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| 2. |
- Calabrese, Claudia, et al.
(författare)
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Genomic basis for RNA alterations in cancer
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 129-136
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Tidskriftsartikel (refereegranskat)abstract
- Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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| 3. |
- 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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| 4. |
- Dou, Yangpeng, et al.
(författare)
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Effects of reducibility of graphene oxide nanosheets on preparation of AgNPs/GO nanocomposites and their electrocatalytic performance
- 2015
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Ingår i: Journal of nanoparticle research. - : Springer Science and Business Media LLC. - 1388-0764 .- 1572-896X. ; 17:12, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Silver nanoparticles/graphene oxide (AgNPs/GO) nanocomposites were prepared in a solution of AgNO3 and GO. The GO serves not only as a reductant but also as a substrate to support the as-reduced silver nanoparticles. The reducibility of GO was investigated by analyzing the influence factors such as pH, duration, the reaction temperature, and the weight ratio of AgNO3 and GO in the AgNP/GO nanocomposite mixture, which were evaluated by the UV–vis absorption spectroscopy. The results demonstrated that Ag nanoparticles with an average diameter of 5–10 nm were uniformly dispersed on the surface of GO nanosheets under the optimum synthesis conditions of pH between 8 and 11, weight ratio of AgNO3 and GO between 55 % and 60 %, and at 80 °C for 6 h. Moreover, the obtained AgNPs/GO nanocomposites exhibit good electrocatalytic activity for the reduction of p-nitrophenol to 4-(hydroxyamino) phenol.
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| 5. |
- Jiao, Wei, et al.
(författare)
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A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
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| 6. |
- Shao, Wei, et al.
(författare)
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Reduce uncertainty in soil hydrological modeling : A comparison of soil hydraulic parameters generated by random sampling and pedotransfer function
- 2023
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Ingår i: Journal of Hydrology. - 0022-1694 .- 1879-2707. ; 623
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Tidskriftsartikel (refereegranskat)abstract
- Numerical simulation of unsaturated soil hydrology relies on calibrated soil hydraulic parameters, which are subject to uncertainty due to imperfect information during the inverse modelling. This study investigates the effectiveness of reducing parameter uncertainty using the recently developed Rosetta 3 pedotransfer function. The GLUE method was employed for numerical modeling using the Darcy-Richards equation under two strategies for sampling Mualem-van Genuchten (MvG) parameters: the first uses conventional random generation of MvG parameters (GLUE-random), while the second adopts Rosetta 3 to transfer soil particle composition to MvG parameter (GLUE-Rosetta). Both approaches were used for inverse modeling of 9 typical soils, each with a recommended parameter set defined as true values and associated soil moisture dynamics as observations. The posterior parameters selected with both GLUE-random and GLUE-Rosetta show an equifinality phenomenon. GLUE-random fails to provide well-constrained posterior parameters to recover the pre-defined true values, and its posterior results of soil water characteristic curve (SWCC) and soil hydraulic conductivity function (HCF) are poorly constrained. In contrast, GLUE-Rosetta significantly improves the accuracy of the inversely-estimated soil hydraulic parameters, and the ensemble of posterior SWCC and HCF also encompasses the predefined true curves. The results demonstrate the effectiveness of using Rosetta 3 to reduce the dimensionality of the optimization problem, which results in reliable estimation of soil hydraulic parameters and soil particle compositions. Moreover, GLUE-Rosetta outperforms GLUE-random in predicting soil moisture dynamics under different rainfall intensities. Overall, it is recommended to integrate Rosetta 3 with existing optimization tools to reduce the uncertainty of soil parameters and support more reliable modeling of unsaturated soil hydrology.
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| 7. |
- Shao, Wei, et al.
(författare)
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Reducing uncertainties in hydromechanical modeling with a recently developed Rosetta 3 podeotransfer function
- 2023
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Ingår i: Engineering Geology. - 0013-7952 .- 1872-6917. ; 324
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Tidskriftsartikel (refereegranskat)abstract
- Stability analysis of unsaturated landslide deposits requires reliable estimates of soil moisture and pore water pressure. However, modeled soil moisture and pore water pressure contain substantial uncertainties due to imperfect information on soil hydraulic properties. Due to the relatively high dimensionality, commonly used parameter optimization strategies can be significantly affected by equifinality problems. This study investigates the effectiveness of reducing parameter estimation dimensionality using soil pedo-transfer functions. Specifically, we first estimated soil hydraulic parameters using the traditional Generalized Likelihood Uncertainty Estimation (GLUE) method, with parameters randomly drawn from the entire space (refer to as GLUE-random). In a second strategy, we use the Rosetta 3 pedotransfer function to constrain soil hydraulic parameters (refer to as GLUE-Rosetta). The two methods were tested in a typical landslide deposit with in-situ measured soil moisture dynamics for inverse modeling. The GLUE-random estimated soil hydraulic parameters contained substantial uncertainties –resulting in poorly constrained soil water retention curves (SWCC) and hydraulic conductivity functions (HCF). As a result, the uncertainty bands of pore water pressure and slope stability can cross values with several orders of magnitudes. In contrast, GLUE-Rosetta provided well-constrained SWCC and HCF, which significantly reduce the uncertainties in pore water pressure and slope stability estimates. These results suggest that the Rosetta 3 pedotransfer function can significantly improve the reliability of soil hydraulic parameters by reducing the dimensionality of the optimization problem and high-quality prior information of soil hydraulic properties. In conclusion, Rosetta 3 can enhance the reliability of soil parameters estimates and the reliability of subsurface hydrology, which may benefit the development of landslide early-warning systems.
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| 8. |
- Tahir, Haroon Elrasheid, et al.
(författare)
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Smart films fabricated from natural pigments for measurement of total volatile basic nitrogen (TVB-N) content of meat for freshness evaluation : A systematic review
- 2022
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Ingår i: Food Chemistry. - : Elsevier. - 0308-8146 .- 1873-7072. ; 396
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Forskningsöversikt (refereegranskat)abstract
- Major databases were searched from January 2012 to August 2021 and 54 eligible studies were included in the meta-analysis to estimate the overall mean of total volatile basic nitrogen (TVB-N) in meat. The mean of TVB-N was 24.96 mg/100 g (95 % CI:23.10-26.82). The pooled estimate of naphthoquinone, curcumin, anthocyanins, alizarin and betalains were 25.98 mg/100 g (95 %CI:19.63-32.33), 30.03 mg/100 g (95 %CI: 24.15-35.91), 24.92 mg/100 g (95 %CI: 22.55-27.30), 23.37 mg/100 g (95 %CI:19.42-27.33) and 19.50 mg/100 g (95 % CI:17.87-21.12), respectively. Meanwhile, subgroups based on meat types showed that smart film was most used in aquatic products at 27.19 mg/100 g (95 %CI:24.97-29.42), followed by red meat at 19.69 mg/100 g (95 % CI:17.44-21.94). Furthermore, 4 degrees C was the most storage temperature used for testing the performance of smart films at 25.48 mg/100 g (95 %CI:23.05-27.90), followed by storage at 25 degrees C of 25.65 mg/100 g (95 % CI:22.17-29.13). Substantial heterogeneity was found across the eligible studies (I-2 = 99 %, p = 0.00). The results of the trim-and-fill method demonstrated publication bias was well controlled.
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| 9. |
- Zhang, Wenliang, et al.
(författare)
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Exploring over-actuation and model complexity for trajectory planning of autonomous vehicles in critical manoeuvres
- 2022
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Ingår i: 15<sup>th</sup> International Symposium on Advanced Vehicle Control, AVEC’22..
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Konferensbidrag (refereegranskat)abstract
- Accurate trajectory planning is crucial for safe driving of autonomous vehicles in critical driving manoeuvres. However, using simple models for trajectory planning in such conditions may result in unrealistic or unsafe trajectories. This paper evaluates various combinations of models, i.e., over-actuation and vehicle and tyre models, for trajectory planning in critical conditions. The trajectory planning is formulated as an optimal control problem, where constraints concerning safety and actuator physical limits are explicitly considered. The results show that, by exploring torque vectoring, the most advanced planner (with the Pacejka tyre model and load transfer) outperformed the others with higher passing velocities and safer trajectories. Moreover, torque vectoring contributed to more consistent passing velocities during trajectory planning and tracking as well as safer trajectories, even with a simpler Dugoff tyre model. Furthermore, the two planners that do not consider torque vectoring had inconsistent or lower passing velocities and less safe trajectories.
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