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| 5. |
- Abdoullaye, Doukary, et al.
(författare)
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Permanent genetic resources added to molecular ecology resources database 1 August 2009 - 30 September 2009
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:1, s. 232-236
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.
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| 6. |
- Chen, Si, et al.
(författare)
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A graphene field-effect capacitor sensor in electrolyte
- 2012
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 101:15, s. 154106-
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Tidskriftsartikel (refereegranskat)abstract
- The unique electronic properties of graphene are exploited for field-effect sensing in both capacitor and transistor modes when operating the sensor device in electrolyte. The device is fabricated using large-area graphene thin films prepared by means of layer-by-layer stacking. Although essentially the same device, its operation in the capacitor mode is found to yield more information than in the transistor mode. The capacitor sensor can simultaneously detect the variations of surface potential and electrical-double-layer capacitance at the graphene/electrolyte interface when altering the ion concentration. The capacitor-mode operation further facilitates studies of the molecular binding-adsorption kinetics by monitoring the capacitance transient
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| 7. |
- Duan, Sai, et al.
(författare)
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A density functional theory approach to mushroom-like platinum clusters on palladium-shell over Au core nanoparticles for high electrocatalytic activity
- 2011
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - Cambridge : ROYAL SOC CHEMISTRY. - 1463-9076 .- 1463-9084. ; 13:12, s. 5441-5449
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Tidskriftsartikel (refereegranskat)abstract
- Recently, it was found that Pt clusters deposited on Pd shell over Au core nanoparticles (Au@Pd@Pt NPs) exhibit unusually high electrocatalytic activity for the electro-oxidation of formic acid (P. P. Fang, S. Duan, et al., Chem. Sci., 2011, 2, 531-539). In an attempt to offer an explanation, we used here carbon monoxide (CO) as probed molecules, and applied density functional theory (DFT) to simulate the surface Raman spectra of CO at this core-shell-cluster NPs with a two monolayer thickness of Pd shell and various Pt cluster coverage. Our DFT results show that the calculated Pt coverage dependent spectra fit the experimental ones well only if the Pt clusters adopt a mushroom-like structure, while currently the island-like structure is the widely accepted model, which follows the Volmer-Weber growth mode. This result infers that there should be a new growth mode, i.e., the mushroom growth mode as proposed in the present work, for Au@Pd@Pt NPs. We suggest that such a mushroom-like structure may offer novel active sites, which accounts for the observed high electrocatalytic activity of Au@Pd@Pt NPs.
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| 8. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 9. |
- Fang, Li Tai, et al.
(författare)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Tidskriftsartikel (refereegranskat)abstract
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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| 10. |
- Georgiou, Konstantinos, et al.
(författare)
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Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas
- 2016
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 127:24, s. 3026-3034
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Tidskriftsartikel (refereegranskat)abstract
- Diffuse large B-cell lymphoma (DLBCL) is one of the most common and aggressive types of B-cell lymphoma. Deregulation of proto-oncogene expression after a translocation, most notably to the immunoglobulin heavy-chain locus (IGH), is one of the hallmarks of DLBCL. Using whole-genome sequencing analysis, we have identified the PD-L1/PD-L2 locus as a recurrent translocation partner for IGH in DLBCL. PIM1 and TP63 were also identified as novel translocation partners for PD-L1/PD-L2. Fluorescence in situ hybridization was furthermore used to rapidly screen an expanded DLBCL cohort. Collectively, a subset of samples was found to be affected by gains (12%), amplifications (3%), and translocations (4%) of the PD-L1/PD-L2 locus. RNA sequencing data coupled with immunohistochemistry revealed that these cytogenetic alterations correlated with increased expression of PD-L1 but not of PD-L2. Moreover, cytogenetic alterations affecting the PD-L1/PD-L2 locus were more frequently observed in the non-germinal center B cell-like (non-GCB) subtype of DLBCL. These findings demonstrate the genetic basis of PD-L1 overexpression in DLBCL and suggest that treatments targeting the PD-1-PD-L1/PD-L2 axis might benefit DLBCL patients, especially those belonging to the more aggressive non-GCB subtype.
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| 11. |
- Harper, David A. T., et al.
(författare)
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Biodiversity, biogeography and phylogeography of Ordovician rhynchonelliform brachiopods
- 2013
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Ingår i: EARLY PALAEOZOIC BIOGEOGRAPHY AND PALAEOGEOGRAPHY. - 0435-4052. ; :38, s. 127-144
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Konferensbidrag (refereegranskat)abstract
- The phylogeographical evolution and the consequent changing distribution and diversity of rhynchonelliform brachiopods through the Ordovician are linked to the dynamic palaeogeography of the period. The Early Ordovician (Tremadocian and Floian) is characterized by globally low-diversity faunas with local biodiversity epicentres, notably on the South China Palaeoplate; low-latitude porambonitoid-dominated faunas with early plectambonitoid and clitambonitoid representatives, as well as high-latitude assemblages mostly dominated by orthoids, can be recognized, but many taxa are rooted in Late Cambrian stocks. The Early Ordovician displays a steady increase in rhynchonelliformean biodiversity, which was mostly driven by the increasing success of the Porambonitoidea and Orthoidea, but the billingsellids and early plectambonitoids also contributed to this expansion. During the Early to Mid Ordovician (Dapingian-Darriwilian), marine life experienced an unprecedented hike in diversity at the species, genus and family levels that firmly installed the suspension-feeding benthos as the main component of the Palaeozoic fauna. However, this may have occurred in response to an early Darriwilian annihilation of existing clades, some of which had been most successful during the Early Ordovician. New clades rapidly expanded. The continents were widely dispersed together with a large number of microcontinents and volcanic arcs related to intense magmatic and tectonic activity. Climates were warm and sea-levels were high. Pivotal to the entire diversification is the role of gamma (inter-provincial) diversity and by implication the spread of the continents and frequency of island arcs and microcontinents. The phylogeographical analysis demonstrates that this new palaeogeographical configuration was particularly well explored and utilized by the strophomenides, especially the Plectambonitoidea, which radiated rapidly during this interval. The porambonitoids, on the other hand, were still in recovery following the early Darriwilian extinctions. Orthides remained dominant, particularly at high latitudes. Biodiversity epicentres were located on most of the larger palaeoplates, as well as within the Iapetus Ocean. Provincial patterns were disrupted during the Sandbian and early Katian with the migration of many elements of the benthos into deeper-water regimes, enjoying a more cosmopolitan distribution. Later Katian faunas exhibit a partition between carbonate and clastic environments. During the latest Katian, biogeographical patterns were disrupted by polewards migrations of warm-water taxa in response to the changing climate; possibly as a consequence of low-latitude cradles being developed in, for instance, carbonate reef settings. Many clades were well established with especially the strophomenides beginning to outnumber the previously successful orthides, although this process had already begun, regionally, in the mid to late Darriwilian. At the same time, atrypoid and pentameroid clades also began to radiate in low-latitude faunas, anticipating their dominance in Silurian faunas. The Hirnantian was marked by severe extinctions particularly across orthidestrophomenide clades within the context of few, but well-defined, climatically controlled provincial belts.
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| 12. |
- Harper, David A.T., et al.
(författare)
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Late Ordovician deep-water brachiopod fauna from Raheen, Waterford harbour, Ireland
- 2017
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Ingår i: Irish Journal of Earth Sciences. - 0790-1763. ; 35, s. 1-18
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Tidskriftsartikel (refereegranskat)abstract
- The Raheen Formation at Newtown Head in Waterford Harbour is a small isolated section of Ordovician rocks, dominated by volcanics of the Duncannon Group, but with interbedded fossiliferous shales. Although a brachiopod and trilobite dominated fauna has been known since the mid-nineteenth century, only the trilobites and cystoids have been assessed in modern terms. This paper describes the brachiopod fauna for the first time. The assemblage from Raheen is overwhelmingly dominated by the dalmanelloid Onniella, with the small plectambonitoid Sericoidea comprising the second most numerous species; both are represented by new species. This revision has also identified a wide range of other genera, but all in very small numbers. These include an obolid, a paterulid, Paracraniops and Orthisocrania divaricata (M‘Coy) amongst the non-articulated brachiopods. Articulated genera present include the orthoids Nicolella, Ptychopleurella, Sulevorthis, Skenidioides and the plectambonitoid Leptestiina. Very rare forms include Idiospira? and Palaeostrophomena, together with possibly Biscuspina and Sowerbyella. The brachiopod revision supports the late Caradoc (early Katian) age indicated by the trilobite fauna. The trilobite fauna generally indicates a probable deeper-water environment and the brachiopod assemblage confirms an outer-shelf environment. Although elements of the assemblage indicate affinity with the well-defined Late Ordovician Foliomena fauna, it probably occupied a more shoreward position.
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| 13. |
- Hinnemo, Malkolm, et al.
(författare)
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Scalable residue-free graphene for surface-enhanced Raman scattering
- 2016
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Ingår i: Carbon. - : Elsevier BV. - 0008-6223 .- 1873-3891. ; 98, s. 567-571
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Tidskriftsartikel (refereegranskat)abstract
- A room-temperature polymer-assisted transfer process is developed for large-area, single-layer graphene grown by means of chemical vapor deposition (CVD). This process leads to transferred graphene layers free of polymer contamination. The absence of polymer residues boosts the surface-enhanced Raman scattering (SERS) of the CVD graphene with gold nanoparticles (Au NPs) deposited atop by evaporation. The SERS enhancement of the CVD graphene reaches similar to 120 for the characteristic 2D peak of graphene, the highest enhancement factor achieved to date, when the Au NPs are at the threshold of percolation. Our simulation supported by experiment suggests that the polymer residues persistently present on the graphene transferred by the conventional polymer-assisted method are equivalent to an ultrathin film of less than 1 nm thickness. The presence of polymer residues drastically reduces SERS due to the separation of the Au NPs from the underlying graphene. The scalability of CVD graphene opens up for the possibility of graphene-based SERS sensors.
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| 14. |
- Hu, Hai-Xi, et al.
(författare)
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Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- The one-dimensional pattern of heterocyst in the model cyanobacterium Anabaena sp. PCC 7120 is coordinated by the transcription factor HetR and PatS peptide. Here we report the complex structures of HetR binding to DNA, and its hood domain (HetR(Hood)) binding to a PatS-derived hexapeptide (PatS6) at 2.80 and 2.10 angstrom, respectively. The intertwined HetR dimer possesses a couple of novel HTH motifs, each of which consists of two canonical alpha-helices in the DNA-binding domain and an auxiliary alpha-helix from the flap domain of the neighboring subunit. Two PatS6 peptides bind to the lateral clefts of HetR(Hood), and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary alpha-helix and eventually release of HetR from the DNA major grove. These findings provide the structural insights into a prokaryotic example of Turing model.
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| 15. |
- Ji, Fuxiang, 1991-, et al.
(författare)
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Remarkable Thermochromism in the Double Perovskite Cs2NaFeCl6
- 2023
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Ingår i: Advanced Optical Materials. - : Wiley-Blackwell. - 2162-7568 .- 2195-1071.
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Tidskriftsartikel (refereegranskat)abstract
- Lead-free halide double perovskites (HDPs) have emerged as a new generation of thermochromic materials. However, further materials development and mechanistic understanding are required. Here, a highly stable HDP Cs2NaFeCl6 single crystal is synthesized, and its remarkable and fully reversible thermochromism with a wide color variation from light-yellow to black over a temperature range of 10 to 423 K is investigated. First-principles, density functional theory (DFT)-based calculations indicate that the thermochromism in Cs2NaFeCl6 is an effect of electron–phonon coupling. The temperature sensitivity of the bandgap in Cs2NaFeCl6 is up to 2.52 meVK−1 based on the Varshni equation, which is significantly higher than that of lead halide perovskites and many conventional group-IV, III–V semiconductors. Meanwhile, this material shows excellent environmental, thermal, and thermochromic cycle stability. This work provides valuable insights into HDPs' thermochromism and sheds new light on developing efficient thermochromic materials.
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| 16. |
- Ji, Fuxiang, 1991-, et al.
(författare)
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Remarkable Thermochromism in the Double Perovskite Cs2NaFeCl6
- 2024
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Ingår i: Advanced Optical Materials. - : John Wiley & Sons. - 2162-7568 .- 2195-1071. ; 12:8
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Tidskriftsartikel (refereegranskat)abstract
- Lead-free halide double perovskites (HDPs) have emerged as a new generation of thermochromic materials. However, further materials development and mechanistic understanding are required. Here, a highly stable HDP Cs2NaFeCl6 single crystal is synthesized, and its remarkable and fully reversible thermochromism with a wide color variation from light-yellow to black over a temperature range of 10 to 423 K is investigated. First-principles, density functional theory (DFT)-based calculations indicate that the thermochromism in Cs2NaFeCl6 is an effect of electron-phonon coupling. The temperature sensitivity of the bandgap in Cs2NaFeCl6 is up to 2.52 meVK(-1) based on the Varshni equation, which is significantly higher than that of lead halide perovskites and many conventional group-IV, III-V semiconductors. Meanwhile, this material shows excellent environmental, thermal, and thermochromic cycle stability. This work provides valuable insights into HDPs' thermochromism and sheds new light on developing efficient thermochromic materials.
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| 17. |
- Jiang, Bin, 1965-, et al.
(författare)
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Geographic space as a living structure for predicting human activities using big data
- 2019
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Ingår i: International Journal of Geographical Information Science. - : Taylor & Francis. - 1365-8816 .- 1365-8824 .- 1362-3087. ; 33:4, s. 764-779
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Tidskriftsartikel (refereegranskat)abstract
- Inspired by Christopher Alexander's conception of the world - space is not lifeless or neutral, but a living structure involving far more small things than large ones - a topological representation has been previously developed to characterize the living structure or the wholeness of geographic space. This paper further develops the topological representation and living structure for predicting human activities in geographic space. Based on millions of street nodes of the United Kingdom extracted from OpenStreetMap, we established living structures at different levels of scale in a nested manner. We found that tweet locations at different levels of scale, such as country and city, can be well predicted by the underlying living structure. The high predictability demonstrates that the living structure and the topological representation are efficient and effective for better understanding geographic forms. Based on this major finding, we argue that the topological representation is a truly multiscale representation, and point out that existing geographic representations are essentially single scale, so they bear many scale problems such as modifiable areal unit problem, the conundrum of length and the ecological fallacy. We further discuss on why the living structure is an efficient and effective instrument for structuring geospatial big data, and why Alexander's organic worldview constitutes the third view of space.
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| 18. |
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| 19. |
- Jiang, Ziyu, et al.
(författare)
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HLA class I genes modulate disease risk and age at onset together with DR-DQ in Chinese patients with insulin-requiring type 1 diabetes
- 2021
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Ingår i: Diabetologia. - : Springer Science and Business Media LLC. - 0012-186X .- 1432-0428. ; 64:9, s. 2026-2036
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Tidskriftsartikel (refereegranskat)abstract
- Aims/hypothesis: The study aimed to investigate the effects of HLA class I genes on susceptibility to type 1 diabetes with different onset ages, in addition to the well-established effects of HLA class II genes. Methods: A total of 361 patients with type 1 diabetes (192 patients with onset <18 years and 169 patients with onset ≥18 years) and 500 healthy control participants from China were enrolled and genotyped for the HLA-A, -B, -C, -DQA1, -DQB1 and -DRB1 genes using next-generation sequencing. Results: The susceptible DR3 (β = −0.09, p = 0.0009) and DR4-DQ8 (β = −0.13, p = 0.0059) haplotypes were negatively associated with onset age, while the protective DR11 (β = 0.21, p = 0.0314) and DR12 (β = 0.27, p < 0.0001) haplotypes were positively associated with onset age. After adjustment for linkage disequilibrium with DR-DQ haplotypes, A*11:01:01 was positively associated with onset age (β = 0.06, p = 0.0370), while the susceptible C*15:02:01 was negatively associated with onset age (β = −0.21, p = 0.0050). The unit for β was double square-root (fourth root) transformed years of change in onset age associated with per copy of the HLA haplotype/allele. In addition, B*46:01:01 was protective (OR 0.41, 0.46; pc [corrected for multiple comparisons] = 0.0044, 0.0040), whereas A*24:02:01 (OR 2.71, 2.25; pc = 0.0003, 0.0002) and B*54:01:01 (OR 3.96, 3.79; pc = 0.0018, 0.0004) were predisposing in both the <18 group and the ≥18 group compared with healthy control participants. In the context of DR4-DQ4, A*11:01:01 (61.29% vs 28.26%, pc = 0.0144) was increased while the predisposing A*24:02:01 (19.35% vs 47.83%, pc = 0.0403) was decreased in patients with onset ≥18 years when compared with patients with onset <18 years. Conclusions/interpretation: In addition to DR-DQ haplotypes, novel HLA class I alleles were detected to play a role in susceptibility to type 1 diabetes with different onset ages, which could improve the understanding of disease heterogeneity and has implications for the design of future studies. Graphical abstract: [Figure not available: see fulltext.].
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| 20. |
- Langer, Judith, et al.
(författare)
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Present and Future of Surface-Enhanced Raman Scattering
- 2020
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-086X .- 1936-0851. ; 14:1, s. 28-117
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Forskningsöversikt (refereegranskat)abstract
- The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article. ©
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| 21. |
- Liao, Shih-Fen, et al.
(författare)
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Immunization of fucose-containing polysaccharides from Reishi mushroom induces antibodies to tumor-associated Globo H-series epitopes.
- 2013
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 110:34, s. 13809-13814
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Tidskriftsartikel (refereegranskat)abstract
- Carbohydrate-based vaccines have shown therapeutic efficacy for infectious disease and cancer. The mushroom Ganoderma lucidum (Reishi) containing complex polysaccharides has been used as antitumor supplement, but the mechanism of immune response has rarely been studied. Here, we show that the mice immunized with a l-fucose (Fuc)-enriched Reishi polysaccharide fraction (designated as FMS) induce antibodies against murine Lewis lung carcinoma cells, with increased antibody-mediated cytotoxicity and reduced production of tumor-associated inflammatory mediators (in particular, monocyte chemoattractant protein-1). The mice showed a significant increase in the peritoneal B1 B-cell population, suggesting FMS-mediated anti-glycan IgM production. Furthermore, the glycan microarray analysis of FMS-induced antisera displayed a high specificity toward tumor-associated glycans, with the antigenic structure located in the nonreducing termini (i.e., Fucα1-2Galβ1-3GalNAc-R, where Gal, GalNAc, and R represent, respectively, D-galactose, D-N-acetyl galactosamine, and reducing end), typically found in Globo H and related tumor antigens. The composition of FMS contains mainly the backbone of 1,4-mannan and 1,6-α-galactan and through the Fucα1-2Gal, Fucα1-3/4Man, Fucα1-4Xyl, and Fucα1-2Fuc linkages (where Man and Xyl represent d-mannose and d-xylose, respectively), underlying the molecular basis of the FMS-induced IgM antibodies against tumor-specific glycans.
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| 22. |
- Llop-Sayson, Jorge, et al.
(författare)
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Constraining the Orbit and Mass of epsilon Eridani b with Radial Velocities, Hipparcos IAD-Gaia DR2 Astrometry, and Multiepoch Vortex Coronagraphy Upper Limits
- 2021
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Ingår i: Astronomical Journal. - : Institute of Physics Publishing (IOPP). - 0004-6256 .- 1538-3881. ; 162:5
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Tidskriftsartikel (refereegranskat)abstract
- epsilon Eridani is a young planetary system hosting a complex multibelt debris disk and a confirmed Jupiter-like planet orbiting at 3.48 au from its host star. Its age and architecture are thus reminiscent of the early Solar System. The most recent study of Mawet et al., which combined radial-velocity data and Ms-band direct imaging upper limits, started to constrain the planet's orbital parameters and mass, but are still affected by large error bars and degeneracies. Here we make use of the most recent data compilation from three different techniques to further refine epsilon Eridani b's properties: RVs, absolute astrometry measurements from the Hipparcos and Gaia missions, and new Keck/NIRC2 Ms-band vortex coronagraph images. We combine this data in a Bayesian framework. We find a new mass, M-b = 0.66(-0.09)(+0.12) M-Jup, and inclination, i = 78.81(-22.41 degrees)(+29.34), with at least a factor 2 of improvement over previous uncertainties. We also report updated constraints on the longitude of the ascending node, the argument of the periastron, and the time of periastron passage. With these updated parameters, we can better predict the position of the planet at any past and future epoch, which can greatly help define the strategy and planning of future observations and with subsequent data analysis. In particular, these results can assist the search for a direct detection with JWST and the Nancy Grace Roman Space Telescope's coronagraph instrument.
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| 23. |
- Peng, Yanling, et al.
(författare)
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Phylogeographic analysis of the fir species in southern China suggests complex origin and genetic admixture
- 2012
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Ingår i: Annals of Forest Science. - 1286-4560 .- 1297-966X. ; 69:3, s. 409-416
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Tidskriftsartikel (refereegranskat)abstract
- ContextFir species are mainly distributed across the high latitudes, preferring cold climates. The phylogeographic origins of those subtropical fir species that occur in low latitudes in southern China remain elusive, as does the nature of any inter-lineage hybridization.AimsIn fir species, mitochondrial DNA (mtDNA) is mater- nally inherited and chloroplast DNA (cpDNA) is paternally inherited, and the genetic variations in the two make them particularly useful for examining species’ hybridizations and evolutionary histories.Materialsand methods We sequenced four DNA frag- ments: two of mtDNA and two of cpDNA for 161 individuals from four subtropical endangered fir species (Abies beshan- zuensis, Abies ziyuanensis, Abies yuanbaoshanensis, and Abies fanjingshanensis) and two more northerly distributed ones (Abies recurvata and Abies fargesii) from central and southwest China.ResultsThree mitotypes and four chlorotypes were recov- ered from the four southern species. In most populations, individuals share a single fixed mitotype and chlorotype. Three mitotypes clustered into two distinct clades, each associated with one of the northern species examined. For four chlorotypes, one occurred in A. ziyuanensis, A. beshan- zuensis, A. fargesii, and A. recurvata, another in A. ziyua- nensis and A. recurvata, the remaining two differed from others by two mutations exclusively in A. fanjingshanenis and A. yuanbaoshanensis.ConclusionPhylogeographic origins of the subtropical fir species are complex, and genetic admixtures occurred dur- ing the evolutionary history of A. ziyuanensis. The geno- typed populations further provide basic frames for genetic delimitation and effective conservation of these endangered species in the future.
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| 24. |
- Qian, Junpeng, et al.
(författare)
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Vision-Based Contactless Pose Estimation for Human Thermal Discomfort
- 2020
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Ingår i: Atmosphere. - : MDPI. - 2073-4433. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- Real-time and effective human thermal discomfort detection plays a critical role in achieving energy efficient control of human centered intelligent buildings because estimation results can provide effective feedback signals to heating, ventilation and air conditioning (HVAC) systems. How to detect occupant thermal discomfort is a challenge. Unfortunately, contact or semi-contact perception methods are inconvenient in practical application. From the contactless perspective, a kind of vision-based contactless human discomfort pose estimation method was proposed in this paper. Firstly, human pose data were captured from a vision-based sensor, and corresponding human skeleton information was extracted. Five thermal discomfort-related human poses were analyzed, and corresponding algorithms were constructed. To verify the effectiveness of the algorithms, 16 subjects were invited for physiological experiments. The validation results show that the proposed algorithms can recognize the five human poses of thermal discomfort.
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| 25. |
- Qiang, Yongjia, et al.
(författare)
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Atypical location of primary cardiac lymphoma in the left heart with atypical clinical presentation: A case report and literature review
- 2023
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Ingår i: Frontiers in Surgery. - : FRONTIERS MEDIA SA. - 2296-875X. ; 9
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Forskningsöversikt (refereegranskat)abstract
- BackgroundPrimary cardiac lymphoma (PCL) is a rare and aggressive cardiac tumor with very poor prognosis that occurs mostly in the right cardiac cavity. Early diagnosis and treatment may improve its prognosis. In the present report, we describe the diagnosis and treatment of a primary cardiac diffuse large B-cell lymphoma (PC-DLBCL) with atypical location and clinical presentation. Additionally, a literature review was conducted to summarize the current knowledge of the disease. Case PresentationA 71-year-old man visited his local hospital because of syncope, recurrent chest tightness, shortness of breath, palpitations, and profuse sweating for more than 20 days. Chest radiography revealed a mediastinal mass. Cardiac computed tomography (CT) showed multiple enlarged mediastinal lymph nodes. Transthoracic echocardiography (TTE) showed a cardiac mass in the posterior-inferior wall of the left atrium. He was then transferred to our hospital for positron emission tomography-CT (PET-CT) which showed active uptake of fluorodeoxyglucose both in the cardiac mass and in the multiple enlarged mediastinal lymph nodes. Biopsy of the enlarged mediastinal lymph nodes was carried out by using video-assisted thoracic surgery (VATS) technique, and pathological examination confirmed the subtype of PC-DLBCL, Stage IV, NCCN IPI 3. Therefore, the patient received a combination of chemotherapy and immunotherapy with R-CDOP (rituximab, cyclophosphamide, liposome doxorubicin, vincristine, and prednisone). After four courses of treatment in 4 months, the cardiac lymphoma and the enlarged mediastinal lymph nodes achieved complete remission with mild side effects of the chemotherapy. ConclusionEarly diagnosis and a precise choice of chemotherapy and immunotherapy based on cardiac imaging and pathological examination may improve the prognosis of PC-DLBCL in an atypical location.
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| 26. |
- Ren, Bin
(författare)
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Crystallographic studies on redox enzymes containing the thioredoxin fold
- 1999
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Three-dimensional structures of two redox enzymes, glutathione peroxidase from human plasma and a protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus, have been determined by X-ray crystallography. Glutathione peroxidases constitute a family of antioxidant seleno-enzymes that catalyze the reduction of a variety of hydroperoxides. Selenocysteine is the active site residue of these enzymes, which presumably shuttles between the selenolate anion state and the selenenic acid state in the catalytic cycle. They usually use glutathione as the reducing substrate. Compared to the other members of this protein family, glutathione peroxidase from human plasma is the only identified extracellular enzyme, whose physiological function remains ambiguous due to the low levels of reduced glutathione in human plasma and the low reactivity of this enzyme. The plasma enzyme was crystallized and the structure was solved by Patterson search methods. Crystallographic refinement of the structure at 2.9 A resolution resulted in a R-factor of 0.222 and a free R-factor of 0.290. The structure of the plasma enzyme was compared with that of the bovine erythrocyte enzyme to understand their structural and functional differences. Like the bovine erythrocyte enzyme, the plasma enzyme shows the structural feature of a thioredoxin fold with a central ß sheet and flanking a helices. The active site selenocysteine is located in a loop preceding the first [alpha] helix. Distinct from the bovine erythrocyte enzyme, however, the plasma enzyme has an intrachain disulfide bridge and a few extra N-terminal residues which form an additional ß strand. Structural variations of residues in the active site region of the plasma enzyme may account for its low affinity for glutathione. Protein disulfide oxidoreductases belong to a superfamily of enzymes that catalyze the reduction, oxidation or rearrangement of protein disulfide bonds. The active site of these enzymes has a CXXC sequence motif, in which the two cysteines undergo reversible oxidation-reduction by shuttling between a dithiol and a disulfide in the catalytic process. The protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus is an enzyme that was first purified without a clearly defined physiological function although it showed the activity of catalyzing the reduction of protein disulfide bonds. The enzyme was crystallized and the structure was determined by multiple isomorphous replacement with anomalous scattering. The structure was refined to 1.9 A resolution with a R-factor of 0.192 and a free R-factor of 0.217. This is the first three-dimensional structure of an archaeal protein disulfide oxidoreductase. It reveals structural details that suggest a relation to eukaryotic protein disulfide isomerase. Compared to the known structures of other oxidoreductases, it shows the unique feature of having two adjacent homologous structural units with low sequence identity. Each unit contains a thioredoxin fold with an active site disulfide formed in a distinct CXXC motif. The two active site disulfides have different solvent accessibilities. They probably differ from each other in their conformational stabilities as well as their redox properties. The structural analysis forms the basis for further functional studies. It is very likely that the enzyme plays a broader functional role than a simple disulfide reductant as shown by recent biochemical experiments.
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| 27. |
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| 28. |
- Ren, Wenqian, et al.
(författare)
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Adult-onset type 1 diabetic patients with less severe clinical manifestation have less risk DR-DQ genotypes than childhood-onset patients
- 2021
-
Ingår i: Diabetes/Metabolism Research and Reviews. - : Wiley. - 1520-7552 .- 1520-7560. ; 37:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The aim of this study was to investigate differences in clinical features and HLA genotypes between adult-onset and childhood-onset patients with type 1 diabetes in a Chinese population. Materials and Methods: This study enrolled 716 Han Chinese patients with type 1 diabetes from Guangdong (258 childhood-onset and 458 adult-onset) to compare their clinical features. Of them 214 patients with classical type 1 diabetes (100 childhood-onset and 114 adult-onset) were selected for HLA DR and DQ genotyping by next-generation sequencing. Results: Adult-onset patients were characterized by longer duration of symptoms before diagnosis, lower frequency of DKA at disease onset, less frequent autoantibody positivity, higher serum C-peptide concentrations, and better glycemic control. These findings were replicated in the restricted cohort of 214 patients with classical type 1 diabetes. Compared with childhood-onset patients, adult-onset patients had a lower frequency of the DR9 haplotype, as well as lower frequency of high-risk DR3/DR4 and DR3/DR9 genotypes, but higher frequency of DR3/DR3 genotype and DR3/X, DR4/X or DR9/X (X, non-risk) genotypes. Conclusions: Adult-onset type 1 diabetic patients with susceptible haplotypes (DR3, DR4 or DR9) were more likely to carry protective DR-DQ haplotypes than childhood-onset patients, which suggested the association between less risk DR-DQ genotypes and the less severe clinical manifestation in adult-onset patients.
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| 29. |
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| 30. |
- Ren, Yaojia, et al.
(författare)
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A comparative study on microstructure, nanomechanical and corrosion behaviors of AlCoCuFeNi high entropy alloys fabricated by selective laser melting and laser metal deposition
- 2022
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Ingår i: Journal of Materials Science and Technology. - : Elsevier BV. - 1005-0302. ; 131, s. 221-230
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Tidskriftsartikel (refereegranskat)abstract
- The present study investigated the microstructure, nanomechanics, and corrosion behavior of AlCoCuFeNi high entropy alloys fabricated by selective laser melting (SLM) and laser metal deposition (LMD). The microstructure of SLM-processed specimens was mainly composed of columnar-grained BCC matrix (∼90 µm in width) and Cu-rich twinned FCC phase. The columnar grains grew epitaxially along the building direction and exhibited a strong {001} texture. In comparison, a coarse columnar-grained BCC matrix (∼150 µm in width) with a stronger 〈001〉 texture, rod-like B2 precipitates, and large core-shell structured FCC phases were formed in the LMD-processed specimens due to the higher heat accumulation effect. Consequently, the LMD-processed specimens showed a lower hardness, wear resistance, and corrosion resistance, but higher creep resistance and reduced Young's modulus than the SLM-processed specimens. Hot cracks occurred in both types of specimens, which could not be completely suppressed due to Cu segregation.
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| 31. |
- Ren, Yaojia, et al.
(författare)
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A novel L12-strengthened AlCoCuFeNi high-entropy alloy with both high hardness and good corrosion resistance
- 2023
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Ingår i: Materials Letters. - : Elsevier BV. - 1873-4979 .- 0167-577X. ; 331
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Tidskriftsartikel (refereegranskat)abstract
- In this work, a high hardness, crack-free AlCoCuFeNi high-entropy alloy with good corrosion resistance was successfully produced by spark plasma sintering at 1000℃ and 30 MPa for 10 min, followed by hot rolling to a thickness reduction of 10 % after holding at 600℃ for 30 min. The microstructure of the alloy was composed of fine equiaxed grains of (Fe, Co, Ni, Al)-enriched BCC, Cu-enriched FCC, nano-sized L12, and Al2O3 phases. The maximum texture index of the material is only 1.53, indicating a low anisotropy. The alloy possessed a high hardness (599 HV), a low friction coefficient (0.1), and a low corrosion current density (1.13 μA/cm2), implying both good wear and corrosion resistance. In addition, the creep mechanism was found to be grain boundary sliding.
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| 32. |
- Ren, Zheng, 1991-, et al.
(författare)
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A topology-based approach to identifying urban centers in America using multi-source geospatial big data
- 2024
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Ingår i: Computers, Environment and Urban Systems. - : Elsevier. - 0198-9715 .- 1873-7587. ; 107
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Tidskriftsartikel (refereegranskat)abstract
- Urban structure can be better comprehended through analyzing its cores. Geospatial big data facilitate the identification of urban centers in terms of high accuracy and accessibility. However, previous studies seldom leverage multi-source geospatial big data to identify urban centers from a topological perspective. This study attempts to identify urban centers through the spatial integration of multi-source geospatial big data, including nighttime light imagery (NTL), building footprints (BFP) and street nodes of OpenStreetMap (OSM). We use a novel topological approach to construct complex networks from intra-urban hotspots based on the theory of centers by Christopher Alexander. We compute the degree of wholeness value for each hotspot as the centric index. The overlapped hotspots with the highest centric indices are regarded as urban centers. The identified urban centers in New York, Los Angeles, and Houston are consistent with their downtown areas, with overall accuracy of 90.23%. In Chicago, a new urban center is identified considering a larger spatial extent. The proposed approach can effectively and objectively prevent counting those hotspots with high intensity values but few neighbors into the result. This study proposes a topological approach for urban center identification and a bottom-up perspective for sustainable urban design.
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| 33. |
- Ren, Zheng, et al.
(författare)
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Capturing and characterizing human activities using building locations in America
- 2019
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Ingår i: ISPRS International Journal of Geo-Information. - : MDPI. - 2220-9964. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- Capturing and characterizing collective human activities in a geographic space have become much easier than ever before in the big era. In the past few decades it has been difficult to acquire the spatiotemporal information of human beings. Thanks to the boom in the use of mobile devices integrated with positioning systems and location-based social media data, we can easily acquire the spatial and temporal information of social media users. Previous studies have successfully used street nodes and geo-tagged social media such as Twitter to predict users’ activities. However, whether human activities can be well represented by social media data remains uncertain. On the other hand, buildings or architectures are permanent and reliable representations of human activities collectively through historical footprints. This study aims to use the big data of US building footprints to investigate the reliability of social media users for human activity prediction. We created spatial clusters from 125 million buildings and 1.48 million Twitter points in the US. We further examined and compared the spatial and statistical distribution of clusters at both country and city levels. The result of this study shows that both building and Twitter data spatial clusters show the scaling pattern measured by the scale of spatial clusters, respectively, characterized by the number points inside clusters and the area of clusters. More specifically, at the country level, the statistical distribution of the building spatial clusters fits power law distribution. Inside the four largest cities, the hotspots are power-law-distributed with the power law exponent around 2.0, meaning that they also follow the Zipf’s law. The correlations between the number of buildings and the number of tweets are very plausible, with the r square ranging from 0.53 to 0.74. The high correlation and the similarity of two datasets in terms of spatial and statistical distribution suggest that, although social media users are only a proportion of the entire population, the spatial clusters from geographical big data is a good and accurate representation of overall human activities. This study also indicates that using an improved method for spatial clustering is more suitable for big data analysis than the conventional clustering methods based on Euclidean geometry.
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| 34. |
- Ren, Zheng, 1991-
(författare)
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Living Structure for Understanding Human Activity Patterns Using Multi-Source Geospatial Big Data
- 2023
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Geographic space is not neutral or lifeless, but an intricate living structure composed of numerous small features and a few large ones across all scales. The living structure is crucial for comprehending how geographic space shapes human activities. With the emerging geospatial big data, researchers now have unprecedented opportunities to study the relationship between geographic space and human behaviour at a finer spatial resolution. This thesis leverages multisource geospatial big data, including Twitter check-in locations, street networks from OpenStreetMap, building footprints, and night-time light images, to explore the fundamental mechanisms of human activities that underlie geographic space. To overcome the limitations of conventional analytics in this era of big data, we propose the topological representation and living structure based on Christopher Alexander's conception of space.We utilize scaling and topological analyses to reveal the underlying living structure of geographic space with various big datasets. Our results demonstrate that tweet locations or human activities at different scales can be accurately predicted by the underlying living structure of street nodes. We also capture and characterize human activities using big data and find that building footprints and tweets show similar scaling patterns in terms of sizes of their spatial clusters. We also propose an improved spatial clustering method to increase the processing speed of geospatial big data. Finally, we adopt topological representation to identify urban centres by the fusion of multi-source geospatial big data. The living structure, together with its topological representation can help us better understand human activities patterns in the geographic space at both city and country levels.
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| 35. |
- Wang, Bolin, et al.
(författare)
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Palladium-Catalyzed Dehydrogenative Carbonylative Esterification of Allenoic Acids for the Synthesis of γ-Butyrolactone Derivatives
- 2024
-
Ingår i: Organic Letters. - 1523-7060 .- 1523-7052. ; 26:12, s. 2430-2434
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Tidskriftsartikel (refereegranskat)abstract
- A highly efficient dehydrogenative carbonylative esterification of allenoic acids using Pd-catalysis was developed, providing a novel approach to synthesizing esterified γ-butyrolactone derivatives with consistently good to excellent results demonstrated across over 50 examples. Additionally, we used a heterogeneous catalyst known as Pd-AmP-MCF and harnessed biomimetic-aerobic-oxidation conditions to facilitate the practical execution of this reaction. Furthermore, our detailed study of γ-butyrolactone products highlighted their potential in synthesizing bioactive compounds.
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| 36. |
- Wang, Jason J., et al.
(författare)
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Keck/NIRC2 L'-Band Imaging of Jovian-Mass Accreting Protoplanets around PDS 70
- 2020
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 159:6
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Tidskriftsartikel (refereegranskat)abstract
- We present L'-band imaging of the PDS 70 planetary system with Keck/NIRC2 using the new infrared pyramid wave front sensor. We detected both PDS 70 b and c in our images, as well as the front rim of the circumstellar disk. After subtracting off a model of the disk, we measured the astrometry and photometry of both planets. Placing priors based on the dynamics of the system, we estimated PDS 70 b to have a semimajor axis of au and PDS 70 c to have a semimajor axis of au (95% credible interval). We fit the spectral energy distribution (SED) of both planets. For PDS 70 b, we were able to place better constraints on the red half of its SED than previous studies and inferred the radius of the photosphere to be 2–3 R Jup. The SED of PDS 70 c is less well constrained, with a range of total luminosities spanning an order of magnitude. With our inferred radii and luminosities, we used evolutionary models of accreting protoplanets to derive a mass of PDS 70 b between 2 and 4 M Jup and a mean mass accretion rate between 3 × 10−7 and 8 × 10−7 M Jup/yr. For PDS 70 c, we computed a mass between 1 and 3 M Jup and mean mass accretion rate between 1 × 10−7 and 5 × 10−7 M Jup/yr. The mass accretion rates imply dust accretion timescales short enough to hide strong molecular absorption features in both planets' SEDs.
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| 37. |
- Wen-Yu, Fang, et al.
(författare)
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Elastic constants, electronic structures and thermal conductivity of monolayer XO2 (X = Ni, Pd, Pt)
- 2021
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Ingår i: Wuli xuebao. - : Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences. - 1000-3290. ; 70:24
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Tidskriftsartikel (refereegranskat)abstract
- Based on the first-principles calculations, the stability, elastic constants, electronic structure, and lattice thermal conductivity of monolayer XO2 (X = Ni, Pd, Pt) are investigated in this work. The results show that XO2 (X = Ni, Pd, Pt) have mechanical and dynamic stability at the same time. In addition, the Young's modulus of monolayer NiO2, PdO2 and PtO2 are 124.69 N.m(-1), 103.31 N.m(-1) and 116.51 N.m(-1), Poisson's ratio of monolayer NiO2, PdO2 and PtO2 are 0.25, 0.24 and 0.27, respectively, and each of them possesses high isotropy. The band structures show that monolayer XO2 (X = Ni, Pd, Pt) are indirect band-gap semiconductors with energy gap of 2.95 eV, 3.00 eV and 3.34 eV, respectively, and the energy levels near the valence band maximum and conduction band minimum are mainly composed of Ni-3d/Pd-4d/Pt-5d and O-2p orbital electrons. Based on deformation potential theory, the carrier mobility of each monolayer is calculated, and the results show that the effective mass and deformation potential of monolayer XO2 (X = Ni, Pd, Pt) along the armchair and zigzag directions show obvious anisotropy, and the highest electron and hole mobility are 13707.96 and 53.25 cm(2) .V-1.s(-1), 1288.12 and 19.18 cm(2).V-1.s(-1), and 404.71 and 270.60 cm(2) .V-1.s(-1) for NiO2, PdO(2 )and PtO2, respectively. Furthermore, the lattice thermal conductivity of monolayer XO2 (X = Ni, Pd, Pt) at 300 K are 53.55 W.m(-1).K-1, 19.06 W.m(-1).K-1 and 17.43 W.m(-1).K-1, respectively. These properties indicate that monolayer XO2 (X = Ni, Pd, Pt) have potential applications in nanometer electronic materials and thermal conductivity devices.
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| 38. |
- Wu, Rong Chang, et al.
(författare)
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Conodont faunal dynamics across the middle and upper ordovician boundary in the Yichang area, western Hubei province, South China
- 2016
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Ingår i: Canadian Journal of Earth Sciences. - : Canadian Science Publishing. - 0008-4077 .- 1480-3313. ; 53:8, s. 856-864
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Tidskriftsartikel (refereegranskat)abstract
- A total of 6094 conodont specimens, assigned to 18 genera and 27 species, have been recovered from the uppermost Kuniutan and Miaopo formations, spanning the latest Darriwilian - early Sandbian in age, at the Jieling section, Yichang, Hubei Province. Three conodont zones have been recognized, i.e., in ascending order, the Pygodus serra Zone, the Pygodus anserinus - Yangtzeplacognathus jianyeensis Zone, and the Baltoniodus alobatus Zone. The conodont biodiversity in the Miaopo Formation shows a decreasing trend at Jieling. Multivariate statistical analysis of the conodont fauna from the Jieling section shows that the Baltoniodus and Periodon biofacies are present in the uppermost Kuniutan Formation, and the Periodon and Scabbardella biofacies can be recognized in the Miaopo Formation.
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| 39. |
- Wu, Sihan, et al.
(författare)
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Circular ecDNA promotes accessible chromatin and high oncogene expression
- 2019
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Ingår i: Nature. - : NATURE PUBLISHING GROUP. - 0028-0836 .- 1476-4687. ; 575:7784, s. 699-703
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Tidskriftsartikel (refereegranskat)abstract
- Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer(1,2), but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Pan-cancer analyses reveal that oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of the tumours, linking increased copy number with high transcription levels. Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. Furthermore, ecDNA is shown to have a significantly greater number of ultra-long-range interactions with active chromatin, which provides insight into how the structure of circular ecDNA affects oncogene function, and connects ecDNA biology with modern cancer genomics and epigenetics.
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| 40. |
- Xia, Yangyang, et al.
(författare)
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Prediction of bending strength of glass fiber reinforced methacrylate-based pipeline UV-CIPP rehabilitation materials based on machine learning
- 2023
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Ingår i: Tunnelling and Underground Space Technology. - : Elsevier. - 0886-7798 .- 1878-4364. ; 140
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Tidskriftsartikel (refereegranskat)abstract
- Ultraviolet cured-in-place-pipe (UV-CIPP) materials are commonly used in trenchless pipeline rehabilitation. Their bending strength is a crucial indicator to evaluate the curing quality. Studies show that this indicator is affected by multiple factors, including the curing time, UV lamp curing power, curing distance, and material thickness. Laboratory experiments have limitations in analyzing the effect of multiple factors on the bending strength of UV-CIPP materials and quantitatively predicting the optimum curing parameters. Aiming at resolving these shortcomings, resolve machine learning techniques were applied to predict the bending strength. In this regard, the surface curing reaction temperature monitoring data and three-point bending data of 30 groups of UV-CIPP material under the influence of different curing parameters were used as a dataset to predict the bending strength of UV-CIPP material. The results show that the influence degree of each factor on the bending strength of the UV-CIPP material, from high to low, is as follows: UV lamp power (−0.439), the temperature at the illuminated side (−0.392), curing time (−0.323), the temperature at the back side (−0.233), curing distance (0.143) and material thickness (−0.140). The best penalty parameter c (44.435) and width g (0.072) of the kernel function in the support vector machine (SVM) model were obtained using the genetic algorithm (GA) optimization, and the results were compared with the grey wolf optimizer (GWO) and particle swarm optimization (PSO). The performed analyses revealed that the developed GA-SVM model exhibits the best prediction results compared to other machine learning algorithms. The optimum bending strength of the UV-CIPP material used in this test is 294.77 MPa, which corresponds to the curing time, UV lamp power, curing distance, material thickness, light side temperature, and back side temperature of 7.59 min, 157.33 mW/cm2, 189.99 mm, 4.38 mm, 79.49 °C, and 76.59 °C, respectively.
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| 41. |
- Xiao, Wenming, et al.
(författare)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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| 42. |
- Xiong, Jing, et al.
(författare)
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Discovery of environmental secrets for historical artefacts : how did micro-climate evolve in ancient tombs in initial phase
- 2018
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Ingår i: 15th Conference of the International Society of Indoor Air Quality and Climate (INDOOR AIR 2018). - : International Society of Indoor Air Quality and Climate. - 9781713826514
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Stable burial environments are vital for historical artefacts' conservations. However, it is still a mystery that how stable burial environments evolve and what the influences of environmental variations on historical artefacts are. In this study, based on field tests and CFD numerical simulations, the temperature and relative humidity evolution in M1 tomb chamber of mausoleum ZHANG An-Shi (~50 BC) were investigated. Whenever the tomb was buried in the coldest or hottest month, the temperature and relative humidity experienced rapid variations and achieved stability shortly after sealing. The changes of atmospheric components inside the ancient tomb relied mainly on the aerobic decomposition at the initial phase of burying. It suggests that historical artifacts are better to be excavated or conserved in the same microclimate as their final burial environment. The study paved the way for finding out environments of the ancient tomb chamber.
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| 43. |
- Xiong, Jing, et al.
(författare)
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Probing the historic thermal and humid environment in a 2000-year-old ancient underground tomb and enlightenment for cultural heritage protection and preventive conservation
- 2021
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Ingår i: Energy and Buildings. - : Elsevier. - 0378-7788 .- 1872-6178. ; 251
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Tidskriftsartikel (refereegranskat)abstract
- The development and utilization of urban underground space have contributed to more excavation of ancient tombs in recent years. The microclimate in the burial environment is crucial for the sustainability of historical artifacts. In this paper, the variation in thermal and humid conditions during the burial time from the closure of a tomb to excavation was investigated by field testing and computational fluid dynamics (CFD) modeling. The selected object is the famous M1 tomb chamber of the mausoleum Zhang An-shi, which has a 2000-year history. It was found that the average air temperature (T) and relative humidity (RH) of the M1 tomb chamber before excavation were 12.7 °C and 93.0%, respectively. The results of the CFD simulation suggest that the burial time of an ancient tomb consists of a very short variable phase and a long stable phase. The very beginning phase may be as short as 0.3 h. The dramatic changes in temperature and RH were more than 10 °C and 20%, respectively. Consequently, dramatic changes in the thermal and humid environment will trigger the deterioration of historical artifacts. Current findings further suggest that the local annual average temperature is optimal for the conservation of underground artifacts excavated from the soil thermostatic layer. This study paves the way for characterizing the environment of an ancient tomb chamber, as well as museum design, energy savings that support cultural heritage protection and preventive conservation.
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| 44. |
- Yang, Bin, 1987-, et al.
(författare)
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Total Synthesis of Strigolactones via Palladium-Catalyzed Cascade Carbonylative Carbocyclization of Enallenes
- 2024
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Ingår i: Organic Letters. - 1523-7060 .- 1523-7052. ; 26:22, s. 4637-4642
-
Tidskriftsartikel (refereegranskat)abstract
- Here we report an efficient route for synthesizing strigolactones (SLs) and their derivatives. Our method relies on a palladium-catalyzed oxidative carbonylation/carbocyclization/carbonylation/alkoxylation cascade reaction, which involves the formation of three new C–C bonds and a new C–O bond while cleaving one C(sp3)–H bond in a single step. With our versatile synthetic strategy, both naturally occurring and artificial SLs were prepared.
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| 45. |
- Yeung, Andy Wai Kan, et al.
(författare)
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Resveratrol, a popular dietary supplement for human and animal health : Quantitative research literature analysis - a review
- 2019
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Ingår i: Animal Science Papers and Reports. - : POLSKA AKAD NAUK, INST GENETYKI I HODOWLI ZWIERZAT. - 0860-4037. ; 37:2, s. 103-118
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Forskningsöversikt (refereegranskat)abstract
- Resveratrol is a stilbene-type bioactive molecule with a broad spectrum of reported biological effects. In this sense, the current work provides a comprehensive literature analysis on resveratrol, representing a highly-researched commercially available dietary ingredient. Bibliometric data were identified by means of the search string TOPIC=("resveratrol*") and analyzed with the VOSviewer software, which yielded 17,561 publications extracted from the Web of Science Core Collection electronic database. 'I'he ratio of original articles to reviews was 9.5:1. More than half of the overall manuscripts have been published since 2013. Major contributing countries were USA, China, Italy, South Korea, and Spain. Most of the publications appeared in journals specialized in biochemistry and molecular biology, pharmacology and pharmacy, food science technology, cell biology, or oncology. The phytochemicals or phytochemical classes that were frequently mentioned in the keywords of analyzed publications included, in descending order: resveratrol, trans-resveratrol, polyphenols, flavonoids, quercetin, stilbenes, curcumin, piceatannol, cis-resveratrol, and anthocyanins.
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| 46. |
- Zhang, Daquan, et al.
(författare)
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Large-scale planar and spherical light-emitting diodes based on arrays of perovskite quantum wires
- 2022
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Ingår i: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 16:4, s. 284-290
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Tidskriftsartikel (refereegranskat)abstract
- Halide perovskites are enticing candidates for highly efficient planar light-emitting diodes (LEDs) with commercial potential in displays and lighting. However, it remains a challenge for conventional solution fabrication processes to fabricate large-scale or non-planar LEDs due to the non-uniformity of perovskite films in conjunction with material stability issues. Here large-area highly uniform arrays of crystalline perovskite quantum wires are grown with emission spectra covering the whole visible range. Photoluminescence quantum yield of up to 92% and 5,644 hours as the time for photoluminescence to degrade down to its 50% of the initial value under ambient conditions are achieved for MAPbBr3 quantum wires. LEDs based on these quantum wires on rigid and flexible planar substrates are fabricated up to a four-inch wafer size and also unique three-dimensional spherical LEDs with outstanding uniformity are reported. The results suggest that the approach developed here can be generalized to other unconventional three-dimensional LEDs in the future.
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| 47. |
- Zhao, Nale, et al.
(författare)
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A Study on The Traffic Organzations of Ring Road Expressways Under Emergency Stituation
- 2013
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Ingår i: Proceedings of the 16th International Conference Road Safety on Four Continents. - Linköping : Statens väg- och transportforskningsinstitut.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- According to the physical and traffic flow characteristics of ring road expressways, the road section elements classification and numbering have been conducted, and three types of traffic organization such as diversion, evacuation and rescue under emergency situation have been studied. Taking the road section between Hongqitai Bridge and Beiliguan Bridge of Shenyang third ring road expressway as an example, the specific diversion, evacuation and rescue routes have been proposed.
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| 48. |
- Zhao, Yongmei, et al.
(författare)
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Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study
- 2021
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- With the rapid advancement of sequencing technologies, next generation sequencing (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS has been adopted in clinical oncology to advance personalized medicine. Clinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during NGS processes or data analysis. Therefore, there is an urgent need to develop best practices in cancer mutation detection using NGS and the need for standard reference data sets for systematically measuring accuracy and reproducibility across platforms and methods. Within the SEQC2 consortium context, we established paired tumor-normal reference samples and generated whole-genome (WGS) and whole-exome sequencing (WES) data using sixteen library protocols, seven sequencing platforms at six different centers. We systematically interrogated somatic mutations in the reference samples to identify factors affecting detection reproducibility and accuracy in cancer genomes. These large cross-platform/site WGS and WES datasets using well-characterized reference samples will represent a powerful resource for benchmarking NGS technologies, bioinformatics pipelines, and for the cancer genomics studies.
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| 49. |
- Zhao, Zeng-Ren, et al.
(författare)
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Significance of mRNA and Protein Expression of MAC30 in Progression of Colorectal Cancer
- 2011
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Ingår i: Chemotherapy. - Basel : Karger AG. - 0009-3157 .- 1421-9794. ; 57:5, s. 394-401
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Tidskriftsartikel (refereegranskat)abstract
- Background: Meningioma-associated protein (MAC30), first described to be overexpressed in meningiomas, exhibits altered expression in certain human tumors. The aim of our study was to investigate the expression of MAC30 mRNA and its correlation with clinicopathological variables in human colorectal cancer (CRC). Methods: MAC30 mRNA expression was first examined in 55 CRCs, along with the samples from the matched distant normal and adjacent noncancerous tissue by RT-PCR, further verified in 18 CRCs by quantitative RT-PCR. MAC30 protein expression was detected by Western blot in 10 CRCs, and DNA sequencing was performed in 1 case of the paired CRC and the matched noncancerous specimen. MAC30 mRNA expression in two colon cancer cell lines, HCT-116(p53-/-) and HCT-116(p53+/+), was detected by quantitative RT-PCR. Results: The mRNA expression of MAC30 was increased in CRC when compared with distant normal (p < 0.01) and adjacent noncancerous mucosa (p < 0.01). The mean value of MAC30 mRNA expression in the tumor located in the colon was higher than in the rectum (0.677 +/- 0.419 vs. 0.412 +/- 0.162, p = 0.005). As the tumor penetrated the wall of the colon/rectum, MAC30 mRNA expression notably increased in tumors with T3+T4 stage compared to tumors with T1+T2 stage (0.571 +/- 0.364 vs. 0.404 +/- 0.115, p = 0.014). MAC30 protein expression in CRCs was also remarkably elevated compared to the adjacent noncancerous mucosa. There was no mutation in the coding region of the MAC30 gene either in CRC or in the noncancerous mucosa. mRNA expression of p53 was notably decreased in HCT-116(p53-/-) compared to HCT-116(p53+/+), while MAC30 did not vary greatly. Conclusion: The overexpression of MAC30 might be involved in the development and aggressiveness of CRCs, especially in the colon.
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| 50. |
- Zhou, Yixuan, et al.
(författare)
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H-Bonding Activation in Highly Regioselective Acetylation of Diols.
- 2013
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Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 78:22, s. 11618-11622
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Tidskriftsartikel (refereegranskat)abstract
- H-bonding activation in the regioselective acetylation of vicinal and 1,3-diols is presented. Herein, the acetylation of the hydroxyl group with acetic anhydride can be activated by the formation of H-bonds between the hydroxyl group and anions. The reaction exhibits high regioselectivity when a catalytic amt. of tetrabutylammonium acetate is employed. Mechanistic studies indicated that acetate anion forms dual H-bonding complexes with the diol, which facilitates the subsequent regioselective monoacetylation. [on SciFinder(R)]
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