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  1. Article ; Online: Identifying driving factors of urban land expansion using Google Earth Engine and machine-learning approaches in Mentougou District, China.

    Cheng, Lin-Lin / Tian, Chao / Yin, Ting-Ting

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 16248

    Abstract: The research on driving mechanisms of urban land expansion is hot topic of land science. However, the relative importance of anthropogenic-natural factors and how they affect urban land expansion change are still unclear. Based on the Google Earth Engine ...

    Abstract The research on driving mechanisms of urban land expansion is hot topic of land science. However, the relative importance of anthropogenic-natural factors and how they affect urban land expansion change are still unclear. Based on the Google Earth Engine platform, this study used the support vector machine classifier to extract land-use datasets of Mentougou district of Beijing, China from 1990 to 2016. Supported by machine-learning approaches, multiple linear regression (MLR) and random forests (RF) were applied and compared to identify the influential factors and their relative importance on urban land expansion. The results show: There was a continuous growth in urban land expansion from 1990 to 2016, the increased area reached 6097.42 ha with an average annual rate of 8.01% and average annual intensity rate of 2.57%, respectively. Factors such as elevation, risk of goaf collapse, accessibility, local fiscal expenditure, industrial restructuring, per capita income in rural area, GDP were important drivers of urban land expansion change. The model comparison indicated that RF had greater ability than MLR to identify the non-linear relationships between urban land expansion and explanatory variables. The influencing factors of urban land expansion should be comprehensively considered to regulate new land policy actions in Mentougou.
    MeSH term(s) China ; Cities ; Machine Learning ; Policy ; Search Engine ; Urbanization
    Language English
    Publishing date 2022-09-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-20478-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Comparative study on clinicopathological features and prognosis of IgA vasculitis nephritis and IgA nephropathy in children.

    Lv, Yan / Fu, Rui / Peng, Xiao-Jie / Wang, Ying / Yin, Ting-Ting / Deng, Yan-Qing

    BMC pediatrics

    2023  Volume 23, Issue 1, Page(s) 423

    Abstract: Background: IgA vasculitis nephritis (IgAVN) and IgA nephropathy (IgAN) share several clinical and pathological characteristics, though distinctions also exist. Their interrelation, however, remains undefined. This study investigates the ... ...

    Abstract Background: IgA vasculitis nephritis (IgAVN) and IgA nephropathy (IgAN) share several clinical and pathological characteristics, though distinctions also exist. Their interrelation, however, remains undefined. This study investigates the clinicopathological divergences and prognostic disparities in pediatric patients with IgAVN and IgAN.
    Methods: Our study encompasses 809 pediatric patients with IgAVN and 236 with IgAN, all of whom underwent kidney biopsy. We utilized the Semiquantitative Classification (SQC) scoring system to juxtapose the pathologies of the two conditions, and performed a COX regression analysis to examine factors influencing their prognoses.
    Results: Both patient groups demonstrated a predominance of males. A seasonality was observed, with a higher incidence of IgAN in the summer, and IgAVN in the fall (P < 0.0001). Patients with IgAN exhibited more severe tubulointerstitial injury, higher chronicity index, and total biopsy scores compared to those with IgAVN (P < 0.0001). Mesangial deposition intensity of complement C3, and the rate of pure IgA deposition, were found to be greater in patients with IgAVN compared to those with IgAN (P < 0.0001). The intensity of IgA deposition was also significantly higher in IgAVN patients (P = 0.003). IgAVN demonstrated a superior prognosis, with a higher rate of kidney remission (P < 0.0001). COX regression analysis indicated that interstitial fibrosis, as identified in the SQC pathology system, was associated with the prognosis of both conditions. Furthermore, the findings suggest that IgA deposition levels (IgA +  + and IgA +  + +) could potentially influence the prognosis of IgAVN.
    Conclusions: Compared to IgAVN, IgAN manifests more severely with regard to renal impairment, interstitial damage, and prognosis. The disparities in immune complex deposition levels and locations within the kidneys support the hypothesis of IgAVN and IgAN as distinct diseases. Interstitial fibrosis may serve as a key pathological indicator within the SQC system associated with kidney prognosis in children with IgAVN and IgAN. The degree of IgA deposition could also be linked with the prognosis of IgAVN.
    MeSH term(s) Male ; Humans ; Child ; Female ; Glomerulonephritis, IGA/diagnosis ; IgA Vasculitis/complications ; IgA Vasculitis/diagnosis ; Nephritis ; Prognosis ; Fibrosis ; Immunoglobulin A
    Chemical Substances Immunoglobulin A
    Language English
    Publishing date 2023-08-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041342-7
    ISSN 1471-2431 ; 1471-2431
    ISSN (online) 1471-2431
    ISSN 1471-2431
    DOI 10.1186/s12887-023-04243-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: 儿童弥漫性毛细血管内增生性紫癜性肾炎的临床、病理及预后.

    Yin, Ting-Ting / Peng, Xiao-Jie / Fu, Rui / Wang, Ying / Lyu, Yan / Deng, Yan-Qing / Fu, Jia-Qi / Zhang, Zhi-Hao

    Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics

    2023  Volume 25, Issue 8, Page(s) 837–842

    Abstract: Objectives: To investigate the clinical characteristics, pathology, and prognosis of children with diffuse endocapillary proliferative Henoch-Schönlein purpura nephritis (DEP-HSPN).: Methods: A retrospective analysis was performed on the clinical, ... ...

    Title translation Clinical characteristics, pathology, and prognosis of children with diffuse endocapillary proliferative Henoch-Schönlein purpura nephritis.
    Abstract Objectives: To investigate the clinical characteristics, pathology, and prognosis of children with diffuse endocapillary proliferative Henoch-Schönlein purpura nephritis (DEP-HSPN).
    Methods: A retrospective analysis was performed on the clinical, pathological, and prognosis data of 44 children with DEP-HSPN and 765 children without DEP-HSPN. The children with DEP-HSPN were diagnosed by renal biopsy in Jiangxi Provincial Children's Hospital from January 2006 to December 2021.
    Results: Among the 809 children with purpura nephritis, 44 (5.4%) had DEP-HSPN, with a mean age of (8±3) years, and there were 29 boys (65.9%) and 15 girls (34.1%). Compared with the non-DEP-HSPN group, the DEP-HSPN group had a significantly shorter time from onset to renal biopsy and a significantly higher proportion of children with respiratory infection or gross hematuria, and most children had nephrotic syndrome. The DEP-HSPN group had significantly higher levels of 24-hour urinary protein, urinary protein grading, microscopic hematuria grading, serum creatinine, and blood urea nitrogen and significantly lower levels of serum albumin and complement C3 (
    Conclusions: Children with DEP-HSPN have a rapid onset, severe clinical manifestations and pathological grading, and high activity scores in the modified semi-quantitative scoring system. However, most of the children with DEP-HSPN have a good prognosis, with a comparable renal complete remission rate to the children without DEP-HSPN.
    MeSH term(s) Male ; Female ; Humans ; Child ; Child, Preschool ; Hematuria ; IgA Vasculitis ; Retrospective Studies ; Prognosis ; Nephritis
    Language Chinese
    Publishing date 2023-08-31
    Publishing country China
    Document type English Abstract ; Journal Article
    ISSN 1008-8830
    ISSN 1008-8830
    DOI 10.7499/j.issn.1008-8830.2303022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Mn-Incorporation-Induced Phase Transition in Bottom-Up Synthesized Colloidal Sub-1-nm Ni(OH)

    Yin, Ting-Ting / Xu, Hou-Ming / Zhang, Xiao-Long / Su, Xiaozhi / Shi, Lei / Gu, Chao / Han, Shi-Kui

    Nano letters

    2023  Volume 23, Issue 8, Page(s) 3259–3266

    Abstract: Sub-1-nm structures are attractive for diverse applications owing to their unique properties compared to those of conventional nanomaterials. Transition-metal hydroxides are promising catalysts for oxygen evolution reaction (OER), yet there remains ... ...

    Abstract Sub-1-nm structures are attractive for diverse applications owing to their unique properties compared to those of conventional nanomaterials. Transition-metal hydroxides are promising catalysts for oxygen evolution reaction (OER), yet there remains difficulty in directly fabricating these materials within the sub-1-nm regime, and the realization of their composition and phase tuning is even more challenging. Here we define a binary-soft-template-mediated colloidal synthesis of phase-selective Ni(OH)
    Language English
    Publishing date 2023-04-13
    Publishing country United States
    Document type Journal Article
    ISSN 1530-6992
    ISSN (online) 1530-6992
    DOI 10.1021/acs.nanolett.3c00067
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Lactate score predicts survival, immune cell infiltration and response to immunotherapy in breast cancer.

    Yin, Ting-Ting / Huang, Meng-Xing / Wang, Fei / Jiang, Yi-Hua / Long, Jie / Li, Liang / Cao, Jie

    Frontiers in genetics

    2022  Volume 13, Page(s) 943849

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2022-08-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.943849
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A Method for Detecting Antioxidant Activity of Antioxidants by Utilizing Oxidative Damage of Pigment Protein

    Liu, CongLing / Zhur, Olena / Yan, XiaoTao / Yin, TingTing / Rao, HaiLian / Xiao, Xun / Zhou, MingYang / Wu, CuiLing / He, HaiLun

    Appl Biochem Biotechnol. 2022 Nov., v. 194, no. 11 p.5522-5536

    2022  

    Abstract: A simple and effective method for detecting the antioxidant activity by utilizing oxidative damage of pigment proteins was developed. In this method, phycocyanin and bovine hemoglobin pigment proteins were used as substrates attacked by free radicals; ... ...

    Abstract A simple and effective method for detecting the antioxidant activity by utilizing oxidative damage of pigment proteins was developed. In this method, phycocyanin and bovine hemoglobin pigment proteins were used as substrates attacked by free radicals; AAPH was used as a free radical initiator; and Trolox as a positive control; and the fermentation products of Lactobacillus plantarum 793, phycocyanin hydrolysates, salmon skin collagen hydrolysates, and synthetic peptides PMRGGYHY and FCVLRP are antioxidants inspected in this study. Because of being attacked by free radicals, the absorbance of the pigment proteins at their characteristic absorption peak changes with time. By recording the time-varying curve at the characteristic absorption peak of the pigment protein in the blank/negative control sample, the Trolox positive control sample, and the samples of inspected antioxidants, the antioxidant activity could be calculated by using the specific equation. The linear detection ranges of Trolox in the phycocyanin assay and the bovine hemoglobin assay were 1–4 μM and 4–24 μM, respectively. Compared with the ORAC assay, the antioxidant activities of the samples measured by this method were slightly lower. The method proposed in this study reflects the protective effects of inspected antioxidants on pigment proteins, which could potentially serve as new biomarkers of oxidative damage processes.
    Keywords Lactobacillus plantarum ; absorbance ; absorption ; antioxidant activity ; antioxidants ; biomarkers ; cattle ; collagen ; equations ; fermentation ; free radicals ; hemoglobin ; phycocyanin ; salmon ; synthetic peptides
    Language English
    Dates of publication 2022-11
    Size p. 5522-5536.
    Publishing place Springer US
    Document type Article ; Online
    ZDB-ID 392344-7
    ISSN 0273-2289
    ISSN 0273-2289
    DOI 10.1007/s12010-022-04058-5
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Germline gene fusions across species reveal the chromosomal instability regions and cancer susceptibility.

    Zhou, Bo-Wen / Wu, Qing-Qin / Mauki, David H / Wang, Xuan / Zhang, Shu-Run / Yin, Ting-Ting / Chen, Fang-Liang / Li, Chao / Liu, Yan-Hu / Wang, Guo-Dong / Zhang, Ya-Ping

    iScience

    2023  Volume 26, Issue 12, Page(s) 108431

    Abstract: The canine transmissible venereal tumor (CTVT) is a clonal cell-mediated cancer with a long evolutionary history and extensive karyotype rearrangements in its genome. However, little is known about its genetic similarity to human tumors. Here, using ... ...

    Abstract The canine transmissible venereal tumor (CTVT) is a clonal cell-mediated cancer with a long evolutionary history and extensive karyotype rearrangements in its genome. However, little is known about its genetic similarity to human tumors. Here, using multi-omics data we identified 11 germline gene fusions (GGFs) in CTVT, which showed higher genetic susceptibility than others. Additionally, we illustrate a mechanism of a complex gene fusion of three gene segments (
    Language English
    Publishing date 2023-11-10
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.108431
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Platelet/Lymphocyte, Lymphocyte/Monocyte, and Neutrophil/Lymphocyte Ratios as Biomarkers in Patients with Rheumatoid Arthritis and Rheumatoid Arthritis-Associated Interstitial Lung Disease.

    Chen, Qiang / Chen, Dong-Yu / Xu, Xi-Zhu / Liu, Ying-Ying / Yin, Ting-Ting / Li, Dong

    Medical science monitor : international medical journal of experimental and clinical research

    2019  Volume 25, Page(s) 6474–6481

    Abstract: BACKGROUND The objective of this study was to assess the diagnostic value of platelet/lymphocyte ratio (PLR), lymphocyte/monocyte ratio (LMR), and neutrophil/lymphocyte ratio (NLR) as biomarkers in patients with rheumatoid arthritis (RA) and rheumatoid ... ...

    Abstract BACKGROUND The objective of this study was to assess the diagnostic value of platelet/lymphocyte ratio (PLR), lymphocyte/monocyte ratio (LMR), and neutrophil/lymphocyte ratio (NLR) as biomarkers in patients with rheumatoid arthritis (RA) and rheumatoid arthritis-associated interstitial lung disease (RA-ILD). MATERIAL AND METHODS Demographic and laboratory data were acquired for 198 RA and 103 RA-ILD patients and 290 healthy controls. The subjects were categorized into female and male groups and further subcategorized based on age into <60 years and ≥60 years subgroups. One-way analysis of variance (ANOVA), receiver operating characteristics (ROC), Pearson analysis, multiple linear regression analysis, and logistic regression analysis were performed to analyze the association of PLR, NLR, and LMR with RA and RA-ILD. RESULTS Mean PLR and NLR were lowest in the control group, followed by the RA and RA-ILD groups (p<0.05). Mean LMR was lowest in the RA-ILD group, followed by the RA and control groups (p<0.05). The area under the ROC (AUROC) values of the PLR to distinguish between RA and controls, RA-ILD and controls, and RA-ILD and RA were 0.676, 0.776, and 0.650, respectively (p<0.001). Multiple linear regression analysis suggested a significantly positive association between the level of PLR and the level of DAS28 (p<0.001). The odds ratio of PLR was 1.101 for RA (p=0.023) and 1.217 for RA-ILD (p<0.001) when compared to the controls. CONCLUSIONS PLR may be applied as a new biomarker for predicting and diagnosing RA and RA-ILD and for distinguishing RA-ILD patients from RA patients and healthy subjects.
    MeSH term(s) Arthritis, Rheumatoid/blood ; Arthritis, Rheumatoid/complications ; Arthritis, Rheumatoid/pathology ; Biomarkers/blood ; Blood Platelets/pathology ; Female ; Humans ; Logistic Models ; Lung Diseases, Interstitial/blood ; Lung Diseases, Interstitial/complications ; Lung Diseases, Interstitial/pathology ; Lymphocytes/pathology ; Male ; Middle Aged ; Monocytes/pathology ; Neutrophils/pathology ; ROC Curve
    Chemical Substances Biomarkers
    Language English
    Publishing date 2019-08-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1439041-3
    ISSN 1643-3750 ; 1234-1010
    ISSN (online) 1643-3750
    ISSN 1234-1010
    DOI 10.12659/MSM.916583
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: A high-throughput SNP discovery strategy for RNA-seq data.

    Zhao, Yun / Wang, Ke / Wang, Wen-Li / Yin, Ting-Ting / Dong, Wei-Qi / Xu, Chang-Jie

    BMC genomics

    2019  Volume 20, Issue 1, Page(s) 160

    Abstract: Background: Single nucleotide polymorphisms (SNP) have been applied as important molecular markers in genetics and breeding studies. The rapid advance of next generation sequencing (NGS) provides a high-throughput means of SNP discovery. However, SNP ... ...

    Abstract Background: Single nucleotide polymorphisms (SNP) have been applied as important molecular markers in genetics and breeding studies. The rapid advance of next generation sequencing (NGS) provides a high-throughput means of SNP discovery. However, SNP development is limited by the availability of reliable SNP discovery methods. Especially, the optimum assembler and SNP caller for accurate SNP prediction from next generation sequencing data are not known.
    Results: Herein we performed SNP prediction based on RNA-seq data of peach and mandarin peel tissue under a comprehensive comparison of two paired-end read lengths (125 bp and 150 bp), five assemblers (Trinity, IDBA, oases, SOAPdenovo, Trans-abyss) and two SNP callers (GATK and GBS). The predicted SNPs were compared with the authentic SNPs identified via PCR amplification followed by gene cloning and sequencing procedures. A total of 40 and 240 authentic SNPs were presented in five anthocyanin biosynthesis related genes in peach and in nine carotenogenic genes in mandarin. Putative SNPs predicted from the same RNA-seq data with different strategies led to quite divergent results. The rate of false positive SNPs was significantly lower when the paired-end read length was 150 bp compared with 125 bp. Trinity was superior to the other four assemblers and GATK was substantially superior to GBS due to a low rate of missing authentic SNPs. The combination of assembler Trinity, SNP caller GATK, and the paired-end read length 150 bp had the best performance in SNP discovery with 100% accuracy both in peach and in mandarin cases. This strategy was applied to the characterization of SNPs in peach and mandarin transcriptomes.
    Conclusions: Through comparison of authentic SNPs obtained by PCR cloning strategy and putative SNPs predicted from different combinations of five assemblers, two SNP callers, and two paired-end read lengths, we provided a reliable and efficient strategy, Trinity-GATK with 150 bp paired-end read length, for SNP discovery from RNA-seq data. This strategy discovered SNP at 100% accuracy in peach and mandarin cases and might be applicable to a wide range of plants and other organisms.
    MeSH term(s) Citrus/genetics ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing/methods ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Prunus persica/genetics ; Sequence Analysis, RNA/methods
    Language English
    Publishing date 2019-02-27
    Publishing country England
    Document type Journal Article
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/s12864-019-5533-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Long amplicon HiFi sequencing for mitochondrial DNA genomes.

    Cai, Zheng-Fei / Hu, Ji-Yuan / Yin, Ting-Ting / Wang, Da / Shen, Quan-Kuan / Ma, Cheng / Ou, Ding-Qin / Xu, Ming-Min / Shi, Xian / Li, Qing-Long / Wu, Ru-Nian / Ajuma, Lameck / Adeola, Adeniyi C / Zhang, Ya-Ping / Peng, Min-Sheng

    Molecular ecology resources

    2023  Volume 23, Issue 5, Page(s) 1014–1022

    Abstract: Long-read sequencing technology is a powerful approach with application in various genetic and genomic research. Herein, we developed the pipeline for long amplicon high-fidelity (HiFi) sequencing and then applied it for sequencing mitochondrial DNA ( ... ...

    Abstract Long-read sequencing technology is a powerful approach with application in various genetic and genomic research. Herein, we developed the pipeline for long amplicon high-fidelity (HiFi) sequencing and then applied it for sequencing mitochondrial DNA (mtDNA) genomes from pools of 79 Tibetan Mastiffs. We amplified the mtDNA genome with long-range PCR using two pairs of primers. Two rounds of circular consensus sequencing (CCS) were conducted and their accuracy was evaluated. The results indicate that the second round of CCS can improve the accuracy of HiFi reads. In addition, the analysis of 79 high-quality mtDNA genomes shows the Tibetan Mastiffs from outside of the Tibetan Plateau experienced hybridization with other dogs. The high quality reads generator (HQGR) software is provided to facilitate data analyses, which is publicly accessible on GitHub (https://github.com/Caizf-script/HQGR). Our long amplicon HiFi sequencing pipeline can also be applied in various target enrichment strategies for small genomes and candidate genes.
    MeSH term(s) Animals ; Dogs ; DNA, Mitochondrial/genetics ; Sequence Analysis, DNA/methods ; Genomics/methods ; Genome, Mitochondrial ; Software ; High-Throughput Nucleotide Sequencing/methods
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2023-02-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406833-0
    ISSN 1755-0998 ; 1755-098X
    ISSN (online) 1755-0998
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13765
    Database MEDical Literature Analysis and Retrieval System OnLINE

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