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  1. Book: Computational Intelligence Methods for Bioinformatics and Biostatistics

    Chicco, Davide / Facchiano, Angelo / Tavazzi, Erica / Cazzaniga, Paolo / Vettoretti, Martina / Bernasconi, Anna / Avesani, Simone / Longato, Enrico

    17th International Meeting, CIBB 2021, Virtual Event, November 15¿17, 2021, Revised Selected Papers

    (Lecture Notes in Bioinformatics)

    2022  

    Series title Lecture Notes in Bioinformatics
    Keywords artificial intelligence ; computational and systems biology ; computer networks ; Computer Systems ; Computer vision ; Correlation Analysis ; Data Mining ; education ; Image Analysis ; image processing ; Image segmentation ; Learning ; Machine Learning ; Neural Networks ; pattern recognition ; Signal Processing ; biostatistics ; computer systems ; computer vision ; correlation analysis ; data mining ; image analysis ; image segmentation ; learning ; machine learning ; neural networks ; signal processing
    Language English
    Size 272 p.
    Edition 1
    Publisher Springer International Publishing
    Document type Book
    Note PDA Manuell_17
    Format 155 x 235 x 15
    ISBN 9783031208362 ; 3031208366
    Database PDA

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  2. Article ; Online: Stardust: improving spatial transcriptomics data analysis through space-aware modularity optimization-based clustering.

    Avesani, Simone / Viesi, Eva / Alessandrì, Luca / Motterle, Giovanni / Bonnici, Vincenzo / Beccuti, Marco / Calogero, Raffaele / Giugno, Rosalba

    GigaScience

    2022  Volume 11

    Abstract: Background: Spatial transcriptomics (ST) combines stained tissue images with spatially resolved high-throughput RNA sequencing. The spatial transcriptomic analysis includes challenging tasks like clustering, where a partition among data points (spots) ... ...

    Abstract Background: Spatial transcriptomics (ST) combines stained tissue images with spatially resolved high-throughput RNA sequencing. The spatial transcriptomic analysis includes challenging tasks like clustering, where a partition among data points (spots) is defined by means of a similarity measure. Improving clustering results is a key factor as clustering affects subsequent downstream analysis. State-of-the-art approaches group data by taking into account transcriptional similarity and some by exploiting spatial information as well. However, it is not yet clear how much the spatial information combined with transcriptomics improves the clustering result.
    Results: We propose a new clustering method, Stardust, that easily exploits the combination of space and transcriptomic information in the clustering procedure through a manual or fully automatic tuning of algorithm parameters. Moreover, a parameter-free version of the method is also provided where the spatial contribution depends dynamically on the expression distances distribution in the space. We evaluated the proposed methods results by analyzing ST data sets available on the 10x Genomics website and comparing clustering performances with state-of-the-art approaches by measuring the spots' stability in the clusters and their biological coherence. Stability is defined by the tendency of each point to remain clustered with the same neighbors when perturbations are applied.
    Conclusions: Stardust is an easy-to-use methodology allowing to define how much spatial information should influence clustering on different tissues and achieving more stable results than state-of-the-art approaches.
    MeSH term(s) Algorithms ; Cluster Analysis ; Data Analysis ; Transcriptome
    Language English
    Publishing date 2022-08-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giac075
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Biometal Dyshomeostasis in Olfactory Mucosa of Alzheimer's Disease Patients.

    Lampinen, Riikka / Górová, Veronika / Avesani, Simone / Liddell, Jeffrey R / Penttilä, Elina / Závodná, Táňa / Krejčík, Zdeněk / Lehtola, Juha-Matti / Saari, Toni / Kalapudas, Juho / Hannonen, Sanna / Löppönen, Heikki / Topinka, Jan / Koivisto, Anne M / White, Anthony R / Giugno, Rosalba / Kanninen, Katja M

    International journal of molecular sciences

    2022  Volume 23, Issue 8

    Abstract: Olfactory function, orchestrated by the cells of the olfactory mucosa at the rooftop of the nasal cavity, is disturbed early in the pathogenesis of Alzheimer's disease (AD). Biometals including zinc and calcium are known to be important for sense of ... ...

    Abstract Olfactory function, orchestrated by the cells of the olfactory mucosa at the rooftop of the nasal cavity, is disturbed early in the pathogenesis of Alzheimer's disease (AD). Biometals including zinc and calcium are known to be important for sense of smell and to be altered in the brains of AD patients. Little is known about elemental homeostasis in the AD patient olfactory mucosa. Here we aimed to assess whether the disease-related alterations to biometal homeostasis observed in the brain are also reflected in the olfactory mucosa. We applied RNA sequencing to discover gene expression changes related to metals in olfactory mucosal cells of cognitively healthy controls, individuals with mild cognitive impairment and AD patients, and performed analysis of the elemental content to determine metal levels. Results demonstrate that the levels of zinc, calcium and sodium are increased in the AD olfactory mucosa concomitantly with alterations to 17 genes related to metal-ion binding or metal-related function of the protein product. A significant elevation in alpha-2-macroglobulin, a known metal-binding biomarker correlated with brain disease burden, was observed on the gene and protein levels in the olfactory mucosa cells of AD patients. These data demonstrate that the olfactory mucosa cells derived from AD patients recapitulate certain impairments of biometal homeostasis observed in the brains of patients.
    MeSH term(s) Alzheimer Disease/metabolism ; Calcium/metabolism ; Chelating Agents/metabolism ; Humans ; Olfactory Mucosa/metabolism ; Trace Elements/metabolism ; Zinc/metabolism
    Chemical Substances Chelating Agents ; Trace Elements ; Zinc (J41CSQ7QDS) ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2022-04-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23084123
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  4. Article ; Online: Emissions from modern engines induce distinct effects in human olfactory mucosa cells, depending on fuel and aftertreatment.

    Mussalo, Laura / Avesani, Simone / Shahbaz, Muhammad Ali / Závodná, Táňa / Saveleva, Liudmila / Järvinen, Anssi / Lampinen, Riikka / Belaya, Irina / Krejčík, Zdeněk / Ivanova, Mariia / Hakkarainen, Henri / Kalapudas, Juho / Penttilä, Elina / Löppönen, Heikki / Koivisto, Anne M / Malm, Tarja / Topinka, Jan / Giugno, Rosalba / Aakko-Saksa, Päivi /
    Chew, Sweelin / Rönkkö, Topi / Jalava, Pasi / Kanninen, Katja M

    The Science of the total environment

    2023  Volume 905, Page(s) 167038

    Abstract: Ultrafine particles (UFP) with a diameter of ≤0.1 μm, are contributors to ambient air pollution and derived mainly from traffic emissions, yet their health effects remain poorly characterized. The olfactory mucosa (OM) is located at the rooftop of the ... ...

    Abstract Ultrafine particles (UFP) with a diameter of ≤0.1 μm, are contributors to ambient air pollution and derived mainly from traffic emissions, yet their health effects remain poorly characterized. The olfactory mucosa (OM) is located at the rooftop of the nasal cavity and directly exposed to both the environment and the brain. Mounting evidence suggests that pollutant particles affect the brain through the olfactory tract, however, the exact cellular mechanisms of how the OM responds to air pollutants remain poorly known. Here we show that the responses of primary human OM cells are altered upon exposure to UFPs and that different fuels and engines elicit different adverse effects. We used UFPs collected from exhausts of a heavy-duty-engine run with renewable diesel (A0) and fossil diesel (A20), and from a modern diesel vehicle run with renewable diesel (Euro6) and compared their health effects on the OM cells by assessing cellular processes on the functional and transcriptomic levels. Quantification revealed all samples as UFPs with the majority of particles being ≤0.1 μm by an aerodynamic diameter. Exposure to A0 and A20 induced substantial alterations in processes associated with inflammatory response, xenobiotic metabolism, olfactory signaling, and epithelial integrity. Euro6 caused only negligible changes, demonstrating the efficacy of aftertreatment devices. Furthermore, when compared to A20, A0 elicited less pronounced effects on OM cells, suggesting renewable diesel induces less adverse effects in OM cells. Prior studies and these results suggest that PAHs may disturb the inflammatory process and xenobiotic metabolism in the OM and that UFPs might mediate harmful effects on the brain through the olfactory route. This study provides important information on the adverse effects of UFPs in a human-based in vitro model, therefore providing new insight to form the basis for mitigation and preventive actions against the possible toxicological impairments caused by UFP exposure.
    MeSH term(s) Humans ; Xenobiotics ; Air Pollutants/toxicity ; Air Pollutants/analysis ; Particulate Matter/toxicity ; Particulate Matter/analysis ; Vehicle Emissions/toxicity ; Vehicle Emissions/analysis ; Olfactory Mucosa/chemistry
    Chemical Substances Xenobiotics ; Air Pollutants ; Particulate Matter ; Vehicle Emissions
    Language English
    Publishing date 2023-09-13
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2023.167038
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  5. Article ; Online: Single-Cell RNA-Seq Analysis of Olfactory Mucosal Cells of Alzheimer's Disease Patients.

    Lampinen, Riikka / Fazaludeen, Mohammad Feroze / Avesani, Simone / Örd, Tiit / Penttilä, Elina / Lehtola, Juha-Matti / Saari, Toni / Hannonen, Sanna / Saveleva, Liudmila / Kaartinen, Emma / Fernández Acosta, Francisco / Cruz-Haces, Marcela / Löppönen, Heikki / Mackay-Sim, Alan / Kaikkonen, Minna U / Koivisto, Anne M / Malm, Tarja / White, Anthony R / Giugno, Rosalba /
    Chew, Sweelin / Kanninen, Katja M

    Cells

    2022  Volume 11, Issue 4

    Abstract: Olfaction is orchestrated by olfactory mucosal cells located in the upper nasal cavity. Olfactory dysfunction manifests early in several neurodegenerative disorders including Alzheimer's disease, however, disease-related alterations to the olfactory ... ...

    Abstract Olfaction is orchestrated by olfactory mucosal cells located in the upper nasal cavity. Olfactory dysfunction manifests early in several neurodegenerative disorders including Alzheimer's disease, however, disease-related alterations to the olfactory mucosal cells remain poorly described. The aim of this study was to evaluate the olfactory mucosa differences between cognitively healthy individuals and Alzheimer's disease patients. We report increased amyloid-beta secretion in Alzheimer's disease olfactory mucosal cells and detail cell-type-specific gene expression patterns, unveiling 240 differentially expressed disease-associated genes compared to the cognitively healthy controls, and five distinct cell populations. Overall, alterations of RNA and protein metabolism, inflammatory processes, and signal transduction were observed in multiple cell populations, suggesting their role in Alzheimer's disease-related olfactory mucosa pathophysiology. Furthermore, the single-cell RNA-sequencing proposed alterations in gene expression of mitochondrially located genes in AD OM cells, which were verified by functional assays, demonstrating altered mitochondrial respiration and a reduction of ATP production. Our results reveal disease-related changes of olfactory mucosal cells in Alzheimer's disease and demonstrate the utility of single-cell RNA sequencing data for investigating molecular and cellular mechanisms associated with the disease.
    MeSH term(s) Alzheimer Disease/metabolism ; Amyloid beta-Peptides/metabolism ; Humans ; Olfactory Mucosa/metabolism ; RNA ; Sequence Analysis, RNA
    Chemical Substances Amyloid beta-Peptides ; RNA (63231-63-0)
    Language English
    Publishing date 2022-02-15
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells11040676
    Database MEDical Literature Analysis and Retrieval System OnLINE

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