LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 293

Search options

  1. Book: Functional coherence of molecular networks in bioinformatics

    Koyutürk, Mehmet / Subramaniam, Shankar / Grama, Ananth

    2012  

    Author's details Mehmet Koyutürk ; Shankar Subramaniam ; Ananth Grama ed
    Language English
    Size X, 228 S. : Ill., graph. Darst., 24 cm
    Publisher Springer
    Publishing place New York u.a.
    Publishing country United States
    Document type Book
    HBZ-ID HT017036731
    ISBN 978-1-461-40319-7 ; 1-461-40319-7 ; 9781461403203 ; 1461403200
    Database Catalogue ZB MED Medicine, Health

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2011 A 4632 order for loan Magazin

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: Multiphase Flows: Rich Physics, Challenging Theory, and Big Simulations

    Subramaniam, Shankar

    Abstract: Understanding multiphase flows is vital to addressing some of our most pressing human needs: clean air, clean water and the sustainable production of food and energy. This article focuses on a subset of multiphase flows called particle-laden suspensions ... ...

    Abstract Understanding multiphase flows is vital to addressing some of our most pressing human needs: clean air, clean water and the sustainable production of food and energy. This article focuses on a subset of multiphase flows called particle-laden suspensions involving non-deforming particles in a carrier fluid. The hydrodynamic interactions in these flows result in rich multiscale physics, such as clustering and pseudo-turbulence, with important practical implications. Theoretical formulations to represent, explain and predict these phenomena encounter peculiar challenges that multiphase flows pose for classical statistical mechanics. A critical analysis of existing approaches leads to the identification of key desirable characteristics that a formulation must possess in order to be successful at representing these physical phenomena. The need to build accurate closure models for unclosed terms that arise in statistical theories has motivated the development of particle-resolved direct numerical simulations (PR--DNS) for model-free simulation at the microscale. A critical perspective on outstanding questions and potential limitations of PR-DNS for model development is provided. Selected highlights of recent progress using PR-DNS to discover new multiphase flow physics and develop models are reviewed. Alternative theoretical formulations and extensions to current formulations are outlined as promising future research directions. The article concludes with a summary perspective on the importance of integrating theoretical, modeling, computational, and experimental efforts at different scales. This article is based on an invited talk given at the 2019 Annual Meeting of the American Physical Society's Division of Fluid Dynamics in Seattle, WA.
    Keywords covid19
    Publisher ArXiv
    Document type Article ; Online
    DOI 10.13140/rg.2.2.28950.16960
    Database COVID19

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: The Janus face of proliferating plasmablasts in dengue and COVID-19 infections.

    Nayak, Priya / Mukund, Kavitha / Subramaniam, Shankar

    Frontiers in immunology

    2023  Volume 14, Page(s) 1068424

    Abstract: Introduction: B cells play an integral role in the immune response to both dengue fever and COVID-19. Prior scRNAseq analyses of peripheral plasmablasts in COVID-19 have revealed a heterogeneous population with distinct cell subsets associated with ... ...

    Abstract Introduction: B cells play an integral role in the immune response to both dengue fever and COVID-19. Prior scRNAseq analyses of peripheral plasmablasts in COVID-19 have revealed a heterogeneous population with distinct cell subsets associated with proliferation; prior studies in patients with dengue fever have likewise shown the presence of proliferative pre-plasmablasts in the circulation. These findings may have implications for disease severity. In this study, we sought to gain a mechanistic understanding of the intracellular processes in naive and memory B cells that are associated with and may lead to an expanded proliferative plasmablast population in the circulation.
    Methods: We analyzed age-controlled (pediatric and adult), peripheral blood mononuclear cell scRNAseq datasets from patients infected with either dengue (primary or secondary) or COVID-19 (non-severe or severe) from previously published studies. Our preliminary analysis showed that pediatric patients with dengue and adults with COVID-19 had an expanded proliferative plasmablast (p-PB) population. By contrast, neither the adults with dengue nor the children with COVID-19 in our dataset had p-PBs. We used this distinctive preliminary signature to guide our analyses design and expanded our analyses to naive and memory B cells.
    Results: In age/disease conditions with and without p-PBs, we found differences in cell sensing and activation, including via the B cell receptor and downstream signal transduction. Likewise, inflammation was mediated differently: relative to groups without p-PBs, those with p-PBs had increased expression of interferon response and S100 genes (particularly severe COVID-19). Furthermore, several transcription factors at the nexus of activation, inflammation, and cell fate decisions were expressed differently in groups with and without p-PBs.
    Discussion: We used dengue and COVID-19 infections in adult and pediatric patients (focusing on naive B, memory B, and plasmablast cells) as a model to better understand the mechanisms that may give rise to p-PB populations in the circulation. Our results indicate that a more pro-inflammatory state in naive and memory B cells correlated with - and could influence the generation of- proliferating plasmablasts. Further exploration of these mechanisms will have implications for immune memory, vaccine development, and post-viral autoimmune syndromes.
    MeSH term(s) Adult ; Humans ; Child ; Leukocytes, Mononuclear ; COVID-19 ; Plasma Cells ; Inflammation ; Dengue
    Language English
    Publishing date 2023-08-11
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2023.1068424
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; Online: Endotype Characterization Reveals Mechanistic Differences Across Brain Regions in Sporadic Alzheimer's Disease.

    Patel, Ashay O / Caldwell, Andrew B / Ramachandran, Srinivasan / Subramaniam, Shankar

    Journal of Alzheimer's disease reports

    2023  Volume 7, Issue 1, Page(s) 957–972

    Abstract: Background: While Alzheimer's disease (AD) pathology is associated with altered brain structure, it is not clear whether gene expression changes mirror the onset and evolution of pathology in distinct brain regions. Deciphering the mechanisms which ... ...

    Abstract Background: While Alzheimer's disease (AD) pathology is associated with altered brain structure, it is not clear whether gene expression changes mirror the onset and evolution of pathology in distinct brain regions. Deciphering the mechanisms which cause the differential manifestation of the disease across different regions has the potential to help early diagnosis.
    Objective: We aimed to identify common and unique endotypes and their regulation in tangle-free neurons in sporadic AD (SAD) across six brain regions: entorhinal cortex (EC), hippocampus (HC), medial temporal gyrus (MTG), posterior cingulate (PC), superior frontal gyrus (SFG), and visual cortex (VCX).
    Methods: To decipher the states of tangle-free neurons across different brain regions in human subjects afflicted with AD, we performed analysis of the neural transcriptome. We explored changes in differential gene expression, functional and transcription factor target enrichment, and co-expression gene module detection analysis to discern disease-state transcriptomic variances and characterize endotypes. Additionally, we compared our results to tangled AD neuron microarray-based study and the Allen Brain Atlas.
    Results: We identified impaired neuron function in EC, MTG, PC, and VCX resulting from REST activation and reversal of mature neurons to a precursor-like state in EC, MTG, and SFG linked to SOX2 activation. Additionally, decreased neuron function and increased dedifferentiation were linked to the activation of SUZ12. Energetic deficit connected to NRF1 inactivation was found in HC, PC, and VCX.
    Conclusions: Our findings suggest that SAD manifestation varies in scale and severity in different brain regions. We identify endotypes, such as energetic shortfalls, impaired neuronal function, and dedifferentiation.
    Language English
    Publishing date 2023-08-29
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2542-4823
    ISSN (online) 2542-4823
    DOI 10.3233/ADR-220098
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Histone Signatures Predict Therapeutic Efficacy in Breast Cancer.

    Mollah, Shamim A / Subramaniam, Shankar

    IEEE open journal of engineering in medicine and biology

    2020  Volume 1, Page(s) 74–82

    Abstract: Objective: ...

    Abstract Objective:
    Language English
    Publishing date 2020-01-17
    Publishing country United States
    Document type Journal Article
    ISSN 2644-1276
    ISSN (online) 2644-1276
    DOI 10.1109/OJEMB.2020.2967105
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: Attractor Ranked Radial Basis Function Network: A Nonparametric Forecasting Approach for Chaotic Dynamic Systems.

    Masnadi-Shirazi, Maryam / Subramaniam, Shankar

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 3780

    Abstract: The curse of dimensionality has long been a hurdle in the analysis of complex data in areas such as computational biology, ecology and econometrics. In this work, we present a forecasting algorithm that exploits the dimensionality of data in a ... ...

    Abstract The curse of dimensionality has long been a hurdle in the analysis of complex data in areas such as computational biology, ecology and econometrics. In this work, we present a forecasting algorithm that exploits the dimensionality of data in a nonparametric autoregressive framework. The main idea is that the dynamics of a chaotic dynamical system consisting of multiple time-series can be reconstructed using a combination of different variables. This nonlinear autoregressive algorithm uses multivariate attractors reconstructed as the inputs of a neural network to predict the future. We show that our approach, attractor ranked radial basis function network (AR-RBFN) provides a better forecast than that obtained using other model-free approaches as well as univariate and multivariate autoregressive models using radial basis function networks. We demonstrate this for simulated ecosystem models and a mesocosm experiment. By taking advantage of dimensionality, we show that AR-RBFN overcomes the shortcomings of noisy and short time-series data.
    MeSH term(s) Algorithms ; Ecosystem ; Forecasting/methods ; Neural Networks, Computer
    Language English
    Publishing date 2020-03-02
    Publishing country England
    Document type Evaluation Study ; Journal Article ; Research Support, N.I.H., Extramural ; 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/s41598-020-60606-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  7. Article ; Online: RefMet: a reference nomenclature for metabolomics.

    Fahy, Eoin / Subramaniam, Shankar

    Nature methods

    2020  Volume 17, Issue 12, Page(s) 1173–1174

    MeSH term(s) Databases, Chemical ; Humans ; Metabolome ; Metabolomics ; Molecular Sequence Annotation ; Terminology as Topic
    Language English
    Publishing date 2020-11-16
    Publishing country United States
    Document type Letter ; Research Support, N.I.H., Extramural
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-020-01009-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6022: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article ; Online: The Mechanistic Metamorphosis.

    Subramaniam, Shankar / Nadeau, Joseph

    WIREs mechanisms of disease

    2020  Volume 13, Issue 1, Page(s) e1517

    MeSH term(s) Humans ; Metamorphosis, Biological
    Language English
    Publishing date 2020-12-26
    Publishing country United States
    Document type Editorial
    ISSN 2692-9368
    ISSN (online) 2692-9368
    DOI 10.1002/wsbm.1517
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  9. Article ; Online: Drug discovery and the maze of biological complexity: an editorial essay.

    Subramaniam, Shankar

    Wiley interdisciplinary reviews. Systems biology and medicine

    2014  Volume 6, Issue 3, Page(s) 225–226

    MeSH term(s) Animals ; Drug Discovery ; Humans ; Systems Biology
    Language English
    Publishing date 2014-05
    Publishing country United States
    Document type Comment ; Editorial
    ZDB-ID 2503323-2
    ISSN 1939-005X ; 1939-5094
    ISSN (online) 1939-005X
    ISSN 1939-5094
    DOI 10.1002/wsbm.1266
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6790: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: Modular and mechanistic changes across stages of colorectal cancer.

    Rahiminejad, Sara / Maurya, Mano R / Mukund, Kavitha / Subramaniam, Shankar

    BMC cancer

    2022  Volume 22, Issue 1, Page(s) 436

    Abstract: Background: While mechanisms contributing to the progression and metastasis of colorectal cancer (CRC) are well studied, cancer stage-specific mechanisms have been less comprehensively explored. This is the focus of this manuscript.: Methods: Using ... ...

    Abstract Background: While mechanisms contributing to the progression and metastasis of colorectal cancer (CRC) are well studied, cancer stage-specific mechanisms have been less comprehensively explored. This is the focus of this manuscript.
    Methods: Using previously published data for CRC (Gene Expression Omnibus ID GSE21510), we identified differentially expressed genes (DEGs) across four stages of the disease. We then generated unweighted and weighted correlation networks for each of the stages. Communities within these networks were detected using the Louvain algorithm and topologically and functionally compared across stages using the normalized mutual information (NMI) metric and pathway enrichment analysis, respectively. We also used Short Time-series Expression Miner (STEM) algorithm to detect potential biomarkers having a role in CRC.
    Results: Sixteen Thousand Sixty Two DEGs were identified between various stages (p-value ≤ 0.05). Comparing communities of different stages revealed that neighboring stages were more similar to each other than non-neighboring stages, at both topological and functional levels. A functional analysis of 24 cancer-related pathways indicated that several signaling pathways were enriched across all stages. However, the stage-unique networks were distinctly enriched only for a subset of these 24 pathways (e.g., MAPK signaling pathway in stages I-III and Notch signaling pathway in stages III and IV). We identified potential biomarkers, including HOXB8 and WNT2 with increasing, and MTUS1 and SFRP2 with decreasing trends from stages I to IV. Extracting subnetworks of 10 cancer-relevant genes and their interacting first neighbors (162 genes in total) revealed that the connectivity patterns for these genes were different across stages. For example, BRAF and CDK4, members of the Ser/Thr kinase, up-regulated in cancer, displayed changing connectivity patterns from stages I to IV.
    Conclusions: Here, we report molecular and modular networks for various stages of CRC, providing a pseudo-temporal view of the mechanistic changes associated with the disease. Our analysis highlighted similarities at both functional and topological levels, across stages. We further identified stage-specific mechanisms and biomarkers potentially contributing to the progression of CRC.
    MeSH term(s) Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Colorectal Neoplasms/pathology ; Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Humans ; Neoplasm Staging ; Signal Transduction/genetics ; Tumor Suppressor Proteins/genetics
    Chemical Substances Biomarkers, Tumor ; MTUS1 protein, human ; Tumor Suppressor Proteins
    Language English
    Publishing date 2022-04-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041352-X
    ISSN 1471-2407 ; 1471-2407
    ISSN (online) 1471-2407
    ISSN 1471-2407
    DOI 10.1186/s12885-022-09479-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top