| 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. |
- Luo, Yifei, et al.
(författare)
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Technology Roadmap for Flexible Sensors
- 2023
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Ingår i: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
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Forskningsöversikt (refereegranskat)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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| 3. |
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| 4. |
- Almgren, Mats, et al.
(författare)
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Contrast Variation SANS Investigation of Composition Distributions in Mixed Surfactant Micelles
- 2007
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 111:25, s. 7133-7141
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Tidskriftsartikel (refereegranskat)abstract
- Small angle neutron scattering measurements have been performed on three systems (HFDeP-d5-C (N-1(1,1,2,2-tetrahydroperfluorodecanoyl)pyridinium-d5 chloride)/C16PC in 63 mM NaCl; HFDeP-d5-C/C12PC in 200 mM NaCl, and as an example of an ideally mixed system, SDS/SDS-d25 in 200 mM NaCl) contg. micelles formed in a binary mixt. of surfactants, in order to investigate the compn. distribution of the mixed micelles. The exptl. data were collected varying the contrast between the av. scattering length d. of micelles and aq. solvent by changing the H2O/D2O ratio. Anal. of data includes a model-independent approach-the indirect Fourier transformation method and direct modeling-simultaneous fit at all contrasts by the scattering from micelles of equal size and shape with compn. distribution and an effective interaction. It has earlier been shown (Almgren, M.; Garamus, V. M. J. Phys. Chem. B 2005, 109, 11348) that for micelles of equal size, independent of the compn., and with negligible intermicellar interactions, the scattered intensity at zero angle varies quadratically with the contrast, with the min. intensity at the nominal match point proportional to s2, the variance of the micelle compn. distribution. Within the regular soln. framework, the compn. distribution and its variance are uniquely defined by the value of the interaction parameter and the micelle aggregation no. At 25 DegC, the first system gave s = 0.37, corresponding to a broad, bimodal compn. distribution, the second s = 0.22, a broad distribution with a shallow min. at the midpoint. For SDS/SDS-d25, we found s = 0.006 +- 0.030, which is a smaller value than that of the binominal compn. distribution expected for an ideally mixed system.
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| 5. |
- Appleton, Katherine Marie, et al.
(författare)
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A mobile phone app for the provision of personalized food-based information in an eating-out situation : development and initial evaluation
- 2019
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Ingår i: JMIR Formative Research. - : JMIR Publications Inc.. - 2561-326X. ; 3:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Increasing pressure from governments, public health bodies, and consumers is driving a need for increased food-based information provision in eating-out situations. Meals eaten outside the home are known to be less healthy than meals eaten at home, and consumers can complain of poor information on the health impact and allergen content of meals eaten out.Objective: This paper aimed to describe the development and early assessment of a mobile phone app that allows the provision of accurate personalized food-based information while considering individual characteristics (allergies, diet type, and preferences) to enable informed consumer choice when eating out.Methods: An app was designed and developed to address these requirements using an agile approach. The developed app was then evaluated at 8 public engagement events using the System Usability Scale (SUS) questionnaire and qualitative feedback.Results: Consideration of the literature and consultation with consumers revealed a need for information provision for consumers in the eating-out situation, including the ability to limit the information provided to that which was personally relevant or interesting. The app was designed to provide information to consumers on the dishes available in a workplace canteen and to allow consumers the freedom to personalize the app and choose the information that they received. Evaluation using the SUS questionnaire revealed positive responses to the app from a range of potential users, and qualitative comments demonstrated broad interest in its use.Conclusions: This paper details the successful development and early assessment of a novel mobile phone app designed to provide food-based information in an eating-out situation in a personalized manner.
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| 6. |
- Chen, Hanwei, et al.
(författare)
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Tumor Volumes Measured From Static and Dynamic F-18-fluoro-2-deoxy-D-glucose Positron Emission Tomography-Computed Tomography Scan : Comparison of Different Methods Using Magnetic Resonance Imaging as the Criterion Standard
- 2014
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Ingår i: Journal of computer assisted tomography. - 0363-8715 .- 1532-3145. ; 38:2, s. 209-215
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Tidskriftsartikel (refereegranskat)abstract
- Objective: The objective of this study was to compare the accuracy of calculating the primary tumor volumes using a gradient-based method and fixed threshold methods on the standardized uptake value (SUV) maps and the net influx of FDG (Ki) maps from positron emission tomography-computed tomography (PET-CT) images. Materials and Methods: Newly diagnosed patients with head and neck cancer were recruited, and dynamic PET-CT scan and T2-weighted magnetic resonance imaging were performed. The maps of Ki and SUV were calculated from PET-CT images. The tumor volumes were calculated using a gradient-based method and a fixed threshold method at 40% of maximal SUV or maximal Ki. Four kinds of volumes, VOLKi-Gra (from the Ki maps using the gradient-based method), VOLKi-40% (from the Ki maps using the threshold of 40% maximal Ki), VOLSUV-Gra (from the SUV maps using the gradient-based method), and VOLSUV-40% (from the SUV maps using the threshold of 40% maximal SUV), were acquired and compared with VOLMRI (the volumes acquired on T2-weighted images) using the Pearson correlation, paired t test, and similarity analysis. Results: Eighteen patients were studied, of which 4 had poorly defined tumors (PDT). The positron emission tomography-derived volumes were as follows: VOLSUV-40%, 2.1 to 41.2 cm(3) (mean [SD], 12.3 [10.6]); VOLSUV-Gra, 2.2 to 28.1 cm(3) (mean [SD], 13.2 [8.4]); VOLKi-Gra, 2.4 to 17.0 cm(3) (mean [SD], 9.5 [4.6]); and VOLKi-40%, 2.7 to 20.3 cm(3) (mean [SD], 12.0 [6.0]). The VOLMRI ranged from 2.9 to 18.1 cm(3) (mean [SD], 9.1 [3.9]). The VOLKi-Gra significantly correlated with VOLMRI with the highest correlation coefficient (PDT included, R = 0.673, P = 0.002; PDT excluded, R = 0.841, P < 0.001) and presented no difference from VOLMRI (P = 0.672 or 0.561, respectively, PDT included and excluded). The difference between VOLKi-Gra and VOLMRI was also the smallest. Conclusions: The tumor volumes delineated on the Ki maps using the gradient-based method are more accurate than those on the SUV maps and using the fixed threshold methods.
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| 7. |
- Dai, Ting, et al.
(författare)
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Assessment of Fast Fluid Dynamics with Different Turbulence Models for Simulating Airflow and Pollutant Dispersion Around Buildings
- 2023
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Ingår i: Proceedings of the 5th International Conference on Building Energy and Environment. - : Springer Nature. ; , s. 51-59
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Konferensbidrag (refereegranskat)abstract
- Fast fluid dynamics (FFD) could provide efficient airflow and concentration simulation. The commonly used turbulence model in FFD was RNG k- ε turbulence model which solved two transport equations to obtain eddy viscosity. To improve computing speed, this investigation implemented no turbulence model, Smagorinsky model and dynamic Smagorinsky model which calculated eddy viscosity without solving equation in FFD in an open-source program, OpenFOAM. By simulating single-building case and comparing with experiment and CFD, this study assessed accuracy and efficiency of FFD with those turbulence models. Compared with CFD, FFD improved computing speed without reducing accuracy. The simulation of FFD without turbulence model was fast but inaccurate. FFD with Smagorinsky model increased computing speed while ensuring the same accuracy as RNG k- ε turbulence model. FFD with dynamic Smagorinsky model provided accurate results with high efficiency. This investigation suggested FFD with dynamic Smagorinsky model for outdoor airflow and pollutant dispersion studies.
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| 8. |
- Dai, Ting, et al.
(författare)
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Evaluation of fast fluid dynamics with different turbulence models for predicting outdoor airflow and pollutant dispersion
- 2022
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Ingår i: Sustainable cities and society. - : Elsevier BV. - 2210-6707. ; 77, s. 103583-
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Tidskriftsartikel (refereegranskat)abstract
- Fast fluid dynamics (FFD) could provide informative and efficient airflow and concentration simulation. The commonly used turbulence model in FFD was Re-Normalization Group (RNG) k-epsilon turbulence model which solved two transport equations to obtain eddy viscosity. To reduce this part of time and further improve computing speed, this investigation implemented no turbulence model, Smagorinsky model and dynamic Smagorinsky model which calculated eddy viscosity without solving equation in FFD in an open-source program, OpenFOAM. By simulating several outdoor cases of varying complexity and comparing with experiment and CFD, this study assessed the accuracy and computing efficiency of FFD with four turbulence models. Compared with CFD, FFD greatly improved the computing speed without reducing accuracy. The simulation of FFD without turbulence model was fast but inaccurate. FFD with Smagorinsky model increased the computing speed while ensuring the same accuracy as RNG k-epsilon turbulence model. FFD with dynamic Smagorinsky model provided accurate results with high efficiency. Computation errors arose mainly from inaccurate prediction of turbulence dispersion. The computing cost was associated with the number of transport equations and calculation method of model coefficient. This investigation recommended the use of FFD with dynamic Smagorinsky model for outdoor airflow and pollutant dispersion studies.
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| 9. |
- Deng, Min, et al.
(författare)
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Genome-wide association analyses in Han Chinese identify two new susceptibility loci for amyotrophic lateral sclerosis
- 2013
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 45:6, s. 697-
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Tidskriftsartikel (refereegranskat)abstract
- To identify susceptibility genes for amyotrophic lateral sclerosis (ALS), we conducted a genome-wide association study (GWAS) in 506 individuals with sporadic ALS and 1,859 controls of Han Chinese ancestry. Ninety top SNPs suggested by the current GWAS and 6 SNPs identified by previous GWAS were analyzed in an independent cohort of 706 individuals with ALS and 1,777 controls of Han Chinese ancestry. We discovered two new susceptibility loci for ALS at 1q32 (CAMK1G, rs6703183, P-combined = 2.92 x 10(-8), odds ratio (OR) = 1.31) and 22p11 (CABIN1 and SUSD2, rs8141797, P-combined = 2.35 x 10(-9), OR = 1.52). These two loci explain 12.48% of the overall variance in disease risk in the Han Chinese population. We found no association evidence for the previously reported loci in the Han Chinese population, suggesting genetic heterogeneity of disease susceptibility for ALS between ancestry groups. Our study identifies two new susceptibility loci and suggests new pathogenic mechanisms of ALS.
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| 10. |
- Deng, Nan, et al.
(författare)
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Significance of Photosynthetic Characters in the Evolution of Asian Gnetum (Gnetales)
- 2019
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Gnetum is a genus in the Gnetales that has a unique but ambiguous placement within seed plant phylogeny. Previous studies have shown that Gnetum has lower values of photosynthetic characters than those of other seed plants, but few Gnetum species have been studied, and those that have been studied are restricted to narrow taxonomic and geographic ranges. In addition, the mechanism underlying the lower values of photosynthetic characters in Gnetum remains poorly understood. Here, we investigated the photosynthetic characters of a Chinese lianoid species, i.e., Gnetum parvifolium, and co-occurring woody angiosperms growing in the wild, as well as seedlings of five Chinese Gnetum species cultivated in a greenhouse. The five Gnetum species had considerably lower values for photosynthesis parameters (net photosynthetic rate, transpiration rate, intercellular CO2 concentration, and stomatal conductance) than those of other seed plant representatives. Interrelated analyses revealed that the low photosynthetic capacity may be an intrinsic property of Gnetum, and may be associated with its evolutionary history. Comparison of the chloroplast genomes (cpDNAs) of Gnetum with those of other seed plant representatives revealed that 17 coding genes are absent from the cpDNAs of all species of Gnetum. This lack of multiple functional genes from the cpDNAs probably leads to the low photosynthetic rates of Gnetum. Our results provide a new perspective on the evolutionary history of the Gnetales, and on the ecophysiological and genomic attributes of tropical biomes in general. These results could also be useful for the breeding and cultivation of Gnetum.
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