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  1. Book ; Online ; E-Book: Environmental contaminants and endocrine health

    Carnevali, Oliana / Hardiman, Gary

    2023  

    Author's details edited by Oliana Carnevali, Gary Hardiman
    Keywords Electronic books
    Language English
    Size 1 Online-Ressource (xvii, 373 Seiten), Illustrationen, Diagramme
    Publisher Elsevier Academic Press
    Publishing place London
    Publishing country Great Britain
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    HBZ-ID HT030046377
    ISBN 978-0-323-85932-5 ; 9780128244647 ; 0-323-85932-1 ; 012824464X
    DOI 10.1007/978-0-323-85932-5
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Book ; Online: Systems Analytics and Integration of Big Omics Data

    Hardiman, Gary

    2020  

    Abstract: A "genotype is essentially an organisms full hereditary information which is obtained from its parents. A phenotype is an organisms actual observed physical and behavioral properties. These may include traits such as morphology, size, height, eye color, ... ...

    Abstract A "genotype is essentially an organisms full hereditary information which is obtained from its parents. A phenotype is an organisms actual observed physical and behavioral properties. These may include traits such as morphology, size, height, eye color, metabolism, etc. One of the pressing challenges in computational and systems biology is genotype-to-phenotype prediction. This is challenging given the amount of data generated by modern Omics technologies. This "Big Data" is so large and complex that traditional data processing applications are not up to the task. Challenges arise in collection, analysis, mining, sharing, transfer, visualization, archiving, and integration of these data. In this Special Issue, there is a focus on the systems-level analysis of Omics data, recent developments in gene ontology annotation, and advances in biological pathways and network biology. The integration of Omics data with clinical and biomedical data using machine learning is explored. This Special Issue covers new methodologies in the context of gene-environment interactions, tissue-specific gene expression, and how external factors or host genetics impact the microbiome
    Keywords Medicine (General) ; Therapeutics. Pharmacology
    Size 1 electronic resource (202 pages)
    Publisher MDPI - Multidisciplinary Digital Publishing Institute
    Document type Book ; Online
    Note eng ; Open Access
    HBZ-ID HT020589469
    ISBN 9783039287444 ; 9783039287451 ; 3039287443 ; 3039287451
    DOI 10.3390/books978-3-03928-745-1
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Article ; Online: An Introduction to Systems Analytics and Integration of Big Omics Data.

    Hardiman, Gary

    Genes

    2020  Volume 11, Issue 3

    Abstract: A major technological shift in the research community in the past decade has been the adoption of high throughput (HT) technologies to interrogate the genome, epigenome, transcriptome, and proteome in a massively parallel fashion [ ... ]. ...

    Abstract A major technological shift in the research community in the past decade has been the adoption of high throughput (HT) technologies to interrogate the genome, epigenome, transcriptome, and proteome in a massively parallel fashion [...].
    MeSH term(s) Big Data ; Data Interpretation, Statistical ; Epigenome/genetics ; Genomics/trends ; Humans ; Proteome/genetics ; Systems Analysis ; Transcriptome/genetics
    Chemical Substances Proteome
    Language English
    Publishing date 2020-02-26
    Publishing country Switzerland
    Document type Editorial ; Introductory Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes11030245
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genetic and epigenetic studies of opioid abuse disorder - the potential for future diagnostics.

    Abdulmalek, Sarah / Hardiman, Gary

    Expert review of molecular diagnostics

    2023  Volume 23, Issue 5, Page(s) 361–373

    Abstract: Introduction: Opioid use disorder (OUD) is a global problem that often begins with prescribed medications. The available treatment and maintenance plans offer solutions for the consumption rate by individuals leaving the outstanding problem of relapse, ... ...

    Abstract Introduction: Opioid use disorder (OUD) is a global problem that often begins with prescribed medications. The available treatment and maintenance plans offer solutions for the consumption rate by individuals leaving the outstanding problem of relapse, which is a major factor hindering the long-term efficacy of treatments.
    Areas covered: Understanding the neurobiology of addiction and relapse would help identifying the core causes of relapse and distinguish vulnerable from resilient individuals, which would lead to more targeted and effective treatment and provide diagnostics to screen individuals who have a propensity to OUD. In this review, we cover the neurobiology of the reward system highlighting the role of multiple brain regions and opioid receptors in the development of the disorder. We also review the current knowledge of the epigenetics of addiction and the available screening tools for aberrant use of opioids.
    Expert opinion: Relapse remains an anticipated limitation in the way of recovery even after long period of abstinence. This highlights the need for diagnostic tools that identify vulnerable patients and prevent the cycle of addiction. Finally, we discuss the limitations of the available screening tools and propose possible solutions for the discovery of addiction diagnostics.
    MeSH term(s) Humans ; Opioid-Related Disorders/diagnosis ; Opioid-Related Disorders/genetics ; Opioid-Related Disorders/drug therapy ; Analgesics, Opioid/therapeutic use ; Brain ; Recurrence
    Chemical Substances Analgesics, Opioid
    Language English
    Publishing date 2023-04-20
    Publishing country England
    Document type Review ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2112530-2
    ISSN 1744-8352 ; 1473-7159
    ISSN (online) 1744-8352
    ISSN 1473-7159
    DOI 10.1080/14737159.2023.2190022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6073: 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)

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  5. Article: An Introduction to Systems Analytics and Integration of Big Omics Data

    Hardiman, Gary

    Genes. 2020 Feb. 26, v. 11, no. 3

    2020  

    Abstract: A major technological shift in the research community in the past decade has been the adoption of high throughput (HT) technologies to interrogate the genome, epigenome, transcriptome, and proteome in a massively parallel fashion [ ... ] ...

    Abstract A major technological shift in the research community in the past decade has been the adoption of high throughput (HT) technologies to interrogate the genome, epigenome, transcriptome, and proteome in a massively parallel fashion [...]
    Keywords epigenome ; proteome ; transcriptome
    Language English
    Dates of publication 2020-0226
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes11030245
    Database NAL-Catalogue (AGRICOLA)

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  6. Book ; Online: Systems Analytics and Integration of Big Omics Data

    Hardiman, Gary

    2020  

    Abstract: A “genotype"" is essentially an organism's full hereditary information which is obtained from its parents. A ""phenotype"" is an organism's actual observed physical and behavioral properties. These may include traits such as morphology, size, height, eye ...

    Abstract A “genotype"" is essentially an organism's full hereditary information which is obtained from its parents. A ""phenotype"" is an organism's actual observed physical and behavioral properties. These may include traits such as morphology, size, height, eye color, metabolism, etc. One of the pressing challenges in computational and systems biology is genotype-to-phenotype prediction. This is challenging given the amount of data generated by modern Omics technologies. This “Big Data” is so large and complex that traditional data processing applications are not up to the task. Challenges arise in collection, analysis, mining, sharing, transfer, visualization, archiving, and integration of these data. In this Special Issue, there is a focus on the systems-level analysis of Omics data, recent developments in gene ontology annotation, and advances in biological pathways and network biology. The integration of Omics data with clinical and biomedical data using machine learning is explored. This Special Issue covers new methodologies in the context of gene–environment interactions, tissue-specific gene expression, and how external factors or host genetics impact the microbiome.
    Keywords tissue-specific expressed genes ; transcriptome ; tissue classification ; support vector machine ; feature selection ; bioinformatics pipelines ; algorithm development for network integration ; miRNA–gene expression networks ; multiomics integration ; network topology analysis ; candidate genes ; gene–environment interactions ; logic forest ; systemic lupus erythematosus ; Gene Ontology ; KEGG pathways ; enrichment analysis ; proteomic analysis ; plot visualization ; Alzheimer’s disease ; dementia ; cognitive impairment ; neurodegeneration ; annotation ; biocuration ; amyloid-beta ; microtubule-associated protein tau ; artificial intelligence ; genotype ; phenotype ; deep phenotype ; data integration ; genomics ; phenomics ; precision medicine informatics ; epigenetics ; chromatin modification ; sequencing ; regulatory genomics ; disease variants ; machine learning ; multi-omics ; curse of dimensionality ; heterogeneous data ; missing data ; class imbalance ; scalability ; pharmacogenomics ; cell lines ; database ; drug sensitivity ; omics data ; RNA expression ; non-omics data ; clinical data ; epidemiological data ; challenges ; integrative analytics ; joint modeling ; multivariate analysis ; multivariate causal mediation ; distance correlation ; direct effect ; indirect effect ; causal inference ; n/a
    Subject code 004
    Language English
    Publisher MDPI - Multidisciplinary Digital Publishing Institute
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  7. Article ; Online: Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle.

    Cahill, Thomas / Chan, Sherine / Overton, Ian M / Hardiman, Gary

    Cells

    2023  Volume 12, Issue 10

    Abstract: The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However, mounting evidence points to torpor-induced protective benefits from the main hazards of space travel, namely, exposure to radiation and microgravity. To ... ...

    Abstract The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However, mounting evidence points to torpor-induced protective benefits from the main hazards of space travel, namely, exposure to radiation and microgravity. To determine the radio-protective effects of an induced torpor-like state we exploited the ectothermic nature of the
    MeSH term(s) Animals ; Hypothermia ; Zebrafish/genetics ; Torpor/physiology ; Gene Expression Profiling ; Muscles
    Language English
    Publishing date 2023-05-11
    Publishing country Switzerland
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; 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/cells12101366
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Modeling Microplastic Transport in the Marine Environment: Testing Empirical Models of Particle Terminal Sinking Velocity for Irregularly Shaped Particles.

    Coyle, Róisín / Service, Matthew / Witte, Ursula / Hardiman, Gary / McKinley, Jennifer

    ACS ES&T water

    2023  Volume 3, Issue 4, Page(s) 984–995

    Abstract: Microplastic (mP) pollution has been indicated as an area of concern in the marine environment. However, there is no consensus on their potential to cause significant ecological harm, and a comprehensive risk assessment of mP pollution is unattainable ... ...

    Abstract Microplastic (mP) pollution has been indicated as an area of concern in the marine environment. However, there is no consensus on their potential to cause significant ecological harm, and a comprehensive risk assessment of mP pollution is unattainable due to gaps in our understanding of their transport, uptake, and exchange processes. This research considers drag models that have been proposed to calculate the terminal settling velocity of regularly and irregularly shaped particles to assess their applicability in a mP modeling context. The evaluation indicates three models that predict the settling velocity of mPs to a high precision and suggests that an explicit model is the most appropriate for implementation in a mP transport model. This research demonstrates that the mP settling velocity does not vary significantly over time and depth relevant to the scale of an ocean model and that the terminal settling velocity is independent of the initial particle velocity. These findings contribute toward efforts to simulate the vertical transport of mPs in the ocean, which will improve our understanding of the residence time of mPs in the water column and subsequently their availability for uptake into the marine ecosystem.
    Language English
    Publishing date 2023-03-22
    Publishing country United States
    Document type Journal Article
    ISSN 2690-0637
    ISSN (online) 2690-0637
    DOI 10.1021/acsestwater.2c00466
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Spaceflight causes strain-dependent gene expression changes associated with lipid and extracellular matrix dysregulation in the mouse kidney in vivo.

    Finch, Rebecca H / Vitry, Geraldine / Siew, Keith / Walsh, Stephen B / Behesti, Afshin / Hardiman, Gary / da Silveira, Willian A

    bioRxiv : the preprint server for biology

    2024  

    Abstract: To explore new worlds we must ensure humans can survive and thrive in the space environment. Incidence of kidney stones in astronauts is a major risk factor associated with long term missions, caused by increased blood calcium levels due to bone ... ...

    Abstract To explore new worlds we must ensure humans can survive and thrive in the space environment. Incidence of kidney stones in astronauts is a major risk factor associated with long term missions, caused by increased blood calcium levels due to bone demineralisation triggered by microgravity and space radiation. Transcriptomic changes have been observed in other tissues during spaceflight, including the kidney. We analysed kidney transcriptome patterns in two different strains of mice flown on the International Space Station, C57BL/6J and BALB/c. Here we show a link between spaceflight and transcriptome patterns associated with dysregulation of lipid and extracellular matrix metabolism and altered transforming growth factor-beta signalling. A stronger response was seen in C57BL/6J mice than BALB/c. Genetic differences in hyaluronan metabolism between strains may confer protection against extracellular matrix remodelling through downregulation of epithelial-mesenchymal transition. We intend for our findings to contribute to development of new countermeasures against kidney disease in astronauts and people here on Earth.
    Highlights: Spaceflight has a significant effect on gene expression in the kidney.Responses in the BALB/c indicate milder transcriptomic perturbations than C57BL/6J.Lipid metabolism was altered in both strains of mice.Extracellular matrix metabolism and TGF-β signalling up in BALB/c down in C57BL/6J.Reduced gene expression of hyaluronan synthesis pathway in BALB/c but not in C57BL/6J.
    Language English
    Publishing date 2024-03-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.13.584781
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Multiscale modeling in the framework of biological systems and its potential for spaceflight biology studies.

    Millar-Wilson, Andrew / Ward, Órla / Duffy, Eolann / Hardiman, Gary

    iScience

    2022  Volume 25, Issue 11, Page(s) 105421

    Abstract: A central tenet of systems biology is that biological systems are greater than the sum of their component parts. Spaceflight is associated with hazards including radiation exposure and microgravity which impact different echelons of biological ... ...

    Abstract A central tenet of systems biology is that biological systems are greater than the sum of their component parts. Spaceflight is associated with hazards including radiation exposure and microgravity which impact different echelons of biological organizations spanning molecular, cellular, organ, and organismal levels. These insults lead to physical damage, including muscle and bone loss, neurological damage, and impaired immunity. Mitochondrial dysfunction and biological alterations occurring during spaceflight have been reported. The health challenges presented by long-term space travel must be addressed and appropriate countermeasures developed to protect astronauts. Increasing quantity of multiomics data are being generated from cells and model organisms flown in space, with physiological data from astronauts. Systems biology approaches leveraging mathematical reasoning and computational modeling are required to characterize these components in a holistic fashion. In this review, we provide an historic perspective on multiscale biological systems modeling, followed by a discussion on its utility for spaceflight biology research.
    Language English
    Publishing date 2022-10-26
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2022.105421
    Database MEDical Literature Analysis and Retrieval System OnLINE

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