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  1. Book: Dendritic cell protocols

    Naik, Shalin H.

    (Methods in molecular biology ; 595 ; Springer protocols)

    2010  

    Author's details ed. by Shalin H. Naik
    Series title Methods in molecular biology ; 595
    Springer protocols
    Collection
    Keywords Dendritic Cells / physiology ; Dendritic Cells / cytology ; Dendritische Zelle
    Language English
    Size XVII, 446 S. : Ill., graph. Darst.
    Edition 2. ed.
    Publisher Humana Press
    Publishing place New York
    Publishing country United States
    Document type Book
    HBZ-ID HT016022777
    ISBN 978-1-60761-420-3 ; 1-60761-420-0
    Database Catalogue ZB MED Medicine, Health

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    2010 A 241 order for loan Magazin

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  2. Article ; Online: tDCs - a distinct subset with dual functional and developmental roles.

    Audiger, Cindy / Tomei, Sara / Naik, Shalin H

    Nature immunology

    2023  Volume 24, Issue 8, Page(s) 1222–1223

    MeSH term(s) Dendritic Cells/immunology
    Language English
    Publishing date 2023-07-14
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2016987-5
    ISSN 1529-2916 ; 1529-2908
    ISSN (online) 1529-2916
    ISSN 1529-2908
    DOI 10.1038/s41590-023-01565-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Dendritic cell development at a clonal level within a revised 'continuous' model of haematopoiesis.

    Naik, Shalin H

    Molecular immunology

    2020  Volume 124, Page(s) 190–197

    Abstract: Understanding development of the dendritic cell (DC) subtypes continues to evolve. The origin and relationship of conventional DC type 1 (cDC1), cDC type 2 (cDC2) and plasmacytoid DCs (pDCs) to each other, and in relation to classic myeloid and lymphoid ... ...

    Abstract Understanding development of the dendritic cell (DC) subtypes continues to evolve. The origin and relationship of conventional DC type 1 (cDC1), cDC type 2 (cDC2) and plasmacytoid DCs (pDCs) to each other, and in relation to classic myeloid and lymphoid cells, has had a long and controversial history and is still not fully resolved. This review summarises the technological developments and findings that have been achieved at a clonal level, and how that has enhanced our knowledge of the process. It summarises the single cell lineage tracing technologies that have emerged, their application in in vitro and in vivo studies, in both mouse and human settings, and places the findings in a wider context of understanding haematopoiesis at a single cell or clonal level. In particular, it addresses the fate heterogeneity observed in many phenotypically defined progenitor subsets and how these findings have led to a departure from the classic ball-and-stick models of haematopoiesis to the emerging continuous model. Prior contradictions in DC development may be reconciled if they are framed within this revised model, where commitment to a lineage or cell type does not occur in an all-or-nothing process in defined progenitors but rather can occur at many stages of haematopoiesis in a dynamic process.
    MeSH term(s) Animals ; Cell Differentiation/immunology ; Cell Lineage/immunology ; Dendritic Cells/cytology ; Hematopoiesis ; Humans
    Language English
    Publishing date 2020-06-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 424427-8
    ISSN 1872-9142 ; 0161-5890
    ISSN (online) 1872-9142
    ISSN 0161-5890
    DOI 10.1016/j.molimm.2020.06.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Death by differentiation: CD4

    Tomei, Sara / Audiger, Cindy / Naik, Shalin H

    Cell stem cell

    2022  Volume 29, Issue 5, Page(s) 655–656

    Abstract: Antigen presentation is typically regarded as the domain of immune cells such as dendritic cells and B cells. Hernandez-Malmierca et al. (2022) upend this notion by observing that hematopoietic stem and progenitor cells process and present antigen via ... ...

    Abstract Antigen presentation is typically regarded as the domain of immune cells such as dendritic cells and B cells. Hernandez-Malmierca et al. (2022) upend this notion by observing that hematopoietic stem and progenitor cells process and present antigen via major histocompatibility class II as a means of CD4
    MeSH term(s) Antigen Presentation ; B-Lymphocytes ; CD4-Positive T-Lymphocytes ; Dendritic Cells ; Histocompatibility Antigens Class II ; Stem Cells
    Chemical Substances Histocompatibility Antigens Class II
    Language English
    Publishing date 2022-05-06
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2375354-7
    ISSN 1875-9777 ; 1934-5909
    ISSN (online) 1875-9777
    ISSN 1934-5909
    DOI 10.1016/j.stem.2022.04.013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Clonal selection parallels between normal and cancer tissues.

    Salavaty, Adrian / Azadian, Esmaeel / Naik, Shalin H / Currie, Peter D

    Trends in genetics : TIG

    2023  Volume 39, Issue 5, Page(s) 358–380

    Abstract: Clonal selection and drift drive both normal tissue and cancer development. However, the biological mechanisms and environmental conditions underpinning these processes remain to be elucidated. Clonal selection models are centered in Darwinian ... ...

    Abstract Clonal selection and drift drive both normal tissue and cancer development. However, the biological mechanisms and environmental conditions underpinning these processes remain to be elucidated. Clonal selection models are centered in Darwinian evolutionary theory, where some clones with the fittest features are selected and populate the tissue or tumor. We suggest that different subclasses of stem cells, each of which is responsible for a distinct feature of the selection process, share common features between normal and cancer conditions. While active stem cells populate the tissue, dormant cells account for tissue replenishment/regeneration in both normal and cancerous tissues. We also discuss potential mechanisms that drive clonal drift, their interactions with clonal selection, and their similarities during normal and cancer tissue development.
    MeSH term(s) Humans ; Neoplasms/genetics ; Neoplasms/pathology ; Stem Cells ; Biological Evolution ; Clone Cells/pathology
    Language English
    Publishing date 2023-02-24
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2023.01.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Mastering the use of cellular barcoding to explore cancer heterogeneity.

    Serrano, Antonin / Berthelet, Jean / Naik, Shalin H / Merino, Delphine

    Nature reviews. Cancer

    2022  Volume 22, Issue 11, Page(s) 609–624

    Abstract: Tumours are often composed of a multitude of malignant clones that are genomically unique, and only a few of them may have the ability to escape cancer therapy and grow as symptomatic lesions. As a result, tumours with a large degree of genomic diversity ...

    Abstract Tumours are often composed of a multitude of malignant clones that are genomically unique, and only a few of them may have the ability to escape cancer therapy and grow as symptomatic lesions. As a result, tumours with a large degree of genomic diversity have a higher chance of leading to patient death. However, clonal fate can be driven by non-genomic features. In this context, new technologies are emerging not only to track the spatiotemporal fate of individual cells and their progeny but also to study their molecular features using various omics analysis. In particular, the recent development of cellular barcoding facilitates the labelling of tens to millions of cancer clones and enables the identification of the complex mechanisms associated with clonal fate in different microenvironments and in response to therapy. In this Review, we highlight the recent discoveries made using lentiviral-based cellular barcoding techniques, namely genetic and optical barcoding. We also emphasize the strengths and limitations of each of these technologies and discuss some of the key concepts that must be taken into consideration when one is designing barcoding experiments. Finally, we suggest new directions to further improve the use of these technologies in cancer research.
    MeSH term(s) Humans ; Clone Cells ; Neoplasms/genetics ; Tumor Microenvironment/genetics
    Language English
    Publishing date 2022-08-18
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2062767-1
    ISSN 1474-1768 ; 1474-175X
    ISSN (online) 1474-1768
    ISSN 1474-175X
    DOI 10.1038/s41568-022-00500-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Self-Organizing Nebulous Growths for Robust and Incremental Data Visualization.

    Senanayake, Damith A / Wang, Wei / Naik, Shalin H / Halgamuge, Saman

    IEEE transactions on neural networks and learning systems

    2021  Volume 32, Issue 10, Page(s) 4588–4602

    Abstract: Nonparametric dimensionality reduction techniques, such as t-distributed Stochastic Neighbor Embedding (t-SNE) and uniform manifold approximation and projection (UMAP), are proficient in providing visualizations for data sets of fixed sizes. However, ... ...

    Abstract Nonparametric dimensionality reduction techniques, such as t-distributed Stochastic Neighbor Embedding (t-SNE) and uniform manifold approximation and projection (UMAP), are proficient in providing visualizations for data sets of fixed sizes. However, they cannot incrementally map and insert new data points into an already provided data visualization. We present self-organizing nebulous growths (SONG), a parametric nonlinear dimensionality reduction technique that supports incremental data visualization, i.e., incremental addition of new data while preserving the structure of the existing visualization. In addition, SONG is capable of handling new data increments, no matter whether they are similar or heterogeneous to the already observed data distribution. We test SONG on a variety of real and simulated data sets. The results show that SONG is superior to Parametric t-SNE, t-SNE, and UMAP in incremental data visualization. Especially, for heterogeneous increments, SONG improves over Parametric t-SNE by 14.98% on the Fashion MNIST data set and 49.73% on the MNIST data set regarding the cluster quality measured by the adjusted mutual information scores. On similar or homogeneous increments, the improvements are 8.36% and 42.26%, respectively. Furthermore, even when the abovementioned data sets are presented all at once, SONG performs better or comparable to UMAP and superior to t-SNE. We also demonstrate that the algorithmic foundations of SONG render it more tolerant to noise compared with UMAP and t-SNE, thus providing greater utility for data with high variance, high mixing of clusters, or noise.
    Language English
    Publishing date 2021-10-05
    Publishing country United States
    Document type Journal Article
    ISSN 2162-2388
    ISSN (online) 2162-2388
    DOI 10.1109/TNNLS.2020.3023941
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Distinct subpopulations of DN1 thymocytes exhibit preferential γδ T lineage potential.

    Oh, Seungyoul / Liu, Xin / Tomei, Sara / Luo, Mengxiao / Skinner, Jarrod P / Berzins, Stuart P / Naik, Shalin H / Gray, Daniel H D / Chong, Mark M W

    Frontiers in immunology

    2023  Volume 14, Page(s) 1106652

    Abstract: The αβ and γδ T cell lineages both differentiate in the thymus from common uncommitted progenitors. The earliest stage of T cell development is known as ... ...

    Abstract The αβ and γδ T cell lineages both differentiate in the thymus from common uncommitted progenitors. The earliest stage of T cell development is known as CD4
    MeSH term(s) Mice ; Animals ; Thymocytes ; Interleukin-17/metabolism ; Thymus Gland ; Cell Differentiation ; Transcription Factors/metabolism
    Chemical Substances Interleukin-17 ; Transcription Factors
    Language English
    Publishing date 2023-04-03
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2023.1106652
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Editorial: Dendritic Cell and Macrophage Nomenclature and Classification.

    Ginhoux, Florent / Guilliams, Martin / Naik, Shalin H

    Frontiers in immunology

    2016  Volume 7, Page(s) 168

    Language English
    Publishing date 2016
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606827-8
    ISSN 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2016.00168
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Late fetal hematopoietic failure results from ZBTB11 deficiency despite abundant HSC specification.

    Cao, Huimin / Naik, Shalin H / Amann-Zalcenstein, Daniela / Hickey, Peter / Salim, Agus / Cao, Benjamin / Nilsson, Susan K / Keightley, M Cristina / Lieschke, Graham J

    Blood advances

    2023  Volume 7, Issue 21, Page(s) 6506–6519

    Abstract: Hematopoiesis produces diverse blood cell lineages to meet the basal needs and sudden demands of injury or infection. A rapid response to such challenges requires the expansion of specific lineages and a prompt return to balanced steady-state levels, ... ...

    Abstract Hematopoiesis produces diverse blood cell lineages to meet the basal needs and sudden demands of injury or infection. A rapid response to such challenges requires the expansion of specific lineages and a prompt return to balanced steady-state levels, necessitating tightly coordinated regulation. Previously we identified a requirement for the zinc finger and broad complex, tramtrak, bric-a-brac domain-containing 11 (ZBTB11) transcription factor in definitive hematopoiesis using a forward genetic screen for zebrafish myeloid mutants. To understand its relevance to mammalian systems, we extended these studies to mice. When Zbtb11 was deleted in the hematopoietic compartment, embryos died at embryonic day (E) 18.5 with hematopoietic failure. Zbtb11 hematopoietic knockout (Zbtb11hKO) hematopoietic stem cells (HSCs) were overabundantly specified from E14.5 to E17.5 compared with those in controls. Overspecification was accompanied by loss of stemness, inability to differentiate into committed progenitors and mature lineages in the fetal liver, failure to seed fetal bone marrow, and total hematopoietic failure. The Zbtb11hKO HSCs did not proliferate in vitro and were constrained in cell cycle progression, demonstrating the cell-intrinsic role of Zbtb11 in proliferation and cell cycle regulation in mammalian HSCs. Single-cell RNA sequencing analysis identified that Zbtb11-deficient HSCs were underrepresented in an erythroid-primed subpopulation and showed downregulation of oxidative phosphorylation pathways and dysregulation of genes associated with the hematopoietic niche. We identified a cell-intrinsic requirement for Zbtb11-mediated gene regulatory networks in sustaining a pool of maturation-capable HSCs and progenitor cells.
    MeSH term(s) Animals ; Mice ; Gene Expression Regulation ; Hematopoiesis/genetics ; Hematopoietic Stem Cells/metabolism ; Mammals/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Zebrafish/metabolism
    Chemical Substances Transcription Factors ; Zbtb11 protein, mouse
    Language English
    Publishing date 2023-08-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2915908-8
    ISSN 2473-9537 ; 2473-9529
    ISSN (online) 2473-9537
    ISSN 2473-9529
    DOI 10.1182/bloodadvances.2022009580
    Database MEDical Literature Analysis and Retrieval System OnLINE

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