| 1. |
- Chen, Zhi-Qiang, et al.
(författare)
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Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
- 2021
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.Results: We identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery.Conclusion: Several important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.
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| 2. |
- Chen, Min Rui, et al.
(författare)
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Effects of nanoparticles on hydraulic cavitation
- 2018
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Ingår i: XI International Conference on Computational Heat, Mass and Momentum Transfer (ICCHMT 2018). - : EDP Sciences. ; 240
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Konferensbidrag (refereegranskat)abstract
- When liquids flowing through a throttling element, such as a perforated plate, the velocity increases and the pressure decreases. If the pressure is below the saturated vapor pressure, the liquid will vaporize into small bubbles, which is called hydraulic cavitation. In fact, vaporization nucleus is another crucial condition for vaporizing. The nanoparticles contained in the nanofluids play a significant role in vaporization of liquids. In this paper, the effects of the nanoparticles on hydraulic cavitation are investigated. Firstly, a geometric model of a pipe channel equipped with a perforated plate is established. Then with different nanoparticle volume fractions and diameters, the nanofluids flowing through the channel is numerically simulated based on a validated numerical method. The operation conditions, such as the temperature and the pressure ratio of inlet to outlet, are the considered variables. As a significant parameter, cavitation numbers under different operation conditions are achieved to investigate the effects of nanoparticles on hydraulic cavitation. Meanwhile, the contours are extracted to research the distribution of bubbles for further investigation. This study is of interests for researchers working on hydraulic cavitation or nanofluids.
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| 3. |
- Chen, Min Rui, et al.
(författare)
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The hydraulic cavitation affected by nanoparticles in nanofluids
- 2018
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Ingår i: Computation. - : MDPI AG. - 2079-3197. ; 6:3
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Tidskriftsartikel (refereegranskat)abstract
- When liquids flow through a throttling element, the velocity increases and the pressure decreases. At this point, if the pressure is below the saturated vapor pressure of this liquid, the liquid will vaporize into small bubbles, causing hydraulic cavitation. In fact, a vaporization nucleus is another crucial condition for vaporizing, and particles contained in the liquid can also work as the vaporization nuclear. As a novel heat transfer medium, nanofluids have attracted the attention of many scholars. The nanoparticles contained in the nanofluids play a significant role in the vaporization of liquids. In this paper, the effects of the nanoparticles on hydraulic cavitation are investigated. Firstly, a geometric model of a perforated plate, the throttling element in this paper, is established. Then with different nanoparticle volume fractions and diameters, the nanofluids flowing through the perforated plate are numerically simulated based on a validated numerical method. The operation conditions, such as the ratio of inlet to outlet pressures and the temperature are the considered variables. Additionally, cavitation numbers under different operating conditions are achieved to investigate the effects of nanoparticles on hydraulic cavitation. Meanwhile, the contours are extracted to research the distribution of bubbles for further investigation. This study is of interest for researchers working on hydraulic cavitation or nanofluids.
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| 4. |
- Ruggeri, Kai, et al.
(författare)
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The globalizability of temporal discounting
- 2022
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Ingår i: Nature Human Behaviour. - : Springer Nature. - 2397-3374. ; 6:10, s. 1386-1397
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Tidskriftsartikel (refereegranskat)abstract
- Economic inequality is associated with preferences for smaller, immediate gains over larger, delayed ones. Such temporal discounting may feed into rising global inequality, yet it is unclear whether it is a function of choice preferences or norms, or rather the absence of sufficient resources for immediate needs. It is also not clear whether these reflect true differences in choice patterns between income groups. We tested temporal discounting and five intertemporal choice anomalies using local currencies and value standards in 61 countries (N = 13,629). Across a diverse sample, we found consistent, robust rates of choice anomalies. Lower-income groups were not significantly different, but economic inequality and broader financial circumstances were clearly correlated with population choice patterns. Ruggeri et al. find in a study of 61 countries that temporal discounting patterns are globally generalizable. Worse financial environments, greater inequality and high inflation are associated with extreme or inconsistent long-term decisions.
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| 5. |
- Wang, Anqi, et al.
(författare)
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Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants
- 2023
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 55:12, s. 2065-2074
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Tidskriftsartikel (refereegranskat)abstract
- The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls of European, African, Asian and Hispanic men, reflecting a 57% increase in the number of non-European cases over previous prostate cancer genome-wide association studies. We identified 187 novel risk variants for prostate cancer, increasing the total number of risk variants to 451. An externally replicated multi-ancestry GRS was associated with risk that ranged from 1.8 (per standard deviation) in African ancestry men to 2.2 in European ancestry men. The GRS was associated with a greater risk of aggressive versus non-aggressive disease in men of African ancestry (P = 0.03). Our study presents novel prostate cancer susceptibility loci and a GRS with effective risk stratification across ancestry groups.
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| 6. |
- Yang, Chen, et al.
(författare)
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Heat transfer study on a hybrid smooth and spirally corrugated tube
- 2018
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Ingår i: XI International Conference on Computational Heat, Mass and Momentum Transfer (ICCHMT 2018). - : EDP Sciences. ; 240
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Konferensbidrag (refereegranskat)abstract
- Corrugated tubes are widely used in a range of applications for heat transfer enhancement. The spirally corrugated tube has a better heat transfer performance than the smooth tube. In this paper, the heat transfer performance of a hybrid smooth and six-start spirally corrugated tube is studied. With a validated numerical model, the effects of the corrugation part length on the vortex in the downstream smooth tube are studied for a range of high Reynolds numbers, where the existence of the corrugation part can turn out the secondary flow and enhance heat transfer. Meanwhile, it is found that in the smooth part, the fluid flow part with whirling can reach a maximum length, even if the length of the corrugation part continuously increases. Thus a series of critical corrugation lengths can be obtained. This work can reveal the enhanced heat transfer mechanism of the hybrid smooth and spirally corrugated tube and be of interest to researchers in heat transfer issues of corrugated tubes.
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| 7. |
- Bernhardsson, Carolina, et al.
(författare)
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Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species
- 2021
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 21:3, s. 880-896
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Tidskriftsartikel (refereegranskat)abstract
- Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome-wide association studies (GWAS) and genomic selection (GS), in Norway spruce and related species, we here report on the design and performance of a 50K single nucleotide polymorphism (SNP) genotyping array for Norway spruce. The array is developed based on whole genome resequencing (WGS), making it the first WGS-based SNP array in any conifer species so far. After identifying SNPs using genome resequencing data from 29 trees collected in northern Europe, we adopted a two-step approach to design the array. First, we built a 450K screening array and used this to genotype a population of 480 trees sampled from both natural and breeding populations across the Norway spruce distribution range. These samples were then used to select high-confidence probes that were put on the final 50K array. The SNPs selected are distributed over 45,552 scaffolds from the P. abies version 1.0 genome assembly and target 19,954 unique gene models with an even coverage of the 12 linkage groups in Norway spruce. We show that the array has a 99.5% probe specificity, >98% Mendelian allelic inheritance concordance, an average sample call rate of 96.30% and an SNP call rate of 98.90% in family trios and haploid tissues. We also observed that 23,797 probes (50%) could be identified with high confidence in three other spruce species (white spruce [Picea glauca], black spruce [P. mariana] and Sitka spruce [P. sitchensis]). The high-quality genotyping array will be a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.
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| 8. |
- Chen, Jie, 1974-
(författare)
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Empirical Essays on Housing Allowance, Housing Wealth, and Aggregate Consumption
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This dissertation consists of four self-contained essays.Essay I (with Cecilia Enström Öst) investigates whether housing allowance affects recipients’ tenure choice in Sweden. A two-stage conditional maxi-mum likelihood probit (2SCMLP) model is applied in a panel data setting to simultaneously control for individual heterogeneity, state dependence and endogeneity. The empirical study is based on administrative data of housing allowance recipients between the years 1994 and 2002. Our results indicate that the housing allowance positively affects recipients’ homeownership propensity in Sweden. Essay II investigates whether the Swedish housing allowance system creates dependence on welfare in recipients. Using longitudinal data from Swedish micro database-LINDA, this paper found that there is no evidence of nega-tive duration dependence among the Swedish housing allowance spells. This finding is consistent across different model specifications and various con-trols of the heterogeneity issue. Essay III analyzes the impacts of the 1997 reform of Swedish housing al-lowance system on affected recipients’ exit hazards using the DD (differ-ence-in-difference) estimation strategy. This paper found strong evidence that the 1997 reform positively shifted up the conditional exiting probability of the couple with children recipient group, and the estimated magnitude of impact is sizable.Essay IV extends the VECM (Vector Error Correction Cointegration Model) and PT (permanent-transitory) variance decomposition framework proposed by Lettau & Ludvigson (2004) to a situation in which total wealth is disag-gregated into housing wealth and financial wealth. The empirical studies are based on the Swedish aggregate quarterly data spanning from 1980q1 to 2004q4. We found strong statistical evidence that the movements of total consumption expenditures, disposable income, housing wealth and financial wealth are tied together. It is also shown that the movements of housing wealth in Sweden contain a large proportion of transitory component.
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| 9. |
- Chen, Zhi-Qiang, et al.
(författare)
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Genetic architecture behind developmental and seasonal control of tree growth and wood properties in Norway spruce
- 2022
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover similar to 130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multilocus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide toots for future Norway spruce breeding and functional studies.
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| 10. |
- Daitch, Allison K., et al.
(författare)
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EstG is a novel esterase required for cell envelope integrity in Caulobacter
- 2023
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Ingår i: Current Biology. - : Cell Press. - 0960-9822 .- 1879-0445. ; 33:2, s. 228-240.e7
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Tidskriftsartikel (refereegranskat)abstract
- Proper regulation of the bacterial cell envelope is critical for cell survival. Identification and characterization of enzymes that maintain cell envelope homeostasis is crucial, as they can be targets for effective antibiotics. In this study, we have identified a novel enzyme, called EstG, whose activity protects cells from a variety of lethal assaults in the ⍺-proteobacterium Caulobacter crescentus. Despite homology to transpeptidase family cell wall enzymes and an ability to protect against cell-wall-targeting antibiotics, EstG does not demonstrate biochemical activity toward cell wall substrates. Instead, EstG is genetically connected to the periplasmic enzymes OpgH and BglX, responsible for synthesis and hydrolysis of osmoregulated periplasmic glucans (OPGs), respectively. The crystal structure of EstG revealed similarities to esterases and transesterases, and we demonstrated esterase activity of EstG in vitro. Using biochemical fractionation, we identified a cyclic hexamer of glucose as a likely substrate of EstG. This molecule is the first OPG described in Caulobacter and establishes a novel class of OPGs, the regulation and modification of which are important for stress survival and adaptation to fluctuating environments. Our data indicate that EstG, BglX, and OpgH comprise a previously unknown OPG pathway in Caulobacter. Ultimately, we propose that EstG is a novel enzyme that instead of acting on the cell wall, acts on cyclic OPGs to provide resistance to a variety of cellular stresses.
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