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  1. Article ; Online: The role of the Mediterranean diet in modulating the gut microbiome: A review of current evidence.

    Gundogdu, Aycan / Nalbantoglu, Ozkan Ufuk

    Nutrition (Burbank, Los Angeles County, Calif.)

    2023  Volume 114, Page(s) 112118

    Abstract: The Mediterranean diet (MedDiet) is recognized as one of the United Nations Educational, Scientific and Cultural Organization Intangible Cultural Heritage assets associated with lower rates of cardiometabolic diseases; lower prevalence of cancer, ... ...

    Abstract The Mediterranean diet (MedDiet) is recognized as one of the United Nations Educational, Scientific and Cultural Organization Intangible Cultural Heritage assets associated with lower rates of cardiometabolic diseases; lower prevalence of cancer, Alzheimer's disease, depression, and onset of inflammatory bowel disease; and more generally low-grade inflammation and mortality risks. Beyond being an input source of beneficial micronutrients, it recently has been discovered that the MedDiet plays a role in a more complex human microbiome-mediated mechanism. An interesting hypothesis suggests a bidirectional relationship between the MedDiet and the gut microbiome, where gut microbiota assembly and biosynthetic capacity are responsive to the diet; in return, the microbiome-reachable nutrients shape and modulate the microbiome toward a characteristic probiotic state. It can be speculated that that primary health benefits of the MedDiet exerted via the gut microbiome are mediated by the bioactive compounds transformed by the microbiome. Furthermore, it is possible that additional probiotic properties of the organisms promoted by diet adherence have secondary benefits. As more detailed omic-based studies take place, more evidence on the MedDiet as a core generic probiotic microbiome modulation strategy surface. However, individual-specific microbiome compositions might impose personal variations on the diet outcome. Therefore, a prospective strategy of a fine-tuned precision nutrition approach might deliver optimized benefits of the MedDiet.
    MeSH term(s) Humans ; Diet, Mediterranean ; Gastrointestinal Microbiome ; Nutrients ; Nutritional Status ; Micronutrients
    Chemical Substances Micronutrients
    Language English
    Publishing date 2023-06-07
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 639259-3
    ISSN 1873-1244 ; 0899-9007
    ISSN (online) 1873-1244
    ISSN 0899-9007
    DOI 10.1016/j.nut.2023.112118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Group testing performance evaluation for SARS-CoV-2 massive scale screening and testing.

    Nalbantoglu, Ozkan Ufuk

    BMC medical research methodology

    2020  Volume 20, Issue 1, Page(s) 176

    Abstract: Background: The capacity of the current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in the current paradigm of shallow tracing is unlikely to reach the silent clusters that ... ...

    Abstract Background: The capacity of the current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in the current paradigm of shallow tracing is unlikely to reach the silent clusters that might be as important as the symptomatic cases in the spread of the disease. Group testing is a feasible and promising approach when the resources are scarce and when a relatively low prevalence regime is observed on the population.
    Methods: We employed group testing with a sparse random pooling scheme and conventional group test decoding algorithms both for exact and inexact recovery.
    Results: Our simulations showed that significant reduction in per case test numbers (or expansion in total test numbers preserving the number of actual tests conducted) for very sparse prevalence regimes is available. Currently proposed COVID-19 group testing schemes offer a gain up to 15X-20X scale-up. There is a good probability that the required scale up to achieve massive scale testing might be greater in certain scenarios. We investigated if further improvement is available, especially in sparse prevalence occurrence where outbreaks are needed to be avoided by population scans.
    Conclusion: Our simulations show that sparse random pooling can provide improved efficiency gains compared to conventional group testing or Reed-Solomon error correcting codes. Therefore, we propose that special designs for different scenarios could be available and it is possible to scale up testing capabilities significantly.
    MeSH term(s) Algorithms ; COVID-19 ; Computer Simulation ; Coronavirus Infections/diagnosis ; Humans ; Mass Screening/methods ; Pandemics ; Pneumonia, Viral/diagnosis ; Random Allocation
    Keywords covid19
    Language English
    Publishing date 2020-07-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041362-2
    ISSN 1471-2288 ; 1471-2288
    ISSN (online) 1471-2288
    ISSN 1471-2288
    DOI 10.1186/s12874-020-01048-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: COVID-19 Pandemic: Group Testing.

    Nalbantoglu, Ozkan Ufuk / Gundogdu, Aycan

    Frontiers in medicine

    2020  Volume 7, Page(s) 522

    Keywords covid19
    Language English
    Publishing date 2020-08-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2775999-4
    ISSN 2296-858X
    ISSN 2296-858X
    DOI 10.3389/fmed.2020.00522
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  4. Article ; Online: The role of the Mediterranean diet in modulating the gut microbiome: A review of current evidence

    Gundogdu, Aycan / Nalbantoglu, Ozkan Ufuk

    Nutrition. 2023 Oct., v. 114 p.112118-

    2023  

    Abstract: The Mediterranean diet (MedDiet) is recognized as one of the United Nations Educational, Scientific and Cultural Organization Intangible Cultural Heritage assets associated with lower rates of cardiometabolic diseases; lower prevalence of cancer, ... ...

    Abstract The Mediterranean diet (MedDiet) is recognized as one of the United Nations Educational, Scientific and Cultural Organization Intangible Cultural Heritage assets associated with lower rates of cardiometabolic diseases; lower prevalence of cancer, Alzheimer's disease, depression, and onset of inflammatory bowel disease; and more generally low-grade inflammation and mortality risks. Beyond being an input source of beneficial micronutrients, it is recently has been discovered that the MedDiet plays a role in a more complex human microbiome–mediated mechanism. An interesting hypothesis suggests a bidirectional relationship between the MedDiet and the gut microbiome, where gut microbiota assembly and biosynthetic capacity are responsive to the diet; in return, the microbiome-reachable nutrients shape and modulate the microbiome toward a characteristic probiotic state. It can be speculated that that primary health benefits of the MedDiet exerted via the gut microbiome are mediated by the bioactive compounds transformed by the microbiome. Furthermore, it is possible that additional probiotic properties of the organisms promoted by diet adherence have secondary benefits. As more detailed omic-based studies take place, more evidence on the MedDiet as a core generic probiotic microbiome modulation strategy surface. However, individual–specific microbiome compositions might impose personal variations on the diet outcome. Therefore, a prospective strategy of a fine-tuned precision nutrition approach might deliver optimized benefits of the MedDiet.
    Keywords Alzheimer disease ; Mediterranean diet ; biosynthesis ; cultural heritage ; humans ; inflammation ; inflammatory bowel disease ; intestinal microorganisms ; microbiome ; mortality ; probiotics ; Gut microbiome ; Microbiota ; Metagenome
    Language English
    Dates of publication 2023-10
    Publishing place Elsevier Inc.
    Document type Article ; Online
    ZDB-ID 639259-3
    ISSN 1873-1244 ; 0899-9007
    ISSN (online) 1873-1244
    ISSN 0899-9007
    DOI 10.1016/j.nut.2023.112118
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 4802: Show issues

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  5. Article ; Online: Group testing performance evaluation for SARS-CoV-2 massive scale screening and testing

    Nalbantoglu, Ozkan Ufuk

    BMC Medical Research Methodology

    2020  Volume 20, Issue 1

    Keywords Health Informatics ; Epidemiology ; covid19
    Language English
    Publisher Springer Science and Business Media LLC
    Publishing country us
    Document type Article ; Online
    ISSN 1471-2288
    DOI 10.1186/s12874-020-01048-1
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Group testing performance evaluation for SARS-CoV-2 massive scale screening and testing

    Ozkan Ufuk Nalbantoglu

    BMC Medical Research Methodology, Vol 20, Iss 1, Pp 1-

    2020  Volume 11

    Abstract: Abstract Background The capacity of the current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in the current paradigm of shallow tracing is unlikely to reach the silent clusters ...

    Abstract Abstract Background The capacity of the current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in the current paradigm of shallow tracing is unlikely to reach the silent clusters that might be as important as the symptomatic cases in the spread of the disease. Group testing is a feasible and promising approach when the resources are scarce and when a relatively low prevalence regime is observed on the population. Methods We employed group testing with a sparse random pooling scheme and conventional group test decoding algorithms both for exact and inexact recovery. Results Our simulations showed that significant reduction in per case test numbers (or expansion in total test numbers preserving the number of actual tests conducted) for very sparse prevalence regimes is available. Currently proposed COVID-19 group testing schemes offer a gain up to 15X-20X scale-up. There is a good probability that the required scale up to achieve massive scale testing might be greater in certain scenarios. We investigated if further improvement is available, especially in sparse prevalence occurrence where outbreaks are needed to be avoided by population scans. Conclusion Our simulations show that sparse random pooling can provide improved efficiency gains compared to conventional group testing or Reed-Solomon error correcting codes. Therefore, we propose that special designs for different scenarios could be available and it is possible to scale up testing capabilities significantly.
    Keywords COVID-19 testing ; Group testing ; Sparse recovery algorithms ; Medicine (General) ; R5-920 ; covid19
    Language English
    Publishing date 2020-07-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: COVID-19 Pandemic

    Ozkan Ufuk Nalbantoglu / Aycan Gundogdu

    Frontiers in Medicine, Vol

    Group Testing

    2020  Volume 7

    Keywords COVID-19 ; pandemia ; molecular diagnostics ; infection control ; group testing ; Medicine (General) ; R5-920 ; covid19
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Group Testing Performance Evaluation for SARS-CoV-2 Massive Scale Screening and Testing

    Nalbantoglu, Ozkan Ufuk

    medRxiv

    Abstract: The capacity of current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in current paradigm of shallow tracing is unlikely to reach the silent clusters that might be as important ... ...

    Abstract The capacity of current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in current paradigm of shallow tracing is unlikely to reach the silent clusters that might be as important as the symptomatic cases in the spread of the disease. Group testing is a feasible and promising approach when the resources are scarce and when a relatively low prevalence regime is observed on the population. We employed group testing with a sparse random pooling scheme and conventional group test decoding algorithms both for exact and inexact recovery. Our simulations showed that significant reduction in per case test numbers (or expansion in total test numbers preserving the number of actual tests conducted) for very sparse prevalence regimes is available. Currently proposed COVID-19 group testing schemes offer a gain up to 10X scale-up. There is a good probability that the required scale up to achieve massive scale testing might be greater in certain scenarios. We investigated if further improvement is available, especially in sparse prevalence occurrence where outbreaks are needed to be avoided by population scans. Our simulations show that sparse random pooling can provide improved efficiency gains compared to row-column group testing or Reed-Solomon error correcting codes. Therefore, we propose that special designs for different scenarios could be available and it is possible to scale up testing capabilities significantly.
    Keywords covid19
    Language English
    Publishing date 2020-05-05
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.05.02.20080390
    Database COVID19

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  9. Article ; Online: Group testing performance evaluation for SARS-CoV-2 massive scale screening and testing

    Nalbantoglu, Ozkan Ufuk

    BMC medical research methodology, 20(1):176

    2020  

    Abstract: BACKGROUND: The capacity of the current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in the current paradigm of shallow tracing is unlikely to reach the silent clusters that ... ...

    Abstract BACKGROUND: The capacity of the current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in the current paradigm of shallow tracing is unlikely to reach the silent clusters that might be as important as the symptomatic cases in the spread of the disease. Group testing is a feasible and promising approach when the resources are scarce and when a relatively low prevalence regime is observed on the population. METHODS: We employed group testing with a sparse random pooling scheme and conventional group test decoding algorithms both for exact and inexact recovery. RESULTS: Our simulations showed that significant reduction in per case test numbers (or expansion in total test numbers preserving the number of actual tests conducted) for very sparse prevalence regimes is available. Currently proposed COVID-19 group testing schemes offer a gain up to 15X-20X scale-up. There is a good probability that the required scale up to achieve massive scale testing might be greater in certain scenarios. We investigated if further improvement is available, especially in sparse prevalence occurrence where outbreaks are needed to be avoided by population scans. CONCLUSION: Our simulations show that sparse random pooling can provide improved efficiency gains compared to conventional group testing or Reed-Solomon error correcting codes. Therefore, we propose that special designs for different scenarios could be available and it is possible to scale up testing capabilities significantly.
    Keywords Group testing ; COVID-19 ; Sparse recovery algorithms ; COVID-19 testing ; covid19
    Language English
    Publishing country de
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: COVID-19 Pandemic

    Nalbantoglu, Ozkan Ufuk / Gundogdu, Aycan

    Frontiers in Medicine

    Group Testing

    2020  Volume 7

    Keywords covid19
    Publisher Frontiers Media SA
    Publishing country ch
    Document type Article ; Online
    ZDB-ID 2775999-4
    ISSN 2296-858X
    ISSN 2296-858X
    DOI 10.3389/fmed.2020.00522
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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