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  1. AU="Vasaikar, Suhas"
  2. AU="Arango, Jesus"
  3. AU="Scott, C. Tim"
  4. AU="Coelho, Luis Francisco Mello(Universidade Estadual Paulista Instituto de Biociências Departamento de Botânica)"
  5. AU="Hesong Zeng"
  6. AU="Babey, Anna-Marie"
  7. AU="Stich, H"
  8. AU=Kuitunen I
  9. AU="Biscaye Pierre E"
  10. AU="Saha, Somen"
  11. AU="Liu, Weihuang"
  12. AU="Nijhuis, Monique"
  13. AU="Ye, Jin-Rong"
  14. AU="Van Not, Hans Pieter"
  15. AU="Liang, Xiao-Hui"
  16. AU="Romano, Raffaella"
  17. AU="Gilles Subra"
  18. AU="Potocnik, Ana"
  19. AU="Butt, Christine"

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  1. Artikel ; Online: A landscape of nanomedicine innovations in India

    Bhatia Pooja / Vasaikar Suhas / Wali Anil

    Nanotechnology Reviews, Vol 7, Iss 2, Pp 131-

    2018  Band 148

    Abstract: Nanomedicine is one of the emerging technologies and a branch of nanotechnology finding applications in healthcare. Many countries, including India, are pursuing active research programs in nanomedicine to explore novel healthcare solutions to address ... ...

    Abstract Nanomedicine is one of the emerging technologies and a branch of nanotechnology finding applications in healthcare. Many countries, including India, are pursuing active research programs in nanomedicine to explore novel healthcare solutions to address specific healthcare needs of the society. At present, the government of India, through its various agencies, is funding nanomedicine research in India. It is anticipated that in the next 5 years or so, several nanomedicine-based products shall reach the market. Thereby, it becomes pertinent to evaluate the extent of India’s involvement in activities related to innovation in nanomedicine. However, a comprehensive landscape of nanomedicine innovation in India is currently lacking. This paper attempts to profile the status of research and innovation in the field of nanomedicine in India. The current study evaluates the innovation on the basis of five indicators: financial ecosystem, technology source, research translation, bibliographic data (patents and publications), and regulation. Public-private partnerships and international collaborations are also discussed in the paper. The landscape elucidates current status of nanomedicine in India and may be relevant for policy-related matters.
    Schlagwörter investments ; nanomedicine ; research indicators ; startups and innovation quotient ; Technology ; T ; Chemical technology ; TP1-1185 ; Physical and theoretical chemistry ; QD450-801
    Thema/Rubrik (Code) 001
    Sprache Englisch
    Erscheinungsdatum 2018-04-01T00:00:00Z
    Verlag De Gruyter
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

    Volltext online

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  2. Artikel ; Online: DLAD4U: deriving and prioritizing disease lists from PubMed literature.

    Shen, Junhui / Vasaikar, Suhas / Zhang, Bing

    BMC bioinformatics

    2018  Band 19, Heft Suppl 17, Seite(n) 495

    Abstract: Background: Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, environmental, and life style ... ...

    Abstract Background: Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, environmental, and life style factors, disease symptoms, and treatment strategies. Here we report DLAD4U (Disease List Automatically Derived For You), an efficient, accurate and easy-to-use disease search engine based on PubMed literature.
    Results: DLAD4U uses the eSearch and eFetch APIs from the National Center for Biotechnology Information (NCBI) to find publications related to a query and to identify diseases from the retrieved publications. The hypergeometric test was used to prioritize identified diseases for displaying to users. DLAD4U accepts any valid queries for PubMed, and the output results include a ranked disease list, information associated with each disease, chronologically-ordered supporting publications, a summary of the run, and links for file export. DLAD4U outperformed other disease search engines in our comparative evaluation using selected genes and drugs as query terms and manually curated data as "gold standard". For 100 genes that are associated with only one disease in the gold standard, the Mean Average Precision (MAP) measure from DLAD4U was 0.77, which clearly outperformed other tools. For 10 genes that are associated with multiple diseases in the gold standard, the mean precision, recall and F-measure scores from DLAD4U were always higher than those from other tools. The superior performance of DLAD4U was further confirmed using 100 drugs as queries, with an MAP of 0.90.
    Conclusions: DLAD4U is a new, intuitive disease search engine that takes advantage of existing resources at NCBI to provide computational efficiency and uses statistical analyses to ensure accuracy. DLAD4U is publicly available at http://dlad4u.zhang-lab.org .
    Mesh-Begriff(e) Disease/genetics ; Genetic Association Studies ; Humans ; Information Storage and Retrieval ; Internet ; Nitric Oxide Synthase Type III/metabolism ; PubMed ; Publications ; Search Engine ; Tumor Necrosis Factor-alpha/metabolism
    Chemische Substanzen Tumor Necrosis Factor-alpha ; NOS3 protein, human (EC 1.14.13.39) ; Nitric Oxide Synthase Type III (EC 1.14.13.39)
    Sprache Englisch
    Erscheinungsdatum 2018-12-28
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-018-2463-0
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Limiting Dilution Tumor Initiation Assay: An In Vivo Approach for the Study of Cancer Stem Cells.

    den Hollander, Petra / Joseph, Robiya / Vasaikar, Suhas / Kuburich, Nick A / Deshmukh, Abhijeet P / Mani, Sendurai A

    Methods in molecular biology (Clifton, N.J.)

    2022  Band 2429, Seite(n) 547–554

    Abstract: Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. Calculating the frequency of tumor-initiating cells is important in the assessment of the number of CSCs present in a cell population. In ... ...

    Abstract Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. Calculating the frequency of tumor-initiating cells is important in the assessment of the number of CSCs present in a cell population. In this chapter, we present a protocol developed for quantification of CSCs from breast cancer tumors that can be adapted to CSCs from other types of tumors.
    Mesh-Begriff(e) Breast Neoplasms/pathology ; Cell Transformation, Neoplastic/metabolism ; Female ; Humans ; Neoplastic Stem Cells/metabolism
    Sprache Englisch
    Erscheinungsdatum 2022-05-04
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1979-7_38
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Enrichment of Cancer Stem Cells in a Tumorsphere Assay.

    Deshmukh, Abhijeet P / den Hollander, Petra / Kuburich, Nick A / Vasaikar, Suhas / Joseph, Robiya / Mani, Sendurai A

    Methods in molecular biology (Clifton, N.J.)

    2022  Band 2429, Seite(n) 501–507

    Abstract: Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. CSCs possess tumor initiation potential as well as the ability to resist toxic compounds and chemotherapeutic agents through the upregulation ...

    Abstract Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. CSCs possess tumor initiation potential as well as the ability to resist toxic compounds and chemotherapeutic agents through the upregulation of drug efflux transporters, DNA repair pathways, and survival cascades. Accumulating evidence suggests that CSCs are responsible for tumor relapse and resistance to chemotherapeutic agents and that targeting CSCs is critical to inhibition of cancer progression. Therefore, isolation and characterization of CSCs is important in studying tumor initiation and progression. In this chapter, we provide a detailed method for the identification and isolation of CSCs.
    Mesh-Begriff(e) Antineoplastic Agents/metabolism ; Antineoplastic Agents/pharmacology ; Humans ; Neoplasm Recurrence, Local/pathology ; Neoplastic Stem Cells/metabolism
    Chemische Substanzen Antineoplastic Agents
    Sprache Englisch
    Erscheinungsdatum 2022-05-04
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1979-7_34
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: In Vitro Quantification of Cancer Stem Cells Using a Mammosphere Formation Assay.

    Kuburich, Nick A / den Hollander, Petra / Deshmukh, Abhijeet P / Vasaikar, Suhas / Joseph, Robiya / Wicha, Max S / Mani, Sendurai A

    Methods in molecular biology (Clifton, N.J.)

    2022  Band 2429, Seite(n) 509–513

    Abstract: Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. In this chapter, we provide a detailed method for the quantification of CSCs in vitro through mammosphere formation. ...

    Abstract Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. In this chapter, we provide a detailed method for the quantification of CSCs in vitro through mammosphere formation.
    Mesh-Begriff(e) Breast Neoplasms/pathology ; Cell Line, Tumor ; Female ; Humans ; Neoplastic Stem Cells/pathology
    Sprache Englisch
    Erscheinungsdatum 2022-05-04
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1979-7_35
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: A comprehensive platform for analyzing longitudinal multi-omics data.

    Vasaikar, Suhas V / Savage, Adam K / Gong, Qiuyu / Swanson, Elliott / Talla, Aarthi / Lord, Cara / Heubeck, Alexander T / Reading, Julian / Graybuck, Lucas T / Meijer, Paul / Torgerson, Troy R / Skene, Peter J / Bumol, Thomas F / Li, Xiao-Jun

    Nature communications

    2023  Band 14, Heft 1, Seite(n) 1684

    Abstract: Longitudinal bulk and single-cell omics data is increasingly generated for biological and clinical research but is challenging to analyze due to its many intrinsic types of variations. We present PALMO ( https://github.com/aifimmunology/PALMO ), a ... ...

    Abstract Longitudinal bulk and single-cell omics data is increasingly generated for biological and clinical research but is challenging to analyze due to its many intrinsic types of variations. We present PALMO ( https://github.com/aifimmunology/PALMO ), a platform that contains five analytical modules to examine longitudinal bulk and single-cell multi-omics data from multiple perspectives, including decomposition of sources of variations within the data, collection of stable or variable features across timepoints and participants, identification of up- or down-regulated markers across timepoints of individual participants, and investigation on samples of same participants for possible outlier events. We have tested PALMO performance on a complex longitudinal multi-omics dataset of five data modalities on the same samples and six external datasets of diverse background. Both PALMO and our longitudinal multi-omics dataset can be valuable resources to the scientific community.
    Mesh-Begriff(e) Humans ; Multiomics ; Software
    Sprache Englisch
    Erscheinungsdatum 2023-03-27
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-37432-w
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit.

    Wang, Jing / Vasaikar, Suhas / Shi, Zhiao / Greer, Michael / Zhang, Bing

    Nucleic acids research

    2017  Band 45, Heft W1, Seite(n) W130–W137

    Abstract: Functional enrichment analysis has played a key role in the biological interpretation of high-throughput omics data. As a long-standing and widely used web application for functional enrichment analysis, WebGestalt has been constantly updated to satisfy ... ...

    Abstract Functional enrichment analysis has played a key role in the biological interpretation of high-throughput omics data. As a long-standing and widely used web application for functional enrichment analysis, WebGestalt has been constantly updated to satisfy the needs of biologists from different research areas. WebGestalt 2017 supports 12 organisms, 324 gene identifiers from various databases and technology platforms, and 150 937 functional categories from public databases and computational analyses. Omics data with gene identifiers not supported by WebGestalt and functional categories not included in the WebGestalt database can also be uploaded for enrichment analysis. In addition to the Over-Representation Analysis in the previous versions, Gene Set Enrichment Analysis and Network Topology-based Analysis have been added to WebGestalt 2017, providing complementary approaches to the interpretation of high-throughput omics data. The new user-friendly output interface and the GOView tool allow interactive and efficient exploration and comparison of enrichment results. Thus, WebGestalt 2017 enables more comprehensive, powerful, flexible and interactive functional enrichment analysis. It is freely available at http://www.webgestalt.org.
    Mesh-Begriff(e) Animals ; Cattle ; Genes ; Humans ; Internet ; Mice ; Neoplasms/genetics ; Rats ; Software ; User-Computer Interface
    Sprache Englisch
    Erscheinungsdatum 2017-05-23
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkx356
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1067: Hefte anzeigen Standort:
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  8. Artikel ; Online: LinkedOmics: analyzing multi-omics data within and across 32 cancer types.

    Vasaikar, Suhas V / Straub, Peter / Wang, Jing / Zhang, Bing

    Nucleic acids research

    2017  Band 46, Heft D1, Seite(n) D956–D963

    Abstract: The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based ... ...

    Abstract The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. Using five case studies, we demonstrate that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. LinkedOmics is freely available at http://www.linkedomics.org.
    Mesh-Begriff(e) Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Databases, Genetic ; Databases, Protein ; Datasets as Topic ; Drug Resistance, Neoplasm ; Female ; Gene Expression Profiling ; Genes, Retinoblastoma ; Genes, erbB-2 ; Genomics ; Humans ; Information Storage and Retrieval ; Intracellular Signaling Peptides and Proteins/genetics ; Mass Spectrometry ; Membrane Proteins/genetics ; Neoplasm Proteins/analysis ; Neoplasm Proteins/biosynthesis ; Neoplasm Proteins/genetics ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/mortality ; Ovarian Neoplasms/chemistry ; Ovarian Neoplasms/mortality ; Phosphorylation/genetics ; Prognosis ; Protein Processing, Post-Translational/genetics ; Proteomics ; RNA, Messenger/genetics ; RNA, Neoplasm/genetics ; Receptor, ErbB-2/genetics ; Retinoblastoma Binding Proteins/genetics ; Retinoblastoma Binding Proteins/physiology ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/physiology ; Urinary Bladder Neoplasms/genetics ; Urinary Bladder Neoplasms/metabolism ; User-Computer Interface
    Chemische Substanzen APCDD1 protein, human ; Intracellular Signaling Peptides and Proteins ; Membrane Proteins ; Neoplasm Proteins ; RB1 protein, human ; RNA, Messenger ; RNA, Neoplasm ; Retinoblastoma Binding Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; ERBB2 protein, human (EC 2.7.10.1) ; Receptor, ErbB-2 (EC 2.7.10.1)
    Sprache Englisch
    Erscheinungsdatum 2017-11-14
    Erscheinungsland England
    Dokumenttyp Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkx1090
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: NPY1R exerts inhibitory action on estradiol-stimulated growth and predicts endocrine sensitivity and better survival in ER-positive breast cancer.

    Bhat, Raksha / Thangavel, Hariprasad / Abdulkareem, Noor Mazin / Vasaikar, Suhas / De Angelis, Carmine / Bae, Leon / Cataldo, Maria Letizia / Nanda, Sarmistha / Fu, Xiaoyong / Zhang, Bing / Schiff, Rachel / Trivedi, Meghana V

    Scientific reports

    2022  Band 12, Heft 1, Seite(n) 1972

    Abstract: G Protein-Coupled Receptors (GPCRs) represent the largest superfamily of cell-surface proteins. However, the expression and function of majority of GPCRs remain unexplored in breast cancer (BC). We interrogated the expression and phosphorylation status ... ...

    Abstract G Protein-Coupled Receptors (GPCRs) represent the largest superfamily of cell-surface proteins. However, the expression and function of majority of GPCRs remain unexplored in breast cancer (BC). We interrogated the expression and phosphorylation status of 398 non-sensory GPCRs using the landmark BC proteogenomics and phosphoproteomic dataset from The Cancer Genome Atlas. Neuropeptide Y Receptor Y1 (NPY1R) gene and protein expression were significantly higher in Luminal A tumors versus other BC subtypes. The trend of NPY1R gene, protein, and phosphosite (NPY1R-S368s) expression was decreasing in the order of Luminal A, Luminal B, Basal, and human epidermal growth factor receptor 2 (HER2) subtypes. NPY1R gene expression increased in response to estrogen and reduced with endocrine therapy in estrogen receptor-positive (ER+) BC cells and xenograft models. Conversely, NPY1R expression decreased in ER+ BC cells resistant to endocrine therapies (estrogen deprivation, tamoxifen, and fulvestrant) in vitro and in vivo. NPY treatment reduced estradiol-stimulated cell growth, which was reversed by NPY1R antagonist (BIBP-3226) in ER+ BC cells. Higher NPY1R gene expression predicted better relapse-free survival and overall survival in ER+ BC. Our study demonstrates that NPY1R mediates the inhibitory action of NPY on estradiol-stimulated growth of ER+ BC cells, and its expression serves as a biomarker to predict endocrine sensitivity and survival in ER+ BC patients.
    Mesh-Begriff(e) Animals ; Antineoplastic Agents, Hormonal/pharmacology ; Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Drug Resistance, Neoplasm/drug effects ; Endocrine Gland Neoplasms/drug therapy ; Endocrine Gland Neoplasms/genetics ; Endocrine Gland Neoplasms/pathology ; Estradiol/pharmacology ; Estrogen Receptor alpha/genetics ; Estrogens/genetics ; Female ; Fulvestrant/pharmacology ; Gene Expression Regulation, Neoplastic ; Heterografts ; Humans ; Mice ; Neoplasm Recurrence, Local/drug therapy ; Neoplasm Recurrence, Local/genetics ; Neoplasm Recurrence, Local/pathology ; Receptor, ErbB-2/genetics ; Receptors, G-Protein-Coupled/genetics ; Receptors, Neuropeptide Y/genetics ; Tamoxifen/pharmacology
    Chemische Substanzen Antineoplastic Agents, Hormonal ; ESR1 protein, human ; Estrogen Receptor alpha ; Estrogens ; Receptors, G-Protein-Coupled ; Receptors, Neuropeptide Y ; neuropeptide Y-Y1 receptor ; Tamoxifen (094ZI81Y45) ; Fulvestrant (22X328QOC4) ; Estradiol (4TI98Z838E) ; ERBB2 protein, human (EC 2.7.10.1) ; Receptor, ErbB-2 (EC 2.7.10.1)
    Sprache Englisch
    Erscheinungsdatum 2022-02-04
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-05949-7
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel: Complementary Approaches to Existing Target Based Drug Discovery for Identifying Novel Drug Targets.

    Vasaikar, Suhas / Bhatia, Pooja / Bhatia, Partap G / Chu Yaiw, Koon

    Biomedicines

    2016  Band 4, Heft 4

    Abstract: In the past decade, it was observed that the relationship between the emerging New Molecular Entities and the quantum of R&D investment has not been favorable. There might be numerous reasons but few studies stress the introduction of target based drug ... ...

    Abstract In the past decade, it was observed that the relationship between the emerging New Molecular Entities and the quantum of R&D investment has not been favorable. There might be numerous reasons but few studies stress the introduction of target based drug discovery approach as one of the factors. Although a number of drugs have been developed with an emphasis on a single protein target, yet identification of valid target is complex. The approach focuses on an in vitro single target, which overlooks the complexity of cell and makes process of validation drug targets uncertain. Thus, it is imperative to search for alternatives rather than looking at success stories of target-based drug discovery. It would be beneficial if the drugs were developed to target multiple components. New approaches like reverse engineering and translational research need to take into account both system and target-based approach. This review evaluates the strengths and limitations of known drug discovery approaches and proposes alternative approaches for increasing efficiency against treatment.
    Sprache Englisch
    Erscheinungsdatum 2016-11-21
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Review
    ZDB-ID 2720867-9
    ISSN 2227-9059
    ISSN 2227-9059
    DOI 10.3390/biomedicines4040027
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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