .- 1873-2577. ; 498-499
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Tidskriftsartikel (refereegranskat)abstract
- Graphene-based nano lubricant additives attract more and more attention because of their superior lubricating performance as well as green and ashless properties. Graphene-based nanocomposites exhibit excellent tribological performances due to the synergistic “slide-roll” effect. In this work, we developed a novel nanocomposite constructed by graphene materials (G) and CuO nanoparticles, named CuO@G, which has superior tribological properties to each component (pure CuO or pure graphene materials) and the mixture (Graphene + CuO) under different testing conditions due to the synergistic effect. By adding 0.5 wt% CuO@G to PAO-6 oil, the coefficient of friction (COF) is reduced by more than 50%, and the wear scar almost disappears. The study provides a novel and promising method for the synthesis of graphene-based lubrication nanomaterials, which has high potential for lubrication applications.
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