| 411. |
- Schreurs, Guido, et al.
(författare)
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Benchmarking analogue models of brittle thrust wedges
- 2016
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Ingår i: Journal of Structural Geology. - : Elsevier BV. - 0191-8141 .- 1873-1201. ; 92, s. 116-139
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Tidskriftsartikel (refereegranskat)abstract
- We performed a quantitative comparison of brittle thrust wedge experiments to evaluate the variability among analogue models and to appraise the reproducibility and limits of model interpretation. Fifteen analogue modeling laboratories participated in this benchmark initiative. Each laboratory received a shipment of the same type of quartz and corundum sand and all laboratories adhered to a stringent model building protocol and used the same type of foil to cover base and sidewalls of the sandbox. Sieve structure, sifting height, filling rate, and details on off-scraping of excess sand followed prescribed procedures. Our analogue benchmark shows that even for simple plane-strain experiments with prescribed stringent model construction techniques, quantitative model results show variability, most notably for surface slope, thrust spacing and number of forward and backthrusts. One of the sources of the variability in model results is related to slight variations in how sand is deposited in the sandbox. Small changes in sifting height, sifting rate, and scraping will result in slightly heterogeneous material bulk densities, which will affect the mechanical properties of the sand, and will result in lateral and vertical differences in peak and boundary friction angles, as well as cohesion values once the model is constructed. Initial variations in basal friction are inferred to play the most important role in causing model variability. Our comparison shows that the human factor plays a decisive role, and even when one modeler repeats the same experiment, quantitative model results still show variability. Our observations highlight the limits of up-scaling quantitative analogue model results to nature or for making comparisons with numerical models. The frictional behavior of sand is highly sensitive to small variations in material state or experimental set-up, and hence, it will remain difficult to scale quantitative results such as number of thrusts, thrust spacing, and pop-up width from model to nature.
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| 412. |
- Senanayake, Indunil C., et al.
(författare)
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Fungal diversity notes 1611–1716: taxonomic and phylogenetic contributions on fungal genera and species emphasis in south China
- 2023
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Ingår i: Fungal Diversity. - 1560-2745 .- 1878-9129. ; 122, s. 161-403
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Tidskriftsartikel (refereegranskat)abstract
- This article is the 15th contribution in the Fungal Diversity Notes series, wherein 115 taxa from three phyla, nine classes, 28 orders, 48 families, and 64 genera are treated. Fungal taxa described and illustrated in the present study include a new family, five new genera, 61 new species, five new combinations, one synonym, one new variety and 31 records on new hosts or new geographical distributions. Ageratinicolaceae fam. nov. is introduced and accommodated in Pleosporales. The new genera introduced in this study are Ageratinicola, Kevinia, Pseudomultiseptospora (Parabambusicolaceae), Marasmiellomycena, and Vizzinia (Porotheleaceae). Newly described species are Abrothallus altoandinus, Ageratinicola kunmingensis, Allocryptovalsa aceris, Allophoma yuccae, Apiospora cannae, A. elliptica, A. pallidesporae, Boeremia wisteriae, Calycina papaeana, Clypeococcum lichenostigmoides, Coniochaeta riskali-shoyakubovii, Cryphonectria kunmingensis, Diaporthe angustiapiculata, D. campylandrae, D. longipapillata, Diatrypella guangdongense, Dothiorella franceschinii, Endocalyx phoenicis, Epicoccum terminosporum, Fulvifomes karaiensis, F. pannaensis, Ganoderma ghatensis, Hysterobrevium baoshanense, Inocybe avellaneorosea, I. lucida, Jahnula oblonga, Kevinia lignicola, Kirschsteiniothelia guangdongensis, Laboulbenia caprina, L. clavulata, L. cobiae, L. cosmodisci, L. nilotica, L. omalii, L. robusta, L. similis, L. stigmatophora, Laccaria rubriporus, Lasiodiplodia morindae, Lyophyllum agnijum, Marasmiellomycena pseudoomphaliiformis, Melomastia beihaiensis, Nemania guangdongensis, Nigrograna thailandica, Nigrospora ficuum, Oxydothis chinensis, O. yunnanensis, Petriella thailandica, Phaeoacremonium chinensis, Phialocephala chinensis, Phytophthora debattistii, Polyplosphaeria nigrospora, Pronectria loweniae, Seriascoma acutispora, Setoseptoria bambusae, Stictis anomianthi, Tarzetta tibetensis, Tarzetta urceolata, Tetraploa obpyriformis, Trichoglossum beninense, and Tricoderma pyrrosiae. We provide an emendation for Urnula ailaoshanensis Agaricus duplocingulatoides var. brevisporus introduced as a new variety based on morphology and phylogeny.
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| 413. |
- Shen, Tianyin, et al.
(författare)
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Secular Changes of the Decadal Relationship Between the Northern Hemisphere Land Monsoon Rainfall and Sea Surface Temperature Over the Past Millennium in Climate Model Simulations
- 2022
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Ingår i: Journal of Geophysical Research: Atmospheres. - 2169-897X .- 2169-8996. ; 127:23
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the decadal variability of Northern Hemisphere land monsoon rainfall (NHLMR) is crucial to social-economic development. However, due to the temporal limitation of instrumental data, the decadal relationship between NHLMR and sea surface temperature (SST) remains uncertain. The extended El Niño–Southern Oscillation (XEN) SST index and the North Atlantic–south Indian Ocean dipole (NAID) SST index can be the predictors to help us understand the decadal relationship between NHLMR and SST. In this study, using the Community Earth System Model-Last Millennium Ensemble (CESM-LME) simulations, we find a significant and stable decadal correlation between the NHLMR and XEN in the all-forcing (AF) (with natural and anthropogenic forcings, AF), control (internal variability only), and other external forcings run over the past millennium, which means that this simulated NHLMR-XEN relationship is caused by internal variability. The AF experiments show that the decadal relationship between NHLMR and NAID is practically non-existent until an abrupt and significant increase in volcanic eruptions at about 1700, which is also indicated by the Paleoclimate Modeling Intercomparison Project Phase 3 (Paleoclimate Modeling Intercomparison Project Phase 3) simulations. Using the volcanic forcing sensitivity experiments, we find that the successive strong volcanic eruptions in the Northern Hemisphere (NH) significantly strengthen the synchronous changes of NHLMR and NAID after 1700, with a periodicity of 20–40-year for NHLMR and NAID. Specifically, successive NH eruptions weaken the north-south hemispheric thermal contrast, contributing to the weakened NAID index. The cross-equator flow is thus weakened, decreasing the NHLMR, which cause a resonant behavior of NHLMR and NAID.
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| 414. |
- Shen, Zhao-Li, et al.
(författare)
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Preconditioned weighted full orothogonalization method for solving singular linear systems from PageRank problems
- 2023
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Ingår i: Numerical Linear Algebra with Applications. - : Wiley. - 1070-5325 .- 1099-1506.
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Tidskriftsartikel (refereegranskat)abstract
- The PageRank model, which was first proposed by Google for its web search engine application, has since become a popular computational tool in a wide range of scientific fields, including chemistry, bioinformatics, neuroscience, bibliometrics, social networks, and others. PageRank calculations necessitate the use of fast computational techniques with low algorithmic and memory complexity. In recent years, much attention has been paid to Krylov subspace algorithms for solving difficult PageRank linear systems, such as those with large damping parameters close to one. In this article, we examine the full orthogonalization method (FOM). We present a convergence study of the method that extends and clarifies part of the conclusions reached in Zhang et al. (J Comput Appl Math. 2016; 296:397–409.). Furthermore, we demonstrate that FOM is breakdown free when solving singular PageRank linear systems with index one and we investigate the effect of using weighted innerâ€products instead of conventional innerâ€products in the orthonormalization procedure on FOM convergence. Finally, we develop a shifted polynomial preconditioner that takes advantage of the special structure of the PageRank linear system and has a good ability to cluster most of the eigenvalues, making it a good choice for an iterative method like FOM or GMRES. Numerical experiments are presented to support the theoretical findings and to evaluate the performance of the new weighted preconditioned FOM PageRank solver in comparison to other established solvers for this class of problem, including conventional stationary methods, hybrid combinations of stationary and Krylov subspace methods, and multiâ€step splitting strategies.
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| 415. |
- Shi, Tian-Le, et al.
(författare)
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Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values
- 2024
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
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| 416. |
- Shi, Tian-Le, et al.
(författare)
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High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar
- 2024
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Ingår i: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 195:1, s. 652-670
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Tidskriftsartikel (refereegranskat)abstract
- Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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| 417. |
- Shi, Xin, et al.
(författare)
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X-ray transient absorption spectroscopy by an ultrashort x-ray-laser pulse in a continuous-wave IR field
- 2020
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 101:2
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Tidskriftsartikel (refereegranskat)abstract
- X-ray transient absorption spectra (XTAS) of molecules are theoretically investigated in a femtosecond x-ray pump and continuous-wave (cw) infrared (IR)-control scenario. The scheme is exemplified by a CO molecule resonantly pumped into carbon and oxygen core-excited 1s -> 7r* states by a weak femtosecond x-ray pulse, while dynamic Stark shifts are induced by the cw IR-control radiation. As a result, significant shoulder structures appear in XTAS showing strong dependence on the phase of IR radiation relative to the envelope of the x-ray pulse. Due to a significant difference in the frequencies of the two pulses, the present XTAS scheme provides much clear interpretation of the dynamic Stark effects as compared to the attosecond UV transient absorption scenario. Within the suggested two-level model, where the total spectrum is decomposed as incoherent superposition of contributions from different vibrational excitations weighted by the Franck-Condon Factors, all spectral structures can be well identified and interpreted in a good agreement with the full-scale molecular simulations. Well-characterized XTAS in the proposed IR-control scheme can be applied for fine phase synchronization between IR and x-ray pulses, highly demanded in modern experiments on x-ray free-electron lasers.
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| 418. |
- Shi, Ying, et al.
(författare)
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Effects of low-molecular-weight polyols on the hydration status of the light-harvesting complex 2 from Rhodobacter sphaeroides 2.4.1
- 2021
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Ingår i: Photochemical and Photobiological Sciences. - : Springer Science and Business Media LLC. - 1474-905X .- 1474-9092. ; 20:5, s. 627-637
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Tidskriftsartikel (refereegranskat)abstract
- Low-molecular-weight (MW) polyols are organic osmolytes influencing water activity. We have investigated the effects of polyol molecules (glycerol and sorbitol) on the optical and triplet excitation dynamics of light-harvesting complex 2 (LH2) from Rhodobacter (Rba.) sphaeroides in buffer-detergent solutions. The resonance Raman spectroscopy demonstrated that, on increasing glycerol and sorbitol volume fractions ranging from 0 to 80% (v/v) (accompanied by the decreasing water activities), the planar and all-trans conformation of carotenoids (Crts) remained unchanged, and the bacteriochlorophyll a (BChl) Qy absorption intensity decreased. The B850 fluorescence amplitude elevated in the 20–80% v/v sorbitol and 20–40% v/v glycerol solution, but decreased in 80% v/v glycerol solution. The change of 3[Crt*–BChl] interaction bands caused by 3Crt*–BChl interaction had no obvious correlation with water activities against polyol volume fractions, which are rationalized by the water activity sensitive of C- and N-termini of protein which binding with BChls. The results suggest that Rba. sphaeroides LH2 is more sensitive to low-molecular-weight polyols compared with that of the thermophiles purple bacterium Thermochromatium (Tch.) tepidum we had investigated before. Graphic abstract: [Figure not available: see fulltext.]
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| 419. |
- Shibayama, Sotaro, et al.
(författare)
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Measuring originality in science
- 2020
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Ingår i: Scientometrics. - : Springer Science and Business Media LLC. - 1588-2861 .- 0138-9130. ; 122:1, s. 409-427
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Tidskriftsartikel (refereegranskat)abstract
- Originality has self-evident importance for science, but objectively measuring originality poses a formidable challenge. We conceptualise originality as the degree to which a scientific discovery provides subsequent studies with unique knowledge that is not available from previous studies. Accordingly, we operationalise a new measure of originality for individual scientific papers building on the network betweenness centrality concept. Specifically, we measure the originality of a paper based on the directed citation network between its references and the subsequent papers citing it. We demonstrate the validity of this measure using survey information. In particular, we find that the proposed measure is positively correlated with the self-assessed theoretical originality but not with the methodological originality. We also find that originality can be reliably measured with only a small number of subsequent citing papers, which lowers computational cost and contributes to practical utility. The measure also predicts future citations, further confirming its validity. We further characterise the measure to guide its future use.
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| 420. |
- Shrivastava, Manish, et al.
(författare)
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Recent advances in understanding secondary organic aerosol : Implications for global climate forcing
- 2017
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Ingår i: Reviews of Geophysics. - 8755-1209. ; 55:2, s. 509-559
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Tidskriftsartikel (refereegranskat)abstract
- Anthropogenic emissions and land use changes have modified atmospheric aerosol concentrations and size distributions over time. Understanding preindustrial conditions and changes in organic aerosol due to anthropogenic activities is important because these features (1) influence estimates of aerosol radiative forcing and (2) can confound estimates of the historical response of climate to increases in greenhouse gases. Secondary organic aerosol (SOA), formed in the atmosphere by oxidation of organic gases, represents a major fraction of global submicron-sized atmospheric organic aerosol. Over the past decade, significant advances in understanding SOA properties and formation mechanisms have occurred through measurements, yet current climate models typically do not comprehensively include all important processes. This review summarizes some of the important developments during the past decade in understanding SOA formation. We highlight the importance of some processes that influence the growth of SOA particles to sizes relevant for clouds and radiative forcing, including formation of extremely low volatility organics in the gas phase, acid-catalyzed multiphase chemistry of isoprene epoxydiols, particle-phase oligomerization, and physical properties such as volatility and viscosity. Several SOA processes highlighted in this review are complex and interdependent and have nonlinear effects on the properties, formation, and evolution of SOA. Current global models neglect this complexity and nonlinearity and thus are less likely to accurately predict the climate forcing of SOA and project future climate sensitivity to greenhouse gases. Efforts are also needed to rank the most influential processes and nonlinear process-related interactions, so that these processes can be accurately represented in atmospheric chemistry-climate models.
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