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  • 1
    Online Resource
    Online Resource
    Cell type–specific genetic regulation of gene expression across human tissues
    American Association for the Advancement of Science (AAAS) ; 2020
    In:  Science Vol. 369, No. 6509 ( 2020-09-11)
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 369, No. 6509 ( 2020-09-11)
    Abstract: The Genotype-Tissue Expression (GTEx) project has identified expression and splicing quantitative trait loci in cis (QTLs) for the majority of genes across a wide range of human tissues. However, the functional characterization of these QTLs has been limited by the heterogeneous cellular composition of GTEx tissue samples. We mapped interactions between computational estimates of cell type abundance and genotype to identify cell type–interaction QTLs for seven cell types and show that cell type–interaction expression QTLs (eQTLs) provide finer resolution to tissue specificity than bulk tissue cis-eQTLs. Analyses of genetic associations with 87 complex traits show a contribution from cell type–interaction QTLs and enables the discovery of hundreds of previously unidentified colocalized loci that are masked in bulk tissue.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.aaz8528
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
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    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 2
    Online Resource
    Online Resource
    Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs
    Springer Science and Business Media LLC ; 2023
    In:  Nature Communications Vol. 14, No. 1 ( 2023-04-19)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2023-04-19)
    Abstract: Expression quantitative trait locus (eQTL) studies illuminate genomic variants that regulate specific genes and contribute to fine-mapped loci discovered via genome-wide association studies (GWAS). Efforts to maximize their accuracy are ongoing. Using 240 glomerular (GLOM) and 311 tubulointerstitial (TUBE) micro-dissected samples from human kidney biopsies, we discovered 5371 GLOM and 9787 TUBE genes with at least one variant significantly associated with expression (eGene) by incorporating kidney single-nucleus open chromatin data and transcription start site distance as an “integrative prior” for Bayesian statistical fine-mapping. The use of an integrative prior resulted in higher resolution eQTLs illustrated by (1) smaller numbers of variants in credible sets with greater confidence, (2) increased enrichment of partitioned heritability for GWAS of two kidney traits, (3) an increased number of variants colocalized with the GWAS loci, and (4) enrichment of computationally predicted functional regulatory variants. A subset of variants and genes were validated experimentally in vitro and using a Drosophila nephrocyte model. More broadly, this study demonstrates that tissue-specific eQTL maps informed by single-nucleus open chromatin data have enhanced utility for diverse downstream analyses.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/s41467-023-37691-7
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
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  • 3
    Online Resource
    Online Resource
    Scott topology on Smyth power posets
    Cambridge University Press (CUP) ; 2023
    In:  Mathematical Structures in Computer Science
    Details
    In: Mathematical Structures in Computer Science, Cambridge University Press (CUP)
    Abstract: For a $T_0$ space X , let $\mathsf{K}(X)$ be the poset of all nonempty compact saturated subsets of X endowed with the Smyth order $\sqsubseteq$ . $(\mathsf{K}(X), \sqsubseteq)$ (shortly $\mathsf{K}(X)$ ) is called the Smyth power poset of X . In this paper, we mainly discuss some basic properties of the Scott topology on Smyth power posets. It is proved that for a well-filtered space X , its Smyth power poset $\mathsf{K}(X)$ with the Scott topology is still well-filtered, and a $T_0$ space Y is well-filtered iff the Smyth power poset $\mathsf{K}(Y)$ with the Scott topology is well-filtered and the upper Vietoris topology is coarser than the Scott topology on $\mathsf{K}(Y)$ . A sober space Z is constructed for which the Smyth power poset $\mathsf{K}(Z)$ with the Scott topology is not sober. A few sufficient conditions are given for a $T_0$ space X under which its Smyth power poset $\mathsf{K}(X)$ with the Scott topology is sober. Some other properties, such as local compactness, first-countability, Rudin property and well-filtered determinedness, of Smyth power spaces, and the Scott topology on Smyth power posets, are also investigated.
    Type of Medium: Online Resource
    ISSN: 0960-1295 , 1469-8072
    URL: Article
    DOI: 10.1017/S0960129523000257
    Language: English
    Publisher: Cambridge University Press (CUP)
    Publication Date: 2023
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    detail.hit.zdb_id: 1070265-9
    SSG: 17,1
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  • 4
    Online Resource
    Online Resource
    A vast resource of allelic expression data spanning human tissues
    Springer Science and Business Media LLC ; 2020
    In:  Genome Biology Vol. 21, No. 1 ( 2020-12)
    Details
    In: Genome Biology, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2020-12)
    Abstract: Allele expression (AE) analysis robustly measures cis -regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis -regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.
    Type of Medium: Online Resource
    ISSN: 1474-760X
    URL: Article
    DOI: 10.1186/s13059-020-02122-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2040529-7
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  • 5
    Online Resource
    Online Resource
    Structural factor equation models for causal network construction via directed acyclic mixed graphs
    Wiley ; 2021
    In:  Biometrics Vol. 77, No. 2 ( 2021-06), p. 573-586
    Details
    In: Biometrics, Wiley, Vol. 77, No. 2 ( 2021-06), p. 573-586
    Abstract: Directed acyclic mixed graphs (DAMGs) provide a useful representation of network topology with both directed and undirected edges subject to the restriction of no directed cycles in the graph. This graphical framework may arise in many biomedical studies, for example, when a directed acyclic graph (DAG) of interest is contaminated with undirected edges induced by some unobserved confounding factors (eg, unmeasured environmental factors). Directed edges in a DAG are widely used to evaluate causal relationships among variables in a network, but detecting them is challenging when the underlying causality is obscured by some shared latent factors. The objective of this paper is to develop an effective structural equation model (SEM) method to extract reliable causal relationships from a DAMG. The proposed approach, termed structural factor equation model (SFEM) , uses the SEM to capture the network topology of the DAG while accounting for the undirected edges in the graph with a factor analysis model. The latent factors in the SFEM enable the identification and removal of undirected edges, leading to a simpler and more interpretable causal network. The proposed method is evaluated and compared to existing methods through extensive simulation studies, and illustrated through the construction of gene regulatory networks related to breast cancer.
    Type of Medium: Online Resource
    ISSN: 0006-341X , 1541-0420
    URL: Issue
    URL: Article
    DOI: 10.1111/biom.v77.2
    DOI: 10.1111/biom.13322
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2021
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    SSG: 12
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  • 6
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    Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions
    eLife Sciences Publications, Ltd ; 2021
    In:  eLife Vol. 10 ( 2021-05-14)
    Details
    In: eLife, eLife Sciences Publications, Ltd, Vol. 10 ( 2021-05-14)
    Abstract: The activity of the genes in a cell depends on the type of cell they are in, the interactions with other genes, the environment and genetics. Active genes produce a greater number of mRNA molecules, which act as messenger molecules to instruct the cell to produce proteins. The amount of mRNA molecules in cells can be measured to assess the levels of gene activity. Genes produce mRNAs through a process called transcription, and the collection of all the mRNA molecules in a cell is called the transcriptome. Cells obtained from human samples can be grown in the lab under different conditions, and this can be used to transform them into different types of cells. These cells can then be exposed to different treatments – such as specific chemicals – to understand how the environment affects them. Cells derived from different people may respond differently to the same treatment based on their unique genetics. Exposing different types of cells from many people to different treatments can help explain how genetics, the environment and cell type affect gene activity. Findley et al. grew three different types of cells from six different people in the lab. The cells were exposed to 28 different treatments, which reflect different environmental changes. Studying all these different factors together allowed Findley et al. to understand how genetics, cell type and environment affect the activity of over 53,000 genes. Around half of the effects due to an interaction between genetics and the environment and had not been seen in other larger studies of the transcriptome. Many of these newly observed changes are in genes that have connections to different diseases, including heart disease. The results of Findley et al. provide evidence indicating to which extent lifestyle and the environment can interact with an individual’s genetic makeup to impact gene activity and long-term health. The more researchers can understand these factors, the more useful they can be in helping to predict, detect and treat illnesses. The findings also show how genes and the environment interact, which may be relevant to understanding disease development. There is more work to be done to understand a wider range of environmental factors across more cell types. It will also be important to establish how this work on cells grown in the lab translates to human health.
    Type of Medium: Online Resource
    ISSN: 2050-084X
    URL: Article
    DOI: 10.7554/eLife.67077
    Language: English
    Publisher: eLife Sciences Publications, Ltd
    Publication Date: 2021
    detail.hit.zdb_id: 2687154-3
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  • 7
    Online Resource
    Online Resource
    Psychosocial experiences modulate asthma-associated genes through gene-environment interactions
    eLife Sciences Publications, Ltd ; 2021
    In:  eLife Vol. 10 ( 2021-06-18)
    Details
    In: eLife, eLife Sciences Publications, Ltd, Vol. 10 ( 2021-06-18)
    Abstract: Social interactions and the overall psychosocial environment have a demonstrated impact on health, particularly for people living in disadvantaged urban areas. Here, we investigated the effect of psychosocial experiences on gene expression in peripheral blood immune cells of children with asthma in Metro Detroit. Using RNA-sequencing and a new machine learning approach, we identified transcriptional signatures of 19 variables including psychosocial factors, blood cell composition, and asthma symptoms. Importantly, we found 169 genes associated with asthma or allergic disease that are regulated by psychosocial factors and 344 significant gene-environment interactions for gene expression levels. These results demonstrate that immune gene expression mediates the link between negative psychosocial experiences and asthma risk.
    Type of Medium: Online Resource
    ISSN: 2050-084X
    URL: Article
    DOI: 10.7554/eLife.63852
    Language: English
    Publisher: eLife Sciences Publications, Ltd
    Publication Date: 2021
    detail.hit.zdb_id: 2687154-3
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  • 8
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    The genome of Dioscorea zingiberensis sheds light on the biosynthesis, origin and evolution of the medicinally important diosgenin saponins
    Oxford University Press (OUP) ; 2022
    In:  Horticulture Research Vol. 9 ( 2022-01-05)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 9 ( 2022-01-05)
    Abstract: Diosgenin saponins isolated from Dioscorea species such as D. zingiberensis exhibit a broad spectrum of pharmacological activities. Diosgenin, the aglycone of diosgenin saponins, is an important starting material for the production of steroidal drugs. However, how plants produce diosgenin saponins and the origin and evolution of the diosgenin saponin biosynthetic pathway remain a mystery. Here we report a high-quality, 629-Mb genome of D. zingiberensis anchored on 10 chromosomes with 30 322 protein-coding genes. We reveal that diosgenin is synthesized in leaves (‘source’), then converted into diosgenin saponins, and finally transported to rhizomes (‘sink’) for storage in plants. By evaluating the distribution and evolutionary patterns of diosgenin saponins in Dioscorea species, we find that diosgenin saponin-containing may be an ancestral trait in Dioscorea and is selectively retained. The results of comparative genomic analysis indicate that tandem duplication coupled with a whole-genome duplication event provided key evolutionary resources for the diosgenin saponin biosynthetic pathway in the D. zingiberensis genome. Furthermore, comparative transcriptome and metabolite analysis among 13 Dioscorea species suggests that specific gene expression patterns of pathway genes promote the differential evolution of the diosgenin saponin biosynthetic pathway in Dioscorea species. Our study provides important insights and valuable resources for further understanding the biosynthesis, evolution, and utilization of plant specialized metabolites such as diosgenin saponins.
    Type of Medium: Online Resource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1093/hr/uhac165
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2781828-7
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  • 9
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    Online Resource
    Research Progress in Alpha-fetoprotein-induced Immunosuppression of Liver Cancer
    Bentham Science Publishers Ltd. ; 2022
    In:  Mini-Reviews in Medicinal Chemistry Vol. 22, No. 17 ( 2022-09), p. 2237-2243
    Details
    In: Mini-Reviews in Medicinal Chemistry, Bentham Science Publishers Ltd., Vol. 22, No. 17 ( 2022-09), p. 2237-2243
    Abstract: Liver cancer is one of the most common malignant tumors, with limited treatment and 8.2% mortality. Liver cancer is the fourth leading cause of cancer-related deaths, which seriously endangers human life and health. Approximately 70% of liver cancer patients show increased serum Alpha- Fetoprotein (AFP) levels. AFP is the main diagnostic and prognostic indicator of liver cancer. AFP, a key marker of liver cancer, plays a crucial role in regulating the proliferation of tumor cells, apoptosis, and induction of cellular immune escape. High levels of AFP during embryonic development protect the embryos from maternal immune attack. AFP also promotes immune escape of liver cancer cells by inhibiting Tumor-Infiltrating Lymphocytes (TILs), Natural Killer cells (NK), Dendritic Cells (DC), and macrophages; thus, it is also used as a target antigen in immunotherapy for liver cancer. AFP is highly expressed in liver cancer cells. In addition to being used in the diagnosis of liver cancer, it has become a target of immunotherapy for liver cancer as a tumor-associated antigen. In immunotherapy, it was also confirmed that early AFP response was positively correlated with the efficacy of immunotherapy. Early AFP responders had longer PFS and OS than non-responders. At present, the methods of immunotherapy for liver cancer mainly include Adoptive Cell Transfer Therapy (ACT), tumor vaccine therapy, immune checkpoint inhibitors (ICIs) therapy, etc. A large number of studies have shown that AFP mainly plays a role in ACT and liver cancer vaccines. This review presents the research progress of AFP and immunosuppression of liver cancer.
    Type of Medium: Online Resource
    ISSN: 1389-5575
    URL: Article
    DOI: 10.2174/1389557522666220218124816
    Language: English
    Publisher: Bentham Science Publishers Ltd.
    Publication Date: 2022
    SSG: 15,3
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  • 10
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    Online Resource
    Integrated Design of Structure and Material of Epoxy Asphalt Mixture Used in Steel Bridge Deck Pavement
    MDPI AG ; 2021
    In:  Buildings Vol. 12, No. 1 ( 2021-12-23), p. 9-
    Details
    In: Buildings, MDPI AG, Vol. 12, No. 1 ( 2021-12-23), p. 9-
    Abstract: To comprehensively investigate the integrated structural and material design of the epoxy asphalt mixture used in steel bridge deck pavement, the following works have been conducted: 1. The strain level of steel bridge deck pavement was calculated; 2. The ultimate strain level of fatigue endurance for epoxy asphalt concrete was measured; 3. The effect of water tightness of epoxy asphalt mixture on the bonding performance of steel plate interface was tested. 4. For better performance evaluation, quantitative analysis of the anti-skid performance of epoxy asphalt mixture was carried out by testing the structure depth using a laser texture tester. Results show the following findings: 1. The fatigue endurance limit strain level of epoxy asphalt mixture (600 με) was higher than that of the steel bridge deck pavement ( 〈 300 με), indicating that the use of epoxy asphalt concrete has better flexibility and can achieve a longer service life in theory; 2. The epoxy asphalt concrete has significant water tightness to protect the steel plate interface from corrosion and ensure good bonding performance; 3. The porosity of epoxy asphalt mixture used in steel bridge deck paving should be controlled within 3%; 4. In terms of anti-skid performance of bridge deck pavement, the FAC-10 graded epoxy asphalt mixture is recommended when compared with EA-10C.
    Type of Medium: Online Resource
    ISSN: 2075-5309
    URL: Article
    DOI: 10.3390/buildings12010009
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2661539-3
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