1. |
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2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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3. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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4. |
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5. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
-
In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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6. |
- Fan, Baobing, et al.
(author)
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Correlation of Local Isomerization Induced Lateral and Terminal Torsions with Performance and Stability of Organic Photovoltaics
- 2023
-
In: Journal of the American Chemical Society. - : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 145:10, s. 5909-5919
-
Journal article (peer-reviewed)abstract
- Organic photovoltaics (OPVs) have achieved great progress in recent years due to delicately designed non-fullerene acceptors (NFAs). Compared with tailoring of the aromatic heterocycles on the NFA backbone, the incorporation of conjugated side-groups is a cost-effective way to improve the photoelectrical properties of NFAs. However, the modifications of side-groups also need to consider their effects on device stability since the molecular planarity changes induced by side-groups are related to the NFA aggregation and the evolution of the blend morphology under stresses. Herein, a new class of NFAs with localisomerized conjugated side-groups are developed and the impact of local isomerization on their geometries and device performance/stability are systematically investigated. The device based on one of the isomers with balanced side- and terminal-group torsion angles can deliver an impressive power conversion efficiency (PCE) of 18.5%, with a low energy loss (0.528 V) and an excellent photo- and thermal stability. A similar approach can also be applied to another polymer donor to achieve an even higher PCE of 18.8%, which is among the highest efficiencies obtained for binary OPVs. This work demonstrates the effectiveness of applying local isomerization to fine-tune the side-group steric effect and non-covalent interactions between side-group and backbone, therefore improving both photovoltaic performance and stability of fused ring NFA-based OPVs.
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7. |
- Abolfathi, Bela, et al.
(author)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
-
In: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
-
Journal article (peer-reviewed)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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8. |
- Donoghue, Philip C. J., et al.
(author)
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Synchrotron X-ray tomographic microscopy of fossil embryos
- 2006
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In: Nature. - 0028-0836. ; 442:7103, s. 601-718
-
Journal article (peer-reviewed)abstract
- Fossilized embryos from the late Neoproterozoic and earliest Phanerozoic have caused much excitement because they preserve the earliest stages of embryology of animals that represent the initial diversification of metazoans1, 2, 3, 4. However, the potential of this material has not been fully realized because of reliance on traditional, non-destructive methods that allow analysis of exposed surfaces only1, 2,3, 4, and destructive methods that preserve only a single two-dimensional view of the interior of the specimen5, 6. Here, we have applied synchrotron-radiation X-ray tomographic microscopy (SRXTM)7, obtaining complete three-dimensional recordings at submicrometre resolution. The embryos are preserved by early diagenetic impregnation and encrustation with calcium phosphate, and differences in X-ray attenuation provide information about the distribution of these two diagenetic phases. Three-dimensional visualization of blastomere arrangement and diagenetic cement in cleavage embryos resolves outstanding questions about their nature, including the identity of the columnar blastomeres. The anterior and posterior anatomy of embryos of the bilaterian worm-like Markuelia confirms its position as a scalidophoran, providing new insights into body-plan assembly among constituent phyla. The structure of the developing germ band in another bilaterian, Pseudooides, indicates a unique mode of germ-band development. SRXTM provides a method of non-invasive analysis that rivals the resolution achieved even by destructive methods, probing the very limits of fossilization and providing insight into embryology during the emergence of metazoan phyla.
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9. |
- Duan, Xiaolin, et al.
(author)
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Early Cambrian (Stage 4) brachiopods from the Shipai Formation in the Three Gorges area of South China
- 2021
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In: Journal of Paleontology. - : Cambridge University Press. - 0022-3360 .- 1937-2337. ; 95:3, s. 497-526
-
Journal article (peer-reviewed)abstract
- Diverse and abundant fossil taxa have been described in the lower Cambrian Shipai Formation in the Three Gorges area of Hubei Province, South China, but the taxonomy and diversity of the co-occurring brachiopod fauna are still far from clear. Here we describe the brachiopod fauna recovered from the Shipai Formation in the Three Gorges area of South China, including representatives of the subphylum Linguliformea: linguloids (Lingulellotreta ergalievi, Eoobolus malongensis, and Neobolidae gen. indet. sp. indet.), and an acrotretoid (Linnarssonia sapushanensis); and representatives from the subphylum Rhynchonelliformea: the calcareous-shelled Kutorginates (Kutorgina sinensis, Kutorgina sp., and Nisusia liantuoensis). This brachiopod assemblage and the first occurrence of Linnarssonia sapushanensis shell beds permit correlation of the Shipai Formation in the Three Gorges area of Hubei Province with the Stage 4 Wulongqing Formation in the Wuding area of eastern Yunnan. This correlation is further strengthened by the first appearance datum (FAD) of the rhynchonelliform brachiopod Nisusia in the upper silty mudstone of both the Shipai and Wulongqing formations. The new well-preserved material, derived from siliciclastic rocks, also gives critical new insights into the fine shell structure of L. sapushanensis. Microstructural studies on micromorphic acrotretoids (like Linnarssonia) have previously been restricted to fossils that were acid-etched from limestones. This is the first study to carry out detailed comparative ultrastructural studies on acrotretoid shells preserved in siliciclastic rocks. This work reveals a hollow tube and solid column microstructure in the acrotretoid shells from the Shipai Formation, which is likely to be equivalent of traditional column and central canal observed in shells dissolved from limestones.
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10. |
- Fan, Ke, et al.
(author)
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Direct Observation of Structural Evolution of Metal Chalcogenide in Electrocatalytic Water Oxidation
- 2018
-
In: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 12:12, s. 12369-12379
-
Journal article (peer-reviewed)abstract
- As one of the most remarkable oxygen evolution reaction (OER) electrocatalysts, metal chalcogenides have been intensively reported during the past few decades because of their high OER activities. It has been reported that electron-chemical conversion of metal OER chalcogenides into oxides/hydroxides would take place after the OER. However, the transition mechanism of such unstable structures, as well as the real active sites and catalytic activity during the OER for these electrocatalysts, has not been understood yet; therefore a direct observation for the electrocatalytic water oxidation process, especially at nano or even angstrom scale, is urgently needed. In this research, by employing advanced Cs-corrected transmission electron microscopy (TEM), a step by step oxidational evolution of amorphous electrocatalyst CoSx into crystallized CoOOH in the OER has been in situ captured: irreversible conversion of CoSx to crystallized CoOOH is initiated on the surface of the electrocatalysts with a morphology change via Co(OH)(2) intermediate during the OER measurement, where CoOOH is confirmed as the real active species. Besides, this transition process has also been confirmed by multiple applications of X-ray photoelectron spectroscopy (XPS), in situ Fourier-transform infrared spectroscopy (FTIR), and other ex situ technologies. Moreover, on the basis of this discovery, a high-efficiency electrocatalyst of a nitrogen-doped graphene foam (NGF) coated by CoSx has been explored through a thorough structure transformation of CoOOH. We believe this in situ and in-depth observation of structural evolution in the OER measurement can provide insights into the fundamental understanding of the mechanism for the OER catalysts, thus enabling the more rational design of low-cost and high-efficient electrocatalysts for water splitting.
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11. |
- Fan, Qunping, et al.
(author)
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Unidirectional Sidechain Engineering to Construct Dual-Asymmetric Acceptors for 19.23 % Efficiency Organic Solar Cells with Low Energy Loss and Efficient Charge Transfer
- 2023
-
In: Angewandte Chemie International Edition. - : WILEY-V C H VERLAG GMBH. - 1433-7851 .- 1521-3773. ; 62:36
-
Journal article (peer-reviewed)abstract
- Achieving both high open-circuit voltage (V-oc) and short-circuit current density (J(sc)) to boost power-conversion efficiency (PCE) is a major challenge for organic solar cells (OSCs), wherein high energy loss (E-loss) and inefficient charge transfer usually take place. Here, three new Y-series acceptors of mono-asymmetric asy-YC11 and dual-asymmetric bi-asy-YC9 and bi-asy-YC12 are developed. They share the same asymmetric D(1)AD(2) (D-1=thieno[3,2-b]thiophene and D-2=selenopheno[3,2-b]thiophene) fused-core but have different unidirectional sidechain on D-1 side, allowing fine-tuned molecular properties, such as intermolecular interaction, packing pattern, and crystallinity. Among the binary blends, the PM6 : bi-asy-YC12 one has better morphology with appropriate phase separation and higher order packing than the PM6 : asy-YC9 and PM6 : bi-asy-YC11 ones. Therefore, the PM6 : bi-asy-YC12-based OSCs offer a higher PCE of 17.16 % with both high V-oc and J(sc), due to the reduced E-loss and efficient charge transfer properties. Inspired by the high V-oc and strong NIR-absorption, bi-asy-YC12 is introduced into efficient binary PM6 : L8-BO to construct ternary OSCs. Thanks to the broadened absorption, optimized morphology, and furtherly minimized E-loss, the PM6 : L8-BO : bi-asy-YC12-based OSCs achieve a champion PCE of 19.23 %, which is one of the highest efficiencies among these annealing-free devices. Our developed unidirectional sidechain engineering for constructing bi-asymmetric Y-series acceptors provides an approach to boost PCE of OSCs.
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12. |
- Fan, W., et al.
(author)
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Investigation of magnetization dynamics damping in Ni80Fe20/Nd-Cu bilayer at room temperature
- 2018
-
In: AIP Advances. - : American Institute of Physics (AIP). - 2158-3226. ; 8:5
-
Journal article (peer-reviewed)abstract
- Focusing on the Ni80Fe20 (Py)/Nd-Cu bilayers, the magnetization dynamic damping from spin pumping effect is investigated systematically by doping itinerant Cu in rear earth metal Nd. Various Ta/Py/Nd1-xCux/Ta/Si films with x = 0%, 16%, 38%, 46% and 58% are prepared by magnetron sputtering. For every content of Cu, the thickness of Nd-Cu layer is changed from 1 nm to 32 nm. The damping coefficient increases with increasing the thickness of Nd-Cu layer, which shows the trend of the spin pumping behavior. Also, with increasing Cu concentration in the Nd-Cu layer, the damping coefficient decreases, implying that the spin-orbit coupling in Nd-Cu layer is indeed cut down by high itinerant of Cu dopants. It is interesting that the spin diffusion length (λSD) in the Nd-Cu layer for different Cu dopants is not found to increase monotonously.
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13. |
- Fan, Xiaoyu, et al.
(author)
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Paper test strip for silver ions detection in drinking water samples based on combined fluorometric and colorimetric methods
- 2023
-
In: Arabian Journal of Chemistry. - : Elsevier. - 1878-5352 .- 1878-5379. ; 16:2
-
Journal article (peer-reviewed)abstract
- In this study, a portable silver ion (Ag+) sensor was fabricated based on a dual signal output system using black phosphorus quantum dots (BPQDs) as probes. It is the first work for Ag+ detection using paper test strip based on BPQDs. The color change of BPQDs paper sensor for the determination of Ag+ was easily identified by naked eye. BPQDs were synthesized from bulk black phosphorus (BP) by mechanical exfoliation combined with a solvothermal method. BPQDs exhibited blue fluorescence with a quantum yield of 8.82 %. The fluorescence of BPQDs can be quenched by Ag+, and the absorbance of BPQDs is increased with increasing Ag+ concentration. The mechanism of the interaction between BPQDs and Ag+ involving fluorescence quenching and bonding was investigated by experimental and computational methods. The detection limit of Ag+ was 1.56 μg/mL and 0.19 μg/mL using fluorometry and colorimetry methods, respectively. A portable visual sensor based on paper test strip was constructed for Ag+ detection using the colorimetric approach. The strategy was employed to determine Ag+ successfully in drinking water samples. Therefore, the proposed portable Ag+ sensor can be potentially utilized for the lab-free analysis of drinking water and even dietary samples.
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14. |
- Fan, Yue, et al.
(author)
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Unveiling inflammatory and prehypertrophic cell populations as key contributors to knee cartilage degeneration in osteoarthritis using multi-omics data integration
- 2024
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In: Annals of the Rheumatic Diseases. - : BMJ Publishing Group Ltd. - 0003-4967 .- 1468-2060. ; 83:7, s. 926-944
-
Journal article (peer-reviewed)abstract
- OBJECTIVES: Single-cell and spatial transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome landscape and osteoarthritis (OA)-critical cell populations.METHODS: Single-cell RNA sequencing and spatially resolved transcriptomic technology have been applied to characterise the cellular heterogeneity of human knee articular cartilage which were collected from 8 OA donors, and 3 non-OA control donors, and a total of 19 samples. The novel chondrocyte population and marker genes of interest were validated by immunohistochemistry staining, quantitative real-time PCR, etc. The OA-critical cell populations were validated through integrative analyses of publicly available bulk RNA sequencing data and large-scale genome-wide association studies.RESULTS: We identified 33 cell population-specific marker genes that define 11 chondrocyte populations, including 9 known populations and 2 new populations, that is, pre-inflammatory chondrocyte population (preInfC) and inflammatory chondrocyte population (InfC). The novel findings that make this an important addition to the literature include: (1) the novel InfC activates the mediator MIF-CD74; (2) the prehypertrophic chondrocyte (preHTC) and hypertrophic chondrocyte (HTC) are potentially OA-critical cell populations; (3) most OA-associated differentially expressed genes reside in the articular surface and superficial zone; (4) the prefibrocartilage chondrocyte (preFC) population is a major contributor to the stratification of patients with OA, resulting in both an inflammatory-related subtype and a non-inflammatory-related subtype.CONCLUSIONS: Our results highlight InfC, preHTC, preFC and HTC as potential cell populations to target for therapy. Also, we conclude that profiling of those cell populations in patients might be used to stratify patient populations for defining cohorts for clinical trials and precision medicine.
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15. |
- Fan, Zheyong, et al.
(author)
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GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations
- 2022
-
In: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 157:11
-
Journal article (peer-reviewed)abstract
- We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in Fan et al. [Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package gpumd. We increase the accuracy of NEP models both by improving the radial functions in the atomic-environment descriptor using a linear combination of Chebyshev basis functions and by extending the angular descriptor with some four-body and five-body contributions as in the atomic cluster expansion approach. We also detail our efficient implementation of the NEP approach in graphics processing units as well as our workflow for the construction of NEP models and demonstrate their application in large-scale atomistic simulations. By comparing to state-of-the-art MLPs, we show that the NEP approach not only achieves above-average accuracy but also is far more computationally efficient. These results demonstrate that the gpumd package is a promising tool for solving challenging problems requiring highly accurate, large-scale atomistic simulations. To enable the construction of MLPs using a minimal training set, we propose an active-learning scheme based on the latent space of a pre-trained NEP model. Finally, we introduce three separate Python packages, viz., gpyumd, calorine, and pynep, that enable the integration of gpumd into Python workflows.
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16. |
- Fang, Ruisen, et al.
(author)
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Late Ediacaran cavity-dwelling filamentous microorganisms accommodated in a valve-like organism from the uppermost Dengying Formation in eastern Yunnan of South China
- 2022
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In: Precambrian Research. - : Elsevier. - 0301-9268 .- 1872-7433. ; 379
-
Journal article (peer-reviewed)abstract
- The EdiacaranâCambrian transition, one of the major turning points in Earthâs history, is characterized by an epoch-making change in biosphere. In South China, the late Ediacaran Dengying Formation (ca. 551â538Â Ma) is an important stratigraphic unit yielding trace fossils, tubular skeletal fossils and some complex forms that represent possible bilateral animals. The fossil-bearing Ediacaran strata of eastern Yunnan is hitherto known from the Jiucheng Member containing the Jiangchuan Biota, together with the enigmatic cosmopolitan taxon Shaanxilithes. Here, we present for the first time cavity-dwelling filamentous microorganisms accommodated within a valve-like fossil from the upper Baiyanshao Member of the Dengying Formation at the Sujiawa Section in Huize County, eastern Yunnan of China. SEM scanning and Micro-CT reconstruction indicate that the well-preserved filaments were characterized by mycelial network structures with abundant branching pattern. Preservation of filamentous microorganisms might result from the decay process of soft parts that were originally accommodated and enclosed within the valve-like organism, and subsequently preserved by early diagenetic phosphatization, which obscures their original organic identity and chemical composition. This paper potentially presents the first fossil evidence of a saprophytic relationship between microorganisms as decomposers and a valve-like organism prior to the eve of the Cambrian Explosion of metazoan animals.
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17. |
- Fu, Rao, et al.
(author)
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First report of Sphenothallus Hall, 1847 from the lower Cambrian of North China
- 2023
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In: Alcheringa. - 0311-5518 .- 1752-0754. ; , s. 1-9
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Journal article (peer-reviewed)abstract
- Sphenothallus is a tubular organism that is one of the most widely distributed and longest-ranging genera through the Palaeozoic. Despite its apparent cosmopolitan distribution, the genus has never been reported from North China. New specimens of Sphenothallus sp. have been discovered in the upper part of the Houjiashan and base of the Mantou formations (early to middle Age 4, Epoch 2, Cambrian) in Jiangsu Province, North China. The specimens are small tubes (up to 5 mm long) and have typical Sphenothallus characteristics, such as a multilayered lamellar structure, and subcircular to elliptical transverse cross-section with a pair of longitudinal thickenings situated at the widest diameter. Our material shows that both the rate of apertural expansion and the curvature of the tubes are significantly larger in early growth stages than in the later growth stages. As the diameter of the aperture increases, the transverse cross-section of the Sphenothallus sp. tube changes from subcircular at the proximal end to elliptical or lenticular at the distal end, and its wall thickness changes from uniform to thickening longitudinally. The discovery of Sphenothallus sp. from the North China Platform represents an extension of its palaeogeographic range during the Cambrian.
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18. |
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19. |
- Ji, Xinyu, et al.
(author)
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Epigenetic–smoking interaction reveals histologically heterogeneous effects of TRIM27 DNA methylation on overall survival among early-stage NSCLC patients
- 2020
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In: Molecular Oncology. - : Wiley. - 1574-7891 .- 1878-0261. ; 14:11, s. 2759-2774
-
Journal article (peer-reviewed)abstract
- Tripartite motif containing 27 (TRIM27) is highly expressed in lung cancer, including non-small-cell lung cancer (NSCLC). Here, we profiled DNA methylation of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tumours from 613 early-stage NSCLC patients and evaluated associations between CpG methylation of TRIM27 and overall survival. Significant CpG probes were confirmed in 617 samples from The Cancer Genome Atlas. The methylation of the CpG probe cg05293407TRIM27 was significantly associated with overall survival in patients with LUSC (HR = 1.65, 95% CI: 1.30–2.09, P = 4.52 × 10−5), but not in patients with LUAD (HR = 1.08, 95% CI: 0.87–1.33, P = 0.493). As incidence of LUSC is associated with higher smoking intensity compared to LUAD, we investigated whether smoking intensity impacted on the prognostic effect of cg05293407TRIM27 methylation in NSCLC. LUSC patients had a higher average pack-year of smoking (37.49LUAD vs 54.79LUSC, P = 1.03 × 10−19) and included a higher proportion of current smokers than LUAD patients (28.24%LUAD vs 34.09%LUSC, P = 0.037). cg05293407TRIM27 was significantly associated with overall survival only in NSCLC patients with medium–high pack-year of smoking (HR = 1.58, 95% CI: 1.26–1.96, P = 5.25 × 10−5). We conclude that cg05293407TRIM27 methylation is a potential predictor of LUSC prognosis, and smoking intensity may impact on its prognostic value across the various types of NSCLC.
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20. |
- Jia, Xiaomin, et al.
(author)
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Single crystal metal-organic framework constructed by vertically self-pillared nanosheets and its derivative for oriented lithium plating
- 2021
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In: Cuihuà xuébào. - : Elsevier BV. - 0253-9837 .- 1872-2067. ; 42:9, s. 1553-1560
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Journal article (peer-reviewed)abstract
- This vertically self-pillared (VSP) structure extends the application range of traditional porous materials with facile mass/ion transport and enhanced reaction kinetics. Here, we prepare a single crystal metal-organic framework (MOF), employing the ZIF-67 structure as a proof of concept, which is constructed by vertically self-pillared nanosheets (VSP-MOF). We further converted VSP-MOF into VSP-cobalt sulfide (VSP-CoS2) through a sulfidation process. Catalysis plays an important role in almost all battery technologies; for metallic batteries, lithium anodes exhibit a high theoretical specific capacity, low density, and low redox potential. However, during the half-cell reaction (Li++e=Li), uncontrolled dendritic Li penetrates the separator and solid electrolyte interphase layer. When employed as a composite scaffold for lithium metal deposition, there are many advantage to using this framework: 1) the VSP-CoS2 substrate provides a high specific surface area to dissipate the ion flux and mass transfer and acts as a pre-catalyst, 2) the catalytic Co center favors the charge transfer process and preferentially binds the Li+ with the enhanced electrical fields, and 3) the VSP structure guides the metallic propagation along the nanosheet 2D orientation without the protrusive dendrites. All these features enable the VSP structure in metallic batteries with encouraging performances.
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21. |
- Kang, Nai-xin, et al.
(author)
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Anemoside B4 inhibits enterovirus 71 propagation in mice through upregulating 14-3-3 expression and type I interferon responses
- 2022
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In: Acta Pharmacologica Sinica. - : Springer Nature. - 1671-4083 .- 1745-7254. ; 43, s. 977-991
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Journal article (peer-reviewed)abstract
- Enterovirus 71 (EV71) is the major pathogens of human hand, foot, and mouth disease (HFMD). EV71 efficiently escapes innate immunity responses of the host to cause infection. At present, no effective antiviral drugs for EV71 are available. Anemoside B4 (B4) is a natural saponin isolated from the roots of Pulsatilla chinensis (Bunge) Regel. P. chinensis extracts that shows a wide variety of biological activities. In this study, we investigated the antiviral activities of B4 against EV71 both in cell culture and in suckling mice. We showed that B4 (12.5-200 mu M) dose dependently increased the viability of EV71-infected RD cells with an IC50 value of 24.95 +/- 0.05 mu M against EV71. The antiviral activity of B4 was associated with enhanced interferon (IFN)-beta response, since knockdown of IFN-beta abolished its antiviral activity. We also confirmed that the enhanced IFN response was mediated via activation of retinoic acid-inducible gene I (RIG-I) like receptors (RLRs) pathway, and it was executed by upregulation of 14-3-3 protein, which disrupted the interaction between yes-associated protein (YAP) and interferon regulatory factor 3 (IRF3). By using amino acids in cell culture (SILAC)-based proteomics profiling, we identified the Hippo pathway as the top-ranking functional cluster in B4-treated EV71-infected cells. In vivo experiments were conducted in suckling mice (2-day-old) infected with EV71 and subsequently B4 (200 mg center dot kg(-1) center dot d(-1), i.p.) was administered for 16 days. We showed that B4 administration effectively suppressed EV71 replication and improved muscle inflammation and limb activity. Meanwhile, B4 administration regulated the expressions of HFMD biomarkers IL-10 and IFN-gamma, attenuating complications of EV71 infection. Collectively, our results suggest that B4 could enhance the antiviral effect of IFN-beta by orchestrating Hippo and RLRs pathway, and B4 would be a potential lead compound for developing an anti-EV71 drug.
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22. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
-
Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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23. |
- Lanigan, Fiona, et al.
(author)
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Delineating Transcriptional Networks of Prognostic Gene Signatures Refines Treatment Recommendations for Lymph Node-negative Breast Cancer Patients.
- 2015
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In: The FEBS Journal. - : Wiley. - 1742-464X. ; 282:18, s. 3455-3473
-
Journal article (peer-reviewed)abstract
- The majority of women diagnosed with lymph node-negative breast cancer are unnecessarily treated with damaging chemotherapeutics following surgical resection. This highlights the importance of understanding and more accurately predicting patient prognosis. Here, we define the transcriptional networks regulating well-established prognostic gene expression signatures. We find that the same set of transcriptional regulators consistently lie upstream of both 'prognosis' and 'proliferation' gene signatures, suggesting that a central transcriptional network underpins a shared phenotype within these signatures. Strikingly, the master transcriptional regulators within this network predict recurrence risk for lymph node-negative breast cancer better than currently used multi-gene prognostic assays, particularly in lymph node-negative, estrogen receptor-positive patients. Simultaneous examination of p16(INK) (4A ) expression, which predicts tumors that have bypassed cellular senescence, revealed that intermediate levels of p16(INK) (4A) correlate with an intact pRB pathway and improved survival. A combination of these master transcriptional regulators and p16(INK) (4A) , termed the OncoMasTR score, stratifies tumours based on their proliferative and senescence capacity, facilitating a clearer delineation of lymph node-negative breast cancer patients at high risk of recurrence, and thus requiring chemotherapy. Furthermore, OncoMasTR accurately classifies over 60% of patients as 'low risk', an improvement on existing prognostic assays, which has the potential to reduce overtreatment in early-stage patients. Taken together, this study provides new insights into the transcriptional regulation of cellular proliferation in breast cancer and provides an opportunity to enhance and streamline breast cancer prognosis. This article is protected by copyright. All rights reserved.
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24. |
- Li, Bo, et al.
(author)
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Therapeutic rationale to target highly expressed CDK7 conferring poor outcomes in triple-negative breast cancer
- 2017
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In: Cancer Research. - 0008-5472. ; 77:14, s. 3834-3845
-
Journal article (peer-reviewed)abstract
- Triple-negative breast cancer (TNBC) patients commonly exhibit poor prognosis and high relapse after treatment, but there remains a lack of biomarkers and effective targeted therapies for this disease. Here, we report evidence highlighting the cell-cycle–related kinase CDK7 as a driver and candidate therapeutic target in TNBC. Using publicly available transcriptomic data from a collated set of TNBC patients (n ¼ 383) and the METABRIC TNBC dataset (n ¼ 217), we found CDK7 mRNA levels to be correlated with patient prognosis. High CDK7 protein expression was associated with poor prognosis within the RATHER TNBC cohort (n ¼ 109) and the METABRIC TNBC cohort (n ¼ 203). The highly specific CDK7 kinase inhibitors, BS-181 and THZ1, each downregulated CDK7-mediated phosphorylation of RNA polymerase II, indicative of transcriptional inhibition, with THZ1 exhibiting 500-fold greater potency than BS-181. Mechanistic investigations revealed that the survival of MDA-MB-231 TNBC cells relied heavily on the BCL-2/BCL-XL signaling axes in cells. Accordingly, we found that combining the BCL-2/BCL-XL inhibitors ABT-263/ABT199 with the CDK7 inhibitor THZ1 synergized in producing growth inhibition and apoptosis of human TNBC cells. Collectively, our results highlight elevated CDK7 expression as a candidate biomarker of poor prognosis in TNBC, and they offer a preclinical proof of concept for combining CDK7 and BCL-2/BCL-XL inhibitors as a mechanism-based therapeutic strategy to improve TNBC treatment.
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25. |
- Li, Xing-Yu, et al.
(author)
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Comparative Study of Dayside Pulsating Auroras Induced by Ultralow-Frequency Waves
- 2023
-
In: Universe. - : MDPI AG. - 2218-1997. ; 9:6
-
Journal article (peer-reviewed)abstract
- Pulsating auroras are usually observed with ultralow-frequency (ULF) waves in the Pc 3-5 band (period 10-600 s). These auroras are thought to result from interactions between energetic electrons and chorus waves, but their relationship with ULF waves remains an open question. In this study, we investigated this question by conducting a comparative study on two ULF wave events with pulsating auroras observed near the magnetic footprints. Conjugate observations from the Magnetospheric Multiscale mission and the Chinese Yellow River Station were used. In both events, lower-band chorus waves were observed, which were suggested to be connected with the auroral pulsations by wavelet analysis. The intensity of these waves oscillates at the period of the ULF waves, but the physics laid behind them differs by events. During the event of 22 January 2019, compressional ULF waves changed the threshold for the whistler anisotropy instability periodically, affecting the emission of chorus waves. In the event on 10 January 2016, poloidal ULF waves modulated the chorus wave generation by regulating electron temperature anisotropy through drift resonance. ULF waves in these events may originate from perturbations in the solar wind. We highlight the role of ULF waves in the solar wind-magnetosphere-ionosphere coupling, which requires further study.
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26. |
- Liang, Yue, et al.
(author)
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Late Ordovician lingulid brachiopods from the Pingliang Formation (Shaanxi Province, North China) : Morphological and ecological implications
- 2024
-
In: Journal of Asian Earth Sciences. - : Elsevier. - 1367-9120 .- 1878-5786. ; 263
-
Journal article (peer-reviewed)abstract
- Brachiopods first appeared in the early Cambrian and persist till present. They are one of the main lineages of marine invertebrates that diversified throughout the Paleozoic and reached their maximum diversity of high-rank taxonomy during the Ordovician. During this time interval, brachiopods were mainly dominated by the articulated Orthida and Strophomenida, which represent major components of the Paleozoic Evolutionary Fauna; however, the inarticulated lingulid brachiopods (Order Lingulida) were comparatively less abundant and received less attention during this time period. Here, we report a new record of the lingulid brachiopod Anomaloglossa porca from the Upper Ordovician (Sandbian) Pingliang Formation of the Xilinggou Section, Shaanxi Province, North China. Collected specimens are preserved as calcium phosphatic shells with highly mineralization which preserve detailed morphology and shell ornamentation of both ventral and dorsal valves. The new occurrence of A. porca extends its paleogeographic distribution from Gondwana and Tarim to North China Platform. Moreover, comprehensive geometric morphometric analysis of A. porca is performed and the results indicate that both the shell shape and pseudointerarea are very close to the recent infaunal lingulids. If interpreted correctly, the fossils represent the first example of infaunal lifestyles achieved by Ordovician lingulids from North China, exhibiting the ecological complexities of the Late Ordovician benthos composed of epibenthos and infaunas as well.
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27. |
- Liu, Suli, et al.
(author)
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A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17
- 2013
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 12:1, s. 49-61
-
Journal article (peer-reviewed)abstract
- We report progress assembling the parts list for chromosome 17 and illustrate the various processes that we have developed to integrate available data from diverse genomic and proteomic knowledge bases. As primary resources, we have used GPMDB, neXtProt, PeptideAtlas, Human Protein Atlas (HPA), and GeneCards. All sites share the common resource of Ensembl for the genome modeling information. We have defined the chromosome 17 parts list with the following information: 1169 protein-coding genes, the numbers of proteins confidently identified by various experimental approaches as documented in GPMDB, neXtProt, PeptideAtlas, and HPA, examples of typical data sets obtained by RNASeq and proteomic studies of epithelial derived tumor cell lines (disease proteome) and a normal proteome (peripheral mononuclear cells), reported evidence of post-translational modifications, and examples of alternative splice variants (ASVs). We have constructed a list of the 59 "missing" proteins as well as 201 proteins that have inconclusive mass spectrometric (MS) identifications. In this report we have defined a process to establish a baseline for the incorporation of new evidence on protein identification and characterization as well as related information from transcriptome analyses. This initial list of "missing" proteins that will guide the selection of appropriate samples for discovery studies as well as antibody reagents. Also we have illustrated the significant diversity of protein variants (including post-translational modifications, PTMs) using regions on chromosome 17 that contain important oncogenes. We emphasize the need for mandated deposition of proteomics data in public databases, the further development of improved PTM, ASV, and single nucleotide variant (SNV) databases, and the construction of Web sites that can integrate and regularly update such information. In addition, we describe the distribution of both clustered and scattered sets of protein families on the chromosome. Since chromosome 17 is rich in cancer-associated genes, we have focused the clustering of cancer-associated genes in such genomic regions and have used the ERBB2 amplicon as an example of the value of a proteogenomic approach in which one integrates transcriptomic with proteomic information and captures evidence of coexpression through coordinated regulation.
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28. |
- Luo, Mei, et al.
(author)
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First Report of Small Skeletal Fossils from the Upper Guojiaba Formation (Series 2, Cambrian), Southern Shaanxi, South China
- 2023
-
In: Biology. - : MDPI. - 2079-7737. ; 12:7
-
Journal article (peer-reviewed)abstract
- A small skeletal fossil assemblage is described for the first time from the bioclastic limestone interbeds of the siltstone-dominated Guojiaba Formation, southern Shaanxi, China. The carbonate-hosted fossils include brachiopods (Eohadrotreta zhujiahensis, Eohadrotreta zhenbaensis, Spinobolus sp., Kuangshanotreta malungensis, Kyrshabaktella sp., Lingulellotreta yuanshanensis, Eoobolus incipiens, and Eoobolus sp.), sphenothallids (Sphenothallus sp.), archaeocyaths (Robustocyathus sp. and Yukonocyathus sp.), bradoriids (Kunmingella douvillei), chancelloriids sclerites (Onychia sp., Allonnia sp., Diminia sp., Archiasterella pentactina, and Chancelloria cf. eros), echinoderm plates, fragments of trilobites (Eoredlichia sp.), and hyolithelminths. The discovery of archaeocyaths in the Guojiaba Formation significantly extends their stratigraphic range in South China from the early Tsanglangpuian at least to the late Chiungchussuan. Thus, the Guojiaba Formation now represents the lowest known stratigraphic horizon where archaeocyath fossils have been found in the southern Shaanxi area. The overall assemblage is most comparable, in terms of composition, to Small skeletal fossil (SSF) assemblages from the early Cambrian Chengjiang fauna recovered from the Yu’anshan Formation in eastern Yunnan Province. The existing position that the Guojiaba Formation is correlated with Stage 3 in Cambrian Series 2 is strongly upheld based on the fossil assemblage recovered in this study.Simple SummarySmall skeletal fossils are reported for the first time from the early Cambrian Guojiaba Formation, southern Shaanxi, China. All specimens were recovered from bioclastic limestone interbeds and encompass a wide variety of skeletal clades, including brachiopods, sphenothallids, archaeocyaths, bradoriids, sponge spicules, echinoderm plates, and trilobite spines. The archaeocyaths described herein are considerably older than those described from the Xiannvdong Formation, which was previously assumed to contain the lowest archaeocyath-bearing horizons in South China. The brachiopod Lingulellotreta yuanshanensis is recorded for the first time from the Fucheng area, with previous records confined mainly to the Chengjiang Fauna-bearing Yu’anshan Formation in the lower Cambrian, the eastern Yunnan Province. Micro-morphological and elemental analyses of the small skeletal fossil assemblages were carried out using SEM, BSEM, and Micro X–ray fluorescence. The skeletal fauna in the Guojiaba Formation resembles the assemblages recovered from the upper Yu’anshan Formation (Chengjiang Fauna) in eastern Yunnan Province. Based on the recovered assemblage, the biostratigraphic age of the Guojiaba Formation correlates with the Chiungchussuan Stage (Stage 3 of Cambrian Series 2).
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29. |
- Lv, Zhong-Peng, et al.
(author)
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Cation field-strength effects on ion irradiation-induced mechanical property changes of borosilicate glass structures
- 2023
-
In: Journal of The American Ceramic Society. - 0002-7820 .- 1551-2916. ; 106:10, s. 5766-5780
-
Journal article (peer-reviewed)abstract
- We examine the impact of the glass network-modifier cation field strength (CFS) on ion irradiation-induced mechanical property changes in borosilicate (BS) glasses for the ternary M2O-B2O3-SiO2 systems with M = {Na, K, Rb} and the quaternary [0.5M((2))O-0.5Na(2)O]-B2O3-SiO2 systems with M = {Li, Na, K, Rb Mg, Ca, Sr, Ba}. B-11 nuclear magnetic resonance (NMR) experiments on the as-prepared BS glasses yielded the fractional population of four-coordinated B species (B-[4]) out of all {B-[3], B-[4]} groups in the glass network, along with the fraction of B-[4]-O-Si linkages out of all B-[4]-O-Si/B bonds. Both parameters correlated linearly with the (average) CFS of the M+ and/or {M(2)+, Na+} cations. Both the nanoindentation-derived hardness and Young's modulus values of the glasses reduced upon their irradiation by Si2+ ions, with the property deterioration decreasing linearly with increasing Mz+ CFS, that is, for higher Mz+center dot center dot center dot O interaction strength. The irradiation damage of the glass network also increased linearly with the fraction of B-[4]-O-Si linkages, which are the second weakest in the structure after the Mz+center dot center dot center dot O bonds. Our results underscore the advantages of employing BS glasses with high-CFS cations for enhancing the radiation resistance for nuclear waste storage.
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30. |
- Ma, Xin, et al.
(author)
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[CH3NH3][M(HCOO)3]-based 2D porous NiCo2S4 nanosheets for high-performance supercapacitors with high power densities
- 2022
-
In: Chemical Engineering Journal. - : Elsevier. - 1385-8947 .- 1873-3212. ; 437
-
Journal article (peer-reviewed)abstract
- Cost-effective and high-performance electrode materials for energy storage and conversion are essential for commercial applications. In this work, the influence of solvent on the morphologies of [CH3NH3][M(HCOO)3] precursors was studied to design and synthesize two-dimensional (2D) porous NiCo2S4 nanosheets with different structures. As an electrode material for supercapacitors, Microflower-NiCo2S4 exhibits excellent capacitance (1,141 F g−1 at 1 A g−1) and stability (88.2% of initial capacitance maintained after 5,000 cycles at 5 A g−1). Moreover, an asymmetric capacitor was constructed using Microflower-NiCo2S4 and porous carbon (PC) and demonstrated an energy density of 51.25 Wh kg−1 at a power density of 397.5 W kg−1. When two Microflower-NiCo2S4//PC asymmetric supercapacitors were assembled in series, the device supplied power for an alarm clock with dimensions of 6.1 × 6.1 cm2 for more than 32 min. Therefore, the preparation of metal sulfides and metal oxides with hollow structures using a [CH3NH3][M(HCOO)3]-template has potential applications in energy storage and conversion.
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31. |
- Mei, J, et al.
(author)
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Development and external validation of a COVID-19 mortality risk prediction algorithm: a multicentre retrospective cohort study
- 2020
-
In: BMJ open. - : BMJ. - 2044-6055. ; 10:12, s. e044028-
-
Journal article (peer-reviewed)abstract
- This study aimed to develop and externally validate a COVID-19 mortality risk prediction algorithm.DesignRetrospective cohort study.SettingFive designated tertiary hospitals for COVID-19 in Hubei province, China.ParticipantsWe routinely collected medical data of 1364 confirmed adult patients with COVID-19 between 8 January and 19 March 2020. Among them, 1088 patients from two designated hospitals in Wuhan were used to develop the prognostic model, and 276 patients from three hospitals outside Wuhan were used for external validation. All patients were followed up for a maximal of 60 days after the diagnosis of COVID-19.MethodsThe model discrimination was assessed by the area under the receiver operating characteristic curve (AUC) and Somers’ D test, and calibration was examined by the calibration plot. Decision curve analysis was conducted.Main outcome measuresThe primary outcome was all-cause mortality within 60 days after the diagnosis of COVID-19.ResultsThe full model included seven predictors of age, respiratory failure, white cell count, lymphocytes, platelets, D-dimer and lactate dehydrogenase. The simple model contained five indicators of age, respiratory failure, coronary heart disease, renal failure and heart failure. After cross-validation, the AUC statistics based on derivation cohort were 0.96 (95% CI, 0.96 to 0.97) for the full model and 0.92 (95% CI, 0.89 to 0.95) for the simple model. The AUC statistics based on the external validation cohort were 0.97 (95% CI, 0.96 to 0.98) for the full model and 0.88 (95% CI, 0.80 to 0.96) for the simple model. Good calibration accuracy of these two models was found in the derivation and validation cohort.ConclusionThe prediction models showed good model performance in identifying patients with COVID-19 with a high risk of death in 60 days. It may be useful for acute risk classification.
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32. |
- Michaut, Magali, et al.
(author)
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Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer.
- 2016
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
-
Journal article (peer-reviewed)abstract
- Invasive lobular carcinoma (ILC) is the second most frequently occurring histological breast cancer subtype after invasive ductal carcinoma (IDC), accounting for around 10% of all breast cancers. The molecular processes that drive the development of ILC are still largely unknown. We have performed a comprehensive genomic, transcriptomic and proteomic analysis of a large ILC patient cohort and present here an integrated molecular portrait of ILC. Mutations in CDH1 and in the PI3K pathway are the most frequent molecular alterations in ILC. We identified two main subtypes of ILCs: (i) an immune related subtype with mRNA up-regulation of PD-L1, PD-1 and CTLA-4 and greater sensitivity to DNA-damaging agents in representative cell line models; (ii) a hormone related subtype, associated with Epithelial to Mesenchymal Transition (EMT), and gain of chromosomes 1q and 8q and loss of chromosome 11q. Using the somatic mutation rate and eIF4B protein level, we identified three groups with different clinical outcomes, including a group with extremely good prognosis. We provide a comprehensive overview of the molecular alterations driving ILC and have explored links with therapy response. This molecular characterization may help to tailor treatment of ILC through the application of specific targeted, chemo- and/or immune-therapies.
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33. |
- O'Hurley, Gillian, et al.
(author)
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Investigation of molecular alterations of AKT-3 in triple-negative breast cancer
- 2014
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In: Histopathology. - : Wiley. - 0309-0167 .- 1365-2559. ; 64:5, s. 660-670
-
Journal article (peer-reviewed)abstract
- Aims Triple-negative breast cancer (TNBC) is responsible for a disproportionate number of breast cancer (BC) deaths, owing to its intrinsic aggressiveness and a lack of treatment options, especially targeted therapies. Thus, there is an urgent need for the development of better targeted treatments for TNBC. Molecular alteration of AKT-3 was previously reported in oestrogen receptor (ER)-positive BC. AKT-3 has also been suggested to play a role in hormone-unresponsive BC. The aim of this study was to investigate molecular alterations of AKT-3 in TNBC, to perform associated survival analysis, and to compare these findings with the incidence of AKT-3 molecular alterations in ER-positive BC. Results Our study revealed AKT-3 amplification and deletions in 11% (9/82) and 13% (11/82) of TNBCs, respectively. In contrast, 1% (2/209) of ER-positive BCs were found to have AKT-3 amplifications and deletions. A higher prevalence of AKT-3 copy number gains was observed in TNBC [26% (21/82)] than in ER-positive BC [9% (19/209)]. AKT-3 amplification together with Akt-3 protein expression was negatively associated with recurrence-free survival in TNBC. Furthermore, a negative association between high AKT-3 copy number and recurrence-free survival was observed. Conclusion AKT-3 amplification could represent a potentially relevant oncogenic event in a subset of TNBCs that may, in turn, select cells sensitive to Akt-3 inhibitors.
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34. |
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35. |
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36. |
- Qian, Zhen, et al.
(author)
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Vectorized dataset of roadside noise barriers in China using street view imagery
- 2022
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In: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 14:9, s. 4057-4076
-
Journal article (peer-reviewed)abstract
- Roadside noise barriers (RNBs) are important urban infrastructures to ensure that cities remain liveable. However, the absence of accurate and large-scale geospatial data on RNBs has impeded the increasing progress of rational urban planning, sustainable cities, and healthy environments. To address this problem, this study creates a vectorized RNB dataset in China using street view imagery and a geospatial artificial intelligence framework. First, intensive sampling is performed on the road network of each city based on OpenStreetMap, which is used as the georeference for downloading 6 x 10(6) Baidu Street View (BSV) images. Furthermore, considering the prior geographic knowledge contained in street view images, convolutional neural networks incorporating image context information (IC-CNNs) based on an ensemble learning strategy are developed to detect RNBs from the BSV images. The RNB dataset presented by polylines is generated based on the identified RNB locations, with a total length of 2667.02 km in 222 cities. Last, the quality of the RNB dataset is evaluated from two perspectives, i.e., the detection accuracy and the completeness and positional accuracy. Specifically, based on a set of randomly selected samples containing 10 000 BSV images, four quantitative metrics are calculated, with an overall accuracy of 98.61 %, recall of 87.14 %, precision of 76.44 %, and F-1 score of 81.44 %. A total length of 254.45 km of roads in different cities are manually surveyed using BSV images to evaluate the mileage deviation and overlap level between the generated and surveyed RNBs. The root mean squared error for the mileage deviation is 0.08 km, and the intersection over union for overlay level is 88.08% +/- 2.95 %. The evaluation results suggest that the generated RNB dataset is of high quality and can be applied as an accurate and reliable dataset for a variety of large-scale urban studies, such as estimating the regional solar photovoltaic potential, developing 3D urban models, and designing rational urban layouts. Besides that, the benchmark dataset of the labeled BSV images can also support more work on RNB detection, such as developing more advanced deep learning algorithms, fine-tuning the existing computer vision models, and analyzing geospatial scenes in BSV. The generated vectorized RNB dataset and the benchmark dataset of labeled BSV imagery are publicly available at https://doi.org/10.11888/Others.tpdc.271914 (Chen, 2021).
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37. |
- Qin, Yue, et al.
(author)
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A multi-scale map of cell structure fusing protein images and interactions
- 2021
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In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 600:7889, s. 536-
-
Journal article (peer-reviewed)abstract
- The cell is a multi-scale structure with modular organization across at least four orders of magnitude(1). Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are typically treated separately(2,3). Here we integrate immunofluorescence images in the Human Protein Atlas(4) with affinity purifications in BioPlex(5) to create a unified hierarchical map of human cell architecture. Integration is achieved by configuring each approach as a general measure of protein distance, then calibrating the two measures using machine learning. The map, known as the multi-scale integrated cell (MuSIC 1.0), resolves 69 subcellular systems, of which approximately half are to our knowledge undocumented. Accordingly, we perform 134 additional affinity purifications and validate subunit associations for the majority of systems. The map reveals a pre-ribosomal RNA processing assembly and accessory factors, which we show govern rRNA maturation, and functional roles for SRRM1 and FAM120C in chromatin and RPS3A in splicing. By integration across scales, MuSIC increases the resolution of imaging while giving protein interactions a spatial dimension, paving the way to incorporate diverse types of data in proteome-wide cell maps.
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38. |
- Schuettpelz, Eric, et al.
(author)
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A community-derived classification for extant lycophytes and ferns
- 2016
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In: Journal of Systematics and Evolution. - : Wiley. - 1674-4918 .- 1759-6831. ; 54:6, s. 563-603
-
Journal article (peer-reviewed)abstract
- Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community-based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.
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39. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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In: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
-
Journal article (peer-reviewed)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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40. |
- Walsh, Louise, et al.
(author)
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BET Inhibition as a Rational Therapeutic Strategy for Invasive Lobular Breast Cancer
- 2019
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In: Clinical cancer research : an official journal of the American Association for Cancer Research. - 1078-0432. ; 25:23, s. 7139-7150
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Journal article (peer-reviewed)abstract
- PURPOSE: Invasive lobular carcinoma (ILC) is a subtype of breast cancer accounting for 10% of breast tumors. The majority of patients are treated with endocrine therapy; however, endocrine resistance is common in estrogen receptor-positive breast cancer and new therapeutic strategies are needed. Bromodomain and extraterminal inhibitors (BETi) are effective in diverse types of breast cancer but they have not yet been assessed in ILC.EXPERIMENTAL DESIGN: We assessed whether targeting the BET proteins with JQ1 could serve as an effective therapeutic strategy in ILC in both 2D and 3D models. We used dynamic BH3 profiling and RNA-sequencing (RNA-seq) to identify transcriptional reprograming enabling resistance to JQ1-induced apoptosis. As part of the RATHER study, we obtained copy-number alterations and RNA-seq on 61 ILC patient samples.RESULTS: Certain ILC cell lines were sensitive to JQ1, while others were intrinsically resistant to JQ1-induced apoptosis. JQ1 treatment led to an enhanced dependence on antiapoptotic proteins and a transcriptional rewiring inducing fibroblast growth factor receptor 1 (FGFR1). This increase in FGFR1 was also evident in invasive ductal carcinoma (IDC) cell lines. The combination of JQ1 and FGFR1 inhibitors was highly effective at inhibiting growth in both 2D and 3D models of ILC and IDC. Interestingly, we found in the RATHER cohort of 61 ILC patients that 20% had FGFR1 amplification and we showed that high BRD3 mRNA expression was associated with poor survival specifically in ILC.CONCLUSIONS: We provide evidence that BETi either alone or in combination with FGFR1 inhibitors or BH3 mimetics may be a useful therapeutic strategy for recurrent ILC patients.
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41. |
- Wang, Di, et al.
(author)
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Enhancing adhesion and durability: A biomimetic approach with dopamine-modified lignin-polydimethylsiloxane coatings
- 2024
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In: Corrosion Science. - : Elsevier. - 0010-938X .- 1879-0496. ; 236
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Journal article (peer-reviewed)abstract
- Corrosion causes significant challenges in industrial settings, leading to economic losses and safety concerns. Previously, we developed a lignin-polydimethylsiloxane (lignin-PDMS) coating that exhibited high corrosion resistance. However, the adhesion of the developed lignin-PDMS coating to carbon steel was limited, affecting its overall performance. To address this, we incorporated dopamine (DOPA), known for its strong adhesive properties, as a pre-treatment before applying the coating. It was found that the adhesion and corrosion resistance of lignin-PDMS coated steel could be improved by adjusting the pH value of the DOPA solution. The steel treated with pH 4.5 DOPA solution showed two times higher adhesion strength to the coating than non-treated steel. After the DOPA treatment, the coating can maintain high barrier property for at least 3 months in 1 M NaCl solution, which is even better than commercial gelcoat, demonstrating super corrosion protection. Quartz Crystal Microbalance with Dissipation (QCM-D) and X-ray Photoelectron Spectroscopy (XPS) analyses confirmed the DOPA deposition on the steel surface. Our findings show that the DOPA-lignin-PDMS system is an environmentally friendly and efficient solution for enhancing the durability of steels in corrosive environments.
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42. |
- Yang, Tien-Nan, et al.
(author)
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Variations in monsoonal rainfall over the last 21 kyr inferred from sedimentary organic matter in Tung-Yuan Pond, southern Taiwan
- 2011
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In: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 30:23-24, s. 3413-3422
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Journal article (peer-reviewed)abstract
- Changes in paleorainfall intensity linked to the strength of the East Asian (EA) summer monsoon since 21 cal kyr BP are inferred from the organic matter contents of a 15-m sediment core from Tung-Yuan Pond in southern Taiwan. High total organic carbon/total nitrogen (TOC/TN) values in association with increased TOC content suggest that more soil-derived material containing terrestrial organic matter (OM) was delivered to the lake during periods of increased runoff associated with extensive precipitation that resulted from intensified summer monsoons, whereas low values indicate OM possessing a dominant algal origin during weakened summer monsoons. Rainfall intensity in terms of the proportion of terrestrial OM was high in four periods: the last deglaciation (similar to 17.2 to similar to 12.2 ka), the early Holocene (similar to 10.6 to similar to 8.6 ka), the middle Holocene Thermal Optimum (similar to 7.7 to similar to 5 ka) and the late Holocene (similar to 4.2 to similar to 2 ka), whereas it was low in the intervening time periods. High TOC/TN values coincide with peak values of summer insolation, and thus the strongest EA summer monsoon during the early and middle Holocene: small drops in these ratios correspond to increasing and decreasing solar radiation in the deglacial period and the late Holocene, respectively. The four intervals with low TOC/TN ratios, as well as episodic drops of the ratios during the deglaciation and the early and late Holocene are concordant with the late last glacial (similar to 21 to similar to 17.2 ka), the Oldest (similar to 14.8 ka), the Older (similar to 13.3 ka) and the Younger Dryas (similar to 13 to similar to 11.5 ka), the 8.2 cold event (similar to 8.6-7.7 ka) and a late Holocene cold event (similar to 5-4.2 ka), and suggest a weakened EA summer monsoon during these times. Moreover, high frequency hydrological variability occurred during the early Holocene, heavy rainfall persisted during the middle Holocene, and precipitation intensity generally diminished after similar to 5 ka. The Tung-Yuan Pond sediment record indicates that the TOC/TN ratio can be used as a paleorainfall intensity proxy to trace variations in the EA summer monsoon strength in other small lakes. Crown Copyright
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43. |
- Yang, Xuan, et al.
(author)
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Geochemical records and environmental analysis of the Ediacaran-Cambrian boundary in Eastern Yunnan, South China
- 2023
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In: Frontiers in Earth Science. - 2296-6463. ; 11
-
Journal article (peer-reviewed)abstract
- The Ediacaran–Cambrian transition is characterized by an unprecedented change in biosphere, lithosphere, and atmosphere. However, the identification of this transition and its global correlation remains debated. East Yunnan is a region of utmost importance in the study of the Ediacaran-Cambrian transition. Although strata from this region have been well studied, recognition of the base of the Cambrian continues to be controversial. This paper presents, a carbon chemostratigraphic isotope and trace element profile through the Dengying and Zhujiaqing formations in the Sujiawa section in East Yunnan. Through carbon isotope and trace element analyses of the Dengying and Zhujiaqing formations we attempt to regionally correlate the section and discuss the paleo-marine redox environment changes during this period. The Fe content of samples is low and the Mn/Sr ratios of the majority of the Sujiawa section samples is lower than 10 and shows no correlations with δ13Ccarb and δ18Ocarb values, indicating that the samples retain near-primary δ13Ccarb characteristics. The carbon isotope profile from the Sujiawa section, shows a prominent negative δ13Ccarb in the basal Zhongyicun Member (N1’, −7.3‰) that most likely represents the prominent negative excursion recorded in Ediacaran-Cambrian strata across the world. REE patterns and Y/Ho ratios were used to screen samples, to ensure that the primary seawater REE features and Ce anomalies were preserved. The samples satisfying this screening process show seawater-like REE distribution patterns in leached carbonates and may have recorded Ce anomalies of the seawater from which the carbonates precipitated. These data show that the Baiyanshao Member has Ce/Ce* values between 0.57 and 0.88, the Daibu Member between 0.56 and 0.83, and the Zhongyicun Member between 0.60 and 0.96. The Ce anomalies through the section indicates that the region experienced suboxic-oxic-anoxic conditions throughout the Ediacaran-Cambrian period. Carbon isotope and trace element analyses indicate that the strata record a negative carbon isotope excursion event and anoxic conditions during the period of deposition. This study complements the carbon chemostratigraphic information and trace element data in the region and provides valuable clues for understanding the lithofacies changes through the Ediacaran and Cambrian in different regions of South China.
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44. |
- Yue, Cong, et al.
(author)
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Numerical Investigation on the Effect of Filler Distribution on Effective Thermal Conductivity of Thermal Interface Material
- 2008
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In: 2008 International Conference on Electronic Packaging Technology and High Density Packaging, ICEPT-HDP 2008; Pudong, Shanghai; China; 28 July 2008 through 31 July 2008. - 9781424427406 ; , s. C1-10
-
Conference paper (peer-reviewed)abstract
- Thermal interface materials have been widely adopted in the thermal management for electronics system. Most of the thermal interface materials are made of polymers with thermally conductive particles distributed inside to enhance the thermal conductivity. Thus it is essential to figure out the effective thermal conductivity of this composite material. In the present paper, a parameterized cubic cell model had been developed and implemented by the finite element method. The numerical simulations were carried out to investigate the effect of the filler distributions on the effective thermal conductivity of the thermal interface materials. The volume percentage loadings of the particles ranging from 13% to 74% had been considered, and different particle distribution patterns had also been analyzed. The simulation results were compared with the experimental data as well as other models. A fairly good agreement was obtained for the particle volume percentage loading under consideration, which verified the developed cubic cell model.
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45. |
- Yue, Siyao, et al.
(author)
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Brown carbon from biomass burning imposes strong circum-Arctic warming
- 2022
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In: ONE EARTH. - : Elsevier BV. - 2590-3330 .- 2590-3322. ; 5:3, s. 293-304
-
Journal article (peer-reviewed)abstract
- Rapid warming in the Arctic has a huge impact on the global environment. Atmospheric brown carbon (BrC) is one of the least understood and uncertain warming agents due to a scarcity of observations. Here, we performed direct observations of atmospheric BrC and quantified its light-absorbing properties during a 2 month circum-Arctic cruise in summer of 2017. Through observation-constrained modeling, we show that BrC, mainly originated from biomass burning in the mid-to high latitudes of the Northern Hemisphere (similar to 60%), can be a strong warming agent in the Arctic region, especially in the summer, with an average radiative forcing of-90 mW m(-2) (similar to 30% relative to black carbon). As climate change is projected to increase the frequency, intensity, and spread of wildfires, we expect BrC to play an increasing role in Arctic warming in the future.
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46. |
- Zhang, Juqing, et al.
(author)
-
Super-enhancers conserved within placental mammals maintain stem cell pluripotency
- 2022
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:40
-
Journal article (peer-reviewed)abstract
- Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolu-tion in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in pla-cental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of plu-ripotency as well as species-specific modulation of the pluripotency-associated regula-tory networks in mammals.
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47. |
- Zhang, Kai, et al.
(author)
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Quantifying the photovoltaic potential of highways in China
- 2022
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In: Applied Energy. - : Elsevier BV. - 0306-2619 .- 1872-9118. ; 324, s. 119600-
-
Journal article (peer-reviewed)abstract
- Installing photovoltaic (PV) modules on highways is considered a promising way to support carbon neutrality in China. However, collecting the area of the highway, and precisely assessing the shadow area of the highway under complex terrain remain challenges. That severely hinders the assessment of highway PV potential. To address these challenges, a spatiotemporal model is developed in this study to estimate the annual solar PV potential on highways over the whole Chinese territory. First, the areas of different highway segments are calculated based on highway network and highway toll stations. Second, hourly shadow area on highways created by nearby terrain is estimated based on a digital elevation model (DEM). When calculating the highway PV potential, the solar irradiation received in these shadow areas is regarded as zero. Finally, the PV potential of all lanes and emergency lanes was estimated at the prefecture-level city scale using surface radiation data and radiation assessment models. Based on the highway data with a total mileage of 143,684 km at the end of 2020, the results show that the annual PV potential is 3,932 TW and that the corresponding installed capacity is 700.85 GW, which can generate clean electricity at a rate of up to 629.06 TWh. The annual PV potential of highways in the southeast is greater than that in the northwest owing to the higher highway density in the southeast. This study provides a reference basis for highway PV construction planning and suitably assessment in each region of China for PV highway development.
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48. |
- Zhang, Shuai, et al.
(author)
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High sensitive assay of formaldehyde using resonance light scattering technique based on carbon dots aggregation
- 2023
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In: Arabian Journal of Chemistry. - : Elsevier. - 1878-5352 .- 1878-5379. ; 16:6
-
Journal article (peer-reviewed)abstract
- Formaldehyde (FA) is widely used in industry and also common in daily life. Finding an efficient method to determine FA is quite an industrial challenge. Herein, a novel method based on a resonance light scattering (RLS) technique was developed for the detection of FA with high sensitivity. Carbon dots (CDs) were used as RLS probes. CDs were obtained via one-pot solvothermal treatment from o-phenylenediamine. CDs showed yellow fluorescence with a quantum yield of 0.41. Due to the multiple amino groups on the surface of CDs, FA can be captured easily by formation of a covalent C = N bond based on the Schiff-base reaction. Owing to the covalent crosslinking, CD nanoparticles aggregated, and even formed precipitate. The aggregation of CDs induced RLS enhancement, where the RLS increment was linearly related to the concentration of FA ranging from 4 nM to 1.6 mM, with a limit of detection (LOD) of 1.6 nM. In comparison with many previous reports, the present RLS method showed a wider linear range and lower LOD. Furthermore, the RLS system was successfully used to detect FA in real food samples. The proposed system has prospective applicability in the detection of FA in food fields.
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49. |
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50. |
- Zhang, Y., et al.
(author)
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Study on the bimodal filler influence on the effective thermal conductivity of thermal conductive adhesive
- 2011
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In: Microsystem Technologies. - : Springer Science and Business Media LLC. - 0946-7076 .- 1432-1858. ; 17:1, s. 93-99
-
Journal article (peer-reviewed)abstract
- The thermal management for electronics systems becomes more crucial to the overall system performance as the packaging density becomes much higher and the IC power increases at the same time. Thermal conductive adhesives (TCAs) have been widely adopted in electronics systems. As an epoxy matrix with conductive fillers, it is essential to figure out the effective thermal conductivity of this composite material. In the present paper, a parameterized cubic cell model (CCM) is developed and then implemented by the finite element method to investigate the effects of the bimodal fillers on the effective thermal conductivity. In addition, a series of bimodal TCA samples are prepared and the thermal conductivities in the in-plane and vertical directions are measured experimentally. An obvious anisotropy with respect to the thermal conductivities has been observed for the bimodal filler loading under consideration. A good agreement between the numerical results and the experimental data is obtained.
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