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  1. Article ; Online: Spatially aware dimension reduction for spatial transcriptomics

    Lulu Shang / Xiang Zhou

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 22

    Abstract: Spatial transcriptomics analyses can be affected by noise and spatial correlation across tissue locations. Here, the authors develop SpatialPCA, a spatially-aware dimensionality reduction method that explicitly models spatial correlation structures, and ... ...

    Abstract Spatial transcriptomics analyses can be affected by noise and spatial correlation across tissue locations. Here, the authors develop SpatialPCA, a spatially-aware dimensionality reduction method that explicitly models spatial correlation structures, and show its application to the analysis of healthy and tumour tissues.
    Keywords Science ; Q
    Language English
    Publishing date 2022-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: BASS

    Zheng Li / Xiang Zhou

    Genome Biology, Vol 23, Iss 1, Pp 1-

    multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies

    2022  Volume 35

    Abstract: Abstract Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a computational method, BASS, that enables multi-scale and multi-sample analysis for single- ... ...

    Abstract Abstract Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a computational method, BASS, that enables multi-scale and multi-sample analysis for single-cell resolution spatial transcriptomics. BASS performs cell type clustering at the single-cell scale and spatial domain detection at the tissue regional scale, with the two tasks carried out simultaneously within a Bayesian hierarchical modeling framework. We illustrate the benefits of BASS through comprehensive simulations and applications to three datasets. The substantial power gain brought by BASS allows us to reveal accurate transcriptomic and cellular landscape in both cortex and hypothalamus.
    Keywords Spatial transcriptomics ; Multi-scale analysis ; Clustering analysis ; Cell type ; Spatial domain ; Multi-sample analysis ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Radiolabeled fibroblast activation protein inhibitors in the evaluation of myocardial fibrosis

    Xiangyu Su / Yiheng Zhao / Xiang Zhou / Peifang Wei

    Chinese Medical Journal, Vol 136, Iss 19, Pp 2377-

    2023  Volume 2379

    Keywords Medicine ; R
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Wolters Kluwer
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Goos–Hänchen and Imbert–Fedorov shifts of the Airy beam in dirac metamaterials

    Qinxin Yue / Xiang Zhou / Dongmei Deng

    New Journal of Physics, Vol 25, Iss 1, p

    2023  Volume 018001

    Abstract: We theoretically derive the expression for the Goos–Hänchen (GH) and Imbert–Fedorov (IF) shifts of the Airy beam in Dirac metamaterial. In this work, the large GH and IF shifts can be found when the Airy beam is reflected near the Dirac and Brewster ... ...

    Abstract We theoretically derive the expression for the Goos–Hänchen (GH) and Imbert–Fedorov (IF) shifts of the Airy beam in Dirac metamaterial. In this work, the large GH and IF shifts can be found when the Airy beam is reflected near the Dirac and Brewster angles. Compared to the Gaussian beam, the GH shifts of the Airy beam are more obvious in the vicinity of the Brewster angle. Interestingly, it is found that the ability to produce an Airy vortex beam at the Dirac point. In addition, the magnitude and the direction of the GH shifts can be controlled by the rotation angles of the Airy beam. We take advantage of this property to design a reflective optical switch based on the rotation angle-controlled GH shifts of the Dirac metamaterial. Our solutions provide the possibility to implement light-tuned optical switches. Moreover, our model can also be used to describe the GH and IF shifts generated by novel beams in other similar photonic systems.
    Keywords shifts ; Airy beam ; dirac metamaterials ; Science ; Q ; Physics ; QC1-999
    Subject code 535
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher IOP Publishing
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Prognostic effect of albumin-to-alkaline phosphatase ratio on patients with hepatocellular carcinoma

    Xinyuan Zhang / Yujing Xin / Yi Chen / Xiang Zhou

    Scientific Reports, Vol 13, Iss 1, Pp 1-

    a systematic review and meta-analysis

    2023  Volume 9

    Abstract: Abstract The prognostic value of albumin-to-alkaline phosphatase ratio (AAPR) in patients with hepatocellular carcinoma (HCC) remains controversial. This meta-analysis aims to evaluate the prognostic role of AAPR in patients with HCC. The databases of ... ...

    Abstract Abstract The prognostic value of albumin-to-alkaline phosphatase ratio (AAPR) in patients with hepatocellular carcinoma (HCC) remains controversial. This meta-analysis aims to evaluate the prognostic role of AAPR in patients with HCC. The databases of Web of Science, Embase, Cochrane Library and PubMed were comprehensively searched from inception to April 25, 2022. Pooled hazard ratio (HR) and 95% confidence interval (CI) were calculated with Stata 16.0 software for the assessment of the relationship between AAPR and overall survival (OS) as well as recurrence-free survival (RFS) in patients with HCC. A total of 2634 patients from 12 cohorts were included in this meta-analysis. The pooled results showed that lower AAPR predicted poorer OS (HR 2.02, 95% CI 1.78–2.30). Similarly, pooled results demonstrated that lower AAPR also predicted poorer RFS (HR 1.88, 95% CI 1.37–2.57). The heterogeneity for RFS by multivariate analytic results and the publication bias for OS existed, however, the subgroup analysis, meta-regression analysis as well as adjustment using trim-and-fill analysis confirmed an association between AAPR and OS as well as RFS. This meta-analysis proves that lower AAPR in patients with HCC predicted inferior survival outcomes, and AAPR might be a promising indicator for the prognosis of HCC.
    Keywords Medicine ; R ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.

    Guodong Hu / Huan-Xiang Zhou

    PLoS Computational Biology, Vol 17, Iss 11, p e

    2021  Volume 1009603

    Abstract: Riboswitches are naturally occurring RNA elements that control bacterial gene expression by binding to specific small molecules. They serve as important models for RNA-small molecule recognition and have also become a novel class of targets for ... ...

    Abstract Riboswitches are naturally occurring RNA elements that control bacterial gene expression by binding to specific small molecules. They serve as important models for RNA-small molecule recognition and have also become a novel class of targets for developing antibiotics. Here, we carried out conventional and enhanced-sampling molecular dynamics (MD) simulations, totaling 153.5 μs, to characterize the determinants of binding free energies and unbinding paths for the cognate and synthetic ligands of a PreQ1 riboswitch. Binding free energy analysis showed that two triplets of nucleotides, U6-C15-A29 and G5-G11-C16, contribute the most to the binding of the cognate ligands, by hydrogen bonding and by base stacking, respectively. Mg2+ ions are essential in stabilizing the binding pocket. For the synthetic ligands, the hydrogen-bonding contributions of the U6-C15-A29 triplet are significantly compromised, and the bound state resembles the apo state in several respects, including the disengagement of the C15-A14-A13 and A32-G33 base stacks. The bulkier synthetic ligands lead to significantly loosening of the binding pocket, including extrusion of the C15 nucleobase and a widening of the C15-C30 groove. Enhanced-sampling simulations further revealed that the cognate and synthetic ligands unbind in almost opposite directions. Our work offers new insight for designing riboswitch ligands.
    Keywords Biology (General) ; QH301-705.5
    Subject code 540
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Impact of Ex-Closure in above and below Ground Carbon Stock Biomass

    Gedion Tsegay / Xiang-Zhou Meng

    Forests, Vol 12, Iss 2, p

    2021  Volume 130

    Abstract: Globally, there is a serious issue in carbon stock due to high deforestation and the loss of land, limited carbon storage pools in aboveground and underground forests in different regions, and increased carbon emissions to the atmosphere. This review ... ...

    Abstract Globally, there is a serious issue in carbon stock due to high deforestation and the loss of land, limited carbon storage pools in aboveground and underground forests in different regions, and increased carbon emissions to the atmosphere. This review paper highlights the impact of exclosures on above and below ground carbon stocks in biomass as a solution to globally curb carbon emissions. The data has been analyzed dependent on the Intergovernmental Panel on Climate Change (IPCC) guidelines, the Food and Agriculture Organization (FAO) Forest Resource Assessment report (FRA, 2020), and scientific journal publications mostly from the last decade, to show the research results of carbon stock and the impact of exclosures, particularly the challenges of deforestation and erosion of land and opportunities of area exclosures to provide a general outlook for policymakers. Overall, the world’s forest regions are declining, and although the forest loss rate has slowed, it has still not stopped sufficiently because the knowledge and practice of exclosures are limited. The global forest loss and carbon stock have decreased from 7.8 million ha/yr to 4.7 million ha/yr and from 668 gigatons to 662 gigatons respectively due to multiple factors that differ across the regions. However, a move toward natural rehabilitation and exclosures to reduce the emissions of Greenhouse Gas (GHGs) is needed. In the global production of carbon, the exclosure of forests plays an important role, in particular for permanent sinks of carbon.
    Keywords communal grazing land ; land degradation ; deforestation ; ex-closure ; carbon stock ; Plant ecology ; QK900-989
    Subject code 333
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Preparation of Mesoporous Si Nanoparticles by Magnesiothermic Reduction for the Enhanced Reactivity

    Xinwen Ma / Weiduo Fei / Xiandie Zhang / Jie Ji / Xiang Zhou

    Molecules, Vol 28, Iss 3274, p

    2023  Volume 3274

    Abstract: In this study, mesoporous silicon nanoparticles (M-Si) were successfully prepared by a magnesiothermic reduction of mesoporous silica nanoparticles, which were synthesized by a templated sol-gel method and used as the precursors. M-Si exhibited a uniform ...

    Abstract In this study, mesoporous silicon nanoparticles (M-Si) were successfully prepared by a magnesiothermic reduction of mesoporous silica nanoparticles, which were synthesized by a templated sol-gel method and used as the precursors. M-Si exhibited a uniform size distribution with an average diameter of about 160 nm. The measured BET surface area was 93.0 m 2 g −1 , and the average pore size calculated by the BJH method was 16 nm. The large internal surface area provides rich reaction sites, resulting in unique interfacial properties and reduced mass diffusion limitations. The mechanism of the magnesiothermic reduction process was discussed. The reactivity of prepared M-Si was compared with that of commercially available non-porous Si nanopowder (with the average diameter of about 30 nm) by performing simultaneous thermogravimetry and differential scanning calorimetry in the air. The results showed that the reaction onset temperature indicated by weight gain was advanced from 772 °C to 468 °C, indicating the promising potential of M-Si as fuel for metastable intermolecular composites.
    Keywords energetic materials ; mesoporous silicon nanoparticles ; magnesiothermic reduction ; thermal analysis ; Organic chemistry ; QD241-441
    Subject code 620
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: The Plant Parasitic Nematodes Database

    Junhao Zhuge / Xiang Zhou / Lifeng Zhou / Jiafu Hu / Kai Guo

    International Journal of Molecular Sciences, Vol 24, Iss 23, p

    A Comprehensive Genomic Data Platform for Plant Parasitic Nematode Research

    2023  Volume 16841

    Abstract: Plant parasitic nematodes are important phytopathogens that greatly affect the growth of agricultural and forestry plants. Scientists have conducted several studies to prevent and treat the diseases they cause. With the advent of the genomics era, the ... ...

    Abstract Plant parasitic nematodes are important phytopathogens that greatly affect the growth of agricultural and forestry plants. Scientists have conducted several studies to prevent and treat the diseases they cause. With the advent of the genomics era, the genome sequencing of plant parasitic nematodes has been considerably accelerated, and a large amount of data has been generated. This study developed the Plant Parasitic Nematodes Database (PPND), a platform to combine these data. The PPND contains genomic, transcriptomic, protein, and functional annotation data, allowing users to conduct BLAST searches and genome browser analyses and download bioinformatics data for in-depth research. PPND will be continuously updated, and new data will be integrated. PPND is anticipated to become a comprehensive genomics data platform for plant parasitic nematode research.
    Keywords plant parasitic nematode ; database ; genome ; bioinformatics ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 580
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Management and outcome of patients with femoral head fractures: the mid-term follow-up with injuries and associated prognostic factors.

    Shakya, Sujan / Chen, Jialei / Sun, Jiachen / Xiang, Zhou

    BMC musculoskeletal disorders

    2023  Volume 24, Issue 1, Page(s) 311

    Abstract: Background: Femoral head fractures are rare injuries often associated with poor functional outcomes and complications. The purpose of this study was to evaluate the incidence, treatment methods and approaches, complications, and functional outcomes of ... ...

    Abstract Background: Femoral head fractures are rare injuries often associated with poor functional outcomes and complications. The purpose of this study was to evaluate the incidence, treatment methods and approaches, complications, and functional outcomes of femoral head fractures.
    Methods: We retrospectively reviewed 50 patients who sustained femoral head fractures between January 2011 and December 2018. There were thirty-seven (74%) males and thirteen (26%) females with a median age of 40 years. According to Pipkin's classification, there were eighteen (36%) Pipkin I, ten (20%) Pipkin II, eight (16%) Pipkin III, and fourteen (28%) Pipkin IV patients. Treatment methods were categorized into non-operative, operative by open reduction and internal fixation (ORIF), and immediate total hip replacement (THR). The recorded surgical approach consists of an anterior(S-P) approach, posterior(K-L) approach, lateral stab, and combined anterior + lateral stab approach for fixation. The patients were also stratified by the Injury Severity Score (ISS), associated injuries, and, mechanism of injuries. The modified harris hip score (MHHS) was used to evaluate the ongoing complications with the clinical outcome of patients with two years or greater follow-up.
    Results: Eight (16%) patients were managed successfully with closed reduction without surgery and thirty-seven (74%) patients required operative reduction and internal fixation (ORIF) of the femoral head and acetabulum, and 5 (10%) patients required immediate THR. Six (12%) patients developed AVN, and four (8%) required a secondary THR. Sixteen patients (33%) developed post-traumatic osteoarthritis (PTOA), eight (16%) developed heterotopic ossification (HO) and six patients (12%) had sciatic nerve injury, none requiring operative treatment. Overall functional results according to MHHS were, excellent in two (4%) patients, good in sixteen (32%) patients, fair in twenty-two (44%) patients, and poor in ten (20%) patients. A statistically significant difference in outcome was observed among four pipkin subtypes.
    Conclusion: Femoral head fractures are rare injuries often associated with poor outcomes. In this study, we report the functional outcomes and complications of all treatment approaches for femoral head fracture based on the Pipkin classification. The treatment aim should always be the anatomical reduction of the fragments. This study, adds to the growing literature on femoral head fracture and provides a reference for the clinical treatment to guide patient management.
    Trial registration: Our study was approved by the Clinical Research and Biomedical Ethical Committee of West China Hospital, Sichuan University, and was performed in accordance with the Declaration of Helsinki. All participants provided written informed consent to participate in this study.
    MeSH term(s) Male ; Female ; Humans ; Adult ; Retrospective Studies ; Follow-Up Studies ; Femur Head/diagnostic imaging ; Femur Head/surgery ; Femur Head/injuries ; Prognosis ; Femoral Fractures/surgery ; Fracture Fixation, Internal/adverse effects ; Fracture Fixation, Internal/methods ; Treatment Outcome ; Hip Fractures/surgery
    Language English
    Publishing date 2023-04-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041355-5
    ISSN 1471-2474 ; 1471-2474
    ISSN (online) 1471-2474
    ISSN 1471-2474
    DOI 10.1186/s12891-023-06317-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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