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| 2. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 3. |
- Zhou, X., et al.
(författare)
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Novel Evaluation Method to Determine the Mixing Time in a Ladle Refining Process
- 2022
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Ingår i: Metallurgical and materials transactions. B, process metallurgy and materials processing science. - : Springer Nature. - 1073-5615 .- 1543-1916. ; 53:6, s. 4114-4123
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Tidskriftsartikel (refereegranskat)abstract
- Mixing plays a key role in mass and heat transfer, as well as chemical reactions in various vessels involving agitation. Several studies have confirmed that the mixing time obtained from several monitor locations cannot reflect the mixing time for the whole bath because stirring situation in different locations is variable due to the change of operation schemes. It is proved that some zones with inefficient stirring cannot be monitored by applying a limited amount of probes in physical and mathematical models. This study provides a novel approach to quantify mixing time evaluation considering the tracer variation for the whole bath using a mathematical model. It was found that the mixing time obtained by considering the whole bath is more representative than that of the probe monitor method. Compared with the traditional probe method, about 50 to 70 pct longer mixing times were obtained for different operations by applying the volume track method. In addition, the volume integral of the concerned variable for the whole bath is more representative to determine the developed flow compared to the points monitoring method for a transient simulation.
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| 4. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 5. |
- Barausse, Enrico, et al.
(författare)
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Prospects for fundamental physics with LISA
- 2020
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Ingår i: General Relativity and Gravitation. - : SPRINGER/PLENUM PUBLISHERS. - 0001-7701 .- 1572-9532. ; 52:8
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In this paper, which is of programmatic rather than quantitative nature, we aim to further delineate and sharpen the future potential of the LISA mission in the area of fundamental physics. Given the very broad range of topics that might be relevant to LISA,we present here a sample of what we view as particularly promising fundamental physics directions. We organize these directions through a "science-first" approach that allows us to classify how LISA data can inform theoretical physics in a variety of areas. For each of these theoretical physics classes, we identify the sources that are currently expected to provide the principal contribution to our knowledge, and the areas that need further development. The classification presented here should not be thought of as cast in stone, but rather as a fluid framework that is amenable to change with the flow of new insights in theoretical physics.
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| 7. |
- Klionsky, DJ, et al.
(författare)
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Autophagy in major human diseases
- 2021
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Ingår i: The EMBO journal. - : EMBO. - 1460-2075 .- 0261-4189. ; 40:19, s. e108863-
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Tidskriftsartikel (refereegranskat)
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| 8. |
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| 11. |
- Liu, X., et al.
(författare)
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Surface roughness prediction method of titanium alloy milling based on CDH platform
- 2022
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Ingår i: The International Journal of Advanced Manufacturing Technology. - : Springer Nature. - 0268-3768 .- 1433-3015. ; 119:11-12, s. 7145-7157
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Tidskriftsartikel (refereegranskat)abstract
- Generally, off-line methods are used for surface roughness prediction of titanium alloy milling. However, studies show that these methods have poor prediction accuracy. In order to resolve this shortcoming, a prediction method based on Cloudera’s Distribution including Apache Hadoop (CDH) platform is proposed in the present study. In this regard, data analysis and process platform are designed based on the CDH, which can upload, calculate, and store data in real time. Then this platform is combined with the Harris hawk optimization (HHO) algorithm and pattern search strategy, and an improved Harris hawk optimization optimization (IHHO) method is proposed accordingly. Then this method is applied to optimize the support vector machine (SVM) algorithm and predict the surface roughness in the CDH platform. The obtained results show that the prediction accuracy of IHHO method reaches 95%, which is higher than the conventional methods of SVM, BAT-SVM, gray wolf optimizer (GWO-SVM), and whale optimization algorithm (WOA-SVM).
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| 12. |
- Magni, Stefano, et al.
(författare)
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Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data
- 2024
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Ingår i: npj Systems Biology and Applications. - : Springer Nature. - 2056-7189. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of upstream regulatory genes of a gene of interest still remains challenging. Here we applied a scalable computational method to unbiasedly predict candidate regulatory genes of critical transcription factors by searching the whole genome. We illustrated our approach with a case study on the master regulator FOXP3 of human primary regulatory T cells (Tregs). While target genes of FOXP3 have been identified, its upstream regulatory machinery still remains elusive. Our methodology selected five top-ranked candidates that were tested via proof-of-concept experiments. Following knockdown, three out of five candidates showed significant effects on the mRNA expression of FOXP3 across multiple donors. This provides insights into the regulatory mechanisms modulating FOXP3 transcriptional expression in Tregs. Overall, at the genome level this represents a high level of accuracy in predicting upstream regulatory genes of key genes of interest.
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| 13. |
- Song, J., et al.
(författare)
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Clinical characteristics and long-term neurodevelopmental outcomes of leukomalacia in preterm infants and term infants: a cohort study
- 2023
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Ingår i: Journal of Neurodevelopmental Disorders. - 1866-1947 .- 1866-1955. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundLeukomalacia is a serious form of neonatal brain injury that often leads to neurodevelopmental impairment, and studies on neonatal leukomalacia and its long-term outcomes are lacking. The aim of this study was to analyze the clinical manifestations, imaging features, and long-term neurodevelopmental outcomes in preterm infants and term infants with leukomalacia.MethodsNewborns diagnosed with leukomalacia by head magnetic resonance imaging (MRI) and who were admitted to intensive care units from January 2015 to June 2020 were enrolled. All infants were followed up to June 2022 (2-7 years old), and their neurodevelopmental outcomes were evaluated. The clinical data and long- term outcomes of preterm infants and term infants was analyzed by Chi-square tests.ResultsA total of 218 surviving infants with leukomalacia including 114 preterm infants and 104 term infants completed the follow-up. The major typesof leukomalacia on MRI were periventricular leukomalacia in the preterm group and subcortical cystic leukomalacia in the term group, respectively (& chi;(2) = 55.166; p < 0.001). When followed up to 2-7 years old, the incidence of neurodevelopmental impairment in the preterm group and term group was not significantly different (& chi;(2) = 0.917; p = 0.338). However, the incidence of cerebral palsy (CP) in the preterm group was significantly higher (& chi;(2) = 4.896; p = 0.027), while the incidence of intellectual disability (ID) (& chi;(2) = 9.445; p = 0.002), epilepsy (EP) (& chi;(2) = 23.049; p < 0.001), and CP combined with ID andEP (& chi;(2) = 4.122; p = 0.042) was significantly lower than that in the term group.ConclusionsPeriventricular leukomalacia mainly occurred in preterm infants while subcortical cystic leukomalacia was commonly seen in term infants. Although the long-term neurodevelopmental outcomes of leukomalacia were both poor, preterm infants were more prone to CP, while term infants were more prone to ID, EP, and the combination of CP with ID and EP.
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| 14. |
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| 15. |
- Wang, Y., et al.
(författare)
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The Impact of Different Degrees of Intraventricular Hemorrhage on Mortality and Neurological Outcomes in Very Preterm Infants: A Prospective Cohort Study
- 2022
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Ingår i: Frontiers in Neurology. - : Frontiers Media SA. - 1664-2295. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- ObjectiveIntraventricular hemorrhage (IVH) is a common complication in preterm infants and is related to neurodevelopmental outcomes. Infants with severe IVH are at higher risk of adverse neurological outcomes and death, but the effect of low-grade IVH remains controversial. The purpose of this study was to evaluate the impact of different degrees of IVH on mortality and neurodevelopmental outcomes in very preterm infants. MethodsPreterm infants with a gestational age of ResultsA total of 1,079 preterm infants were included, and 380 (35.2%) infants had grade I-II IVH, 74 (6.9%) infants had grade III-IV IVH, and 625 (57.9%) infants did not have IVH. The mortality in the non-IVH, I-II IVH, and III-IV IVH groups was 20.1, 19.7, and 55.2%, respectively (p < 0.05), and the incidence of neurodevelopmental disabilities was 13.9, 16.1, and 43.3%, respectively (p < 0.05), at 18-24 months of corrected age. After adjusting for confounding factors, preterm infants with III-IV IVH had higher rates of cerebral palsy [26.7 vs. 2.4%, OR = 6.10, 95% CI (1.840-20.231), p = 0.003], disability [43.3 vs. 13.9%, OR = 2.49, 95% CI (1.059-5.873), p = 0.037], death [55.2 vs. 20.1%, OR = 3.84, 95% CI (2.090-7.067), p < 0.001], and disability + death [73.7 vs. 28.7%, OR = 4.77, 95% CI (2.518-9.021), p < 0.001] compared to those without IVH. However, the mortality and the incidence of neurodevelopmental disability in infants with I-II IVH were similar to those without IVH (p > 0.05). ConclusionsSevere IVH but not mild IVH increased the risk of mortality and neurodevelopmental disability in very preterm infants.
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| 16. |
- Wei, X., et al.
(författare)
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Research on parallel distributed clustering algorithm applied to cutting parameter optimization
- 2022
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Ingår i: The International Journal of Advanced Manufacturing Technology. - : Springer Nature. - 0268-3768 .- 1433-3015. ; 120:11-12, s. 7895-7904
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Tidskriftsartikel (refereegranskat)abstract
- In the big data era, traditional data mining technology cannot meet the requirements of massive data processing with the background of intelligent manufacturing. Aiming at insufficient computing power and low efficiency in mining process, this paper proposes a improved K-means clustering algorithm based on the concept of distributed clustering in cloud computing environment. The improved algorithm (T.K-means) is combined with MapReduce computing framework of Hadoop platform to realize parallel computing, so as to perform processing tasks of massive data. In order to verify the practical performance of T.K-means algorithm, taking machining data of milling Ti-6Al-4V alloy as the mining object. The mapping relationship among cutting parameters, surface roughness, and material removal rate is mined, and the optimized value for cutting parameters is obtained. The results show that T.K-means algorithm can be used to mine the optimal cutting parameters, so that the best surface roughness can be obtained in milling Ti-6Al-4V titanium alloy.
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| 17. |
- You, Q. L., et al.
(författare)
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Recent frontiers of climate changes in East Asia at global warming of 1.5 degrees C and 2 degrees C
- 2022
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Ingår i: npj Climate and Atmospheric Science. - : Springer Science and Business Media LLC. - 2397-3722. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- East Asia is undergoing significant climate changes and these changes are likely to grow in the future. It is urgent to characterize both the mechanisms controlling climate and the response of the East Asian climate system at global warming of 1.5 and 2 degrees C above pre-industrial levels (GW1.5 and GW2 hereafter). This study reviews recent studies on East Asian climate change at GW1.5 and GW2. The intensity and variability of the East Asian summer monsoon are expected to increase modestly, accompanied by an enhancement of water vapor transport. Other expected changes include the intensification of the Western Pacific Subtropical High and an intensified and southward shift of the East Asian jet, while the intensity of the East Asian winter monsoon is projected to reduce with high uncertainty. Meanwhile, the frequency of ENSO may increase in a warming world with great uncertainty. Significant warming and wetting occur in East Asia, with more pronounced intensity, frequency, and duration of climate extremes at GW2 than that at GW1.5. The fine structure of regional climate changes and the presence and location of various warming hotspots, however, show substantial divergence among different model simulations. Furthermore, the Asian climate responses can differ substantially between the transient and stabilized GW1.5 and GW2, which has important implications for emission policies. Thus, to better plan effective mitigation and adaptation activities, further research including an in-depth exploration of the divergent responses in transient versus stabilized scenarios, the quantification of future projection uncertainties, and improvements of the methods to reduce model uncertainties are required.
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| 18. |
- Zhou, X., et al.
(författare)
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Study on the Cavity Forming Induced by a Gas Jet Impinging on a Liquid Surface Based on a Deformed Mesh Method
- 2021
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Ingår i: JOM. - : Springer. - 1047-4838 .- 1543-1851. ; 73:10, s. 2953-2962
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Tidskriftsartikel (refereegranskat)abstract
- The current study focuses on the cavity formation induced by jet impingement with the help of numerical simulations based on a deformed mesh method. The interface between the liquid phase and gas phase separates the calculation domain into two single-phase domains, which exchange momentum data except for mass transfer. For the subsonic jet flow, the results show that the cavity depth is a decreasing function when the blowing height is increased, while the cavity diameter increases when increasing the blowing height. In addition, larger diameter of the nozzle will result in a deeper cavity because the jet flow attenuation becomes weaker. The simulation result shows good agreement with that of the theoretical equation on the cavity depth and diameter for the subsonic jet flow. In addition, the cavity formation created by the supersonic flow, which is treated as a compressible flow, can also be described by the developed model.
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