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  1. Article ; Online: Recent Advances and Future Perspectives in the Use of Machine Learning and Mathematical Models in Nephrology.

    Galuzio, Paulo Paneque / Cherif, Alhaji

    Advances in chronic kidney disease

    2022  Volume 29, Issue 5, Page(s) 472–479

    Abstract: We reviewed some of the latest advancements in the use of mathematical models in nephrology. We looked over 2 distinct categories of mathematical models that are widely used in biological research and pointed out some of their strengths and weaknesses ... ...

    Abstract We reviewed some of the latest advancements in the use of mathematical models in nephrology. We looked over 2 distinct categories of mathematical models that are widely used in biological research and pointed out some of their strengths and weaknesses when applied to health care, especially in the context of nephrology. A mechanistic dynamical system allows the representation of causal relations among the system variables but with a more complex and longer development/implementation phase. Artificial intelligence/machine learning provides predictive tools that allow identifying correlative patterns in large data sets, but they are usually harder-to-interpret black boxes. Chronic kidney disease (CKD), a major worldwide health problem, generates copious quantities of data that can be leveraged by choice of the appropriate model; also, there is a large number of dialysis parameters that need to be determined at every treatment session that can benefit from predictive mechanistic models. Following important steps in the use of mathematical methods in medical science might be in the intersection of seemingly antagonistic frameworks, by leveraging the strength of each to provide better care.
    MeSH term(s) Artificial Intelligence ; Forecasting ; Humans ; Machine Learning ; Models, Theoretical ; Nephrology
    Language English
    Publishing date 2022-10-17
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1548-5609 ; 1548-5595
    ISSN (online) 1548-5609
    ISSN 1548-5595
    DOI 10.1053/j.ackd.2022.07.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Mathematical analysis of a multiple strain, multi-locus-allele system for antigenically variable infectious diseases revisited.

    Cherif, Alhaji

    Mathematical biosciences

    2015  Volume 267, Page(s) 24–40

    Abstract: Many important pathogens such as HIV/AIDS, influenza, malaria, dengue and meningitis generally exist in phenotypically distinct serotypes that compete for hosts. Models used to study these diseases appear as meta-population systems. Herein, we revisit ... ...

    Abstract Many important pathogens such as HIV/AIDS, influenza, malaria, dengue and meningitis generally exist in phenotypically distinct serotypes that compete for hosts. Models used to study these diseases appear as meta-population systems. Herein, we revisit one of the multiple strain models that have been used to investigate the dynamics of infectious diseases with co-circulating serotypes or strains, and provide analytical results underlying the numerical investigations. In particular, we establish the necessary conditions for the local asymptotic stability of the steady states and for the existence of oscillatory behaviors via Hopf bifurcation. In addition, we show that the existence of discrete antigenic forms among pathogens can either fully or partially self-organize, where (i) strains exhibit no strain structures and coexist or (ii) antigenic variants sort into non-overlapping or minimally overlapping clusters that either undergo the principle of competitive exclusion exhibiting discrete strain structures, or co-exist cyclically.
    MeSH term(s) Alleles ; Antigenic Variation ; Communicable Diseases/epidemiology ; Communicable Diseases/genetics ; Communicable Diseases/immunology ; Endemic Diseases ; Host-Pathogen Interactions/genetics ; Host-Pathogen Interactions/immunology ; Humans ; Mathematical Concepts ; Models, Biological
    Language English
    Publishing date 2015-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1126-5
    ISSN 1879-3134 ; 0025-5564
    ISSN (online) 1879-3134
    ISSN 0025-5564
    DOI 10.1016/j.mbs.2015.06.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Simulation of Pool Testing to Identify Patients With Coronavirus Disease 2019 Under Conditions of Limited Test Availability.

    Cherif, Alhaji / Grobe, Nadja / Wang, Xiaoling / Kotanko, Peter

    JAMA network open

    2020  Volume 3, Issue 6, Page(s) e2013075

    MeSH term(s) Adult ; Aged ; Betacoronavirus ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Computer Simulation ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Decision Support Techniques ; False Negative Reactions ; Female ; Health Services Accessibility ; Humans ; Male ; Middle Aged ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Population Surveillance/methods ; Prevalence ; SARS-CoV-2 ; Sensitivity and Specificity ; Statistics as Topic/methods
    Keywords covid19
    Language English
    Publishing date 2020-06-01
    Publishing country United States
    Document type Journal Article
    ISSN 2574-3805
    ISSN (online) 2574-3805
    DOI 10.1001/jamanetworkopen.2020.13075
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Comparative Analysis of SARS-CoV-2 Reproduction Rates in the Dialysis and General Populations.

    Cherif, Alhaji / Willetts, Joanna L / Usvyat, Len / Wang, Yuedong / Kotanko, Peter

    Journal of the American Society of Nephrology : JASN

    2021  Volume 32, Issue 4, Page(s) 791–794

    Language English
    Publishing date 2021-03-08
    Publishing country United States
    Document type Letter
    ZDB-ID 1085942-1
    ISSN 1533-3450 ; 1046-6673
    ISSN (online) 1533-3450
    ISSN 1046-6673
    DOI 10.1681/ASN.2020121691
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Sample pooling: burden or solution?

    Grobe, Nadja / Cherif, Alhaji / Wang, Xiaoling / Dong, Zijun / Kotanko, Peter

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases

    2021  Volume 27, Issue 9, Page(s) 1212–1220

    Abstract: Background: Pool-testing strategies combine samples from multiple people and test them as a group. A pool-testing approach may shorten the screening time and increase the test rate during times of limited test availability and inadequate reporting speed. ...

    Abstract Background: Pool-testing strategies combine samples from multiple people and test them as a group. A pool-testing approach may shorten the screening time and increase the test rate during times of limited test availability and inadequate reporting speed. Pool testing has been effectively used for a wide variety of infectious disease screening settings. Historically, it originated from serological testing in syphilis. During the current coronavirus disease 2019 (COVID-19) pandemic, pool testing is considered across the globe to inform opening strategies and to monitor infection rates after the implementation of interventions.
    Aims: This narrative review aims to provide a comprehensive overview of the global efforts to implement pool testing, specifically for COVID-19 screening.
    Sources: Data were retrieved from a detailed search for peer-reviewed articles and preprint reports using Medline/PubMed, medRxiv, Web of Science, and Google up to 21st March 2021, using search terms "pool testing", "viral", "serum", "SARS-CoV-2" and "COVID-19".
    Content: This review summarizes the history and theory of pool testing. We identified numerous peer-reviewed articles that describe specific details and practical implementation of pool testing. Successful examples as well as limitations of pool testing, in general and specifically related to the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and antibodies, are reviewed. While promising, significant operational, pre-analytical, logistical, and economic challenges need to be overcome to advance pool testing.
    Implications: The theory of pool testing is well understood and numerous successful examples from the past are available. Operationalization of pool testing requires sophisticated processes that can be adapted to the local medical circumstances. Special attention needs to be paid to sample collection, sample pooling, and strategies to avoid re-sampling.
    MeSH term(s) Antibodies, Viral/analysis ; COVID-19/diagnosis ; COVID-19 Testing/methods ; Diagnostic Tests, Routine ; Humans ; Mass Screening ; RNA, Viral/genetics ; Research Design ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; SARS-CoV-2/isolation & purification ; Sensitivity and Specificity ; Specimen Handling/methods
    Chemical Substances Antibodies, Viral ; RNA, Viral
    Language English
    Publishing date 2021-04-18
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1328418-6
    ISSN 1469-0691 ; 1470-9465 ; 1198-743X
    ISSN (online) 1469-0691
    ISSN 1470-9465 ; 1198-743X
    DOI 10.1016/j.cmi.2021.04.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Identification of arterial oxygen intermittency in oximetry data.

    Galuzio, Paulo P / Cherif, Alhaji / Tao, Xia / Thwin, Ohnmar / Zhang, Hanjie / Thijssen, Stephan / Kotanko, Peter

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 16023

    Abstract: In patients with kidney failure treated by hemodialysis, intradialytic arterial oxygen saturation ( ... ...

    Abstract In patients with kidney failure treated by hemodialysis, intradialytic arterial oxygen saturation (SaO
    MeSH term(s) Humans ; Oximetry/methods ; Oxygen ; Polysomnography ; Sleep Apnea Syndromes/diagnosis ; Sleep Apnea, Obstructive
    Chemical Substances Oxygen (S88TT14065)
    Language English
    Publishing date 2022-09-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-20493-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Simulation of Pool Testing to Identify Patients With Coronavirus Disease 2019 Under Conditions of Limited Test Availability

    Cherif, Alhaji / Grobe, Nadja / Wang, Xiaoling / Kotanko, Peter

    JAMA Netw Open

    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #612402
    Database COVID19

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  8. Article ; Online: Modeling osteoporosis to design and optimize pharmacological therapies comprising multiple drug types.

    Jörg, David J / Fuertinger, Doris H / Cherif, Alhaji / Bushinsky, David A / Mermelstein, Ariella / Raimann, Jochen G / Kotanko, Peter

    eLife

    2022  Volume 11

    Abstract: For the treatment of postmenopausal osteoporosis, several drug classes with different mechanisms of action are available. Since only a limited set of dosing regimens and drug combinations can be tested in clinical trials, it is currently unclear whether ... ...

    Abstract For the treatment of postmenopausal osteoporosis, several drug classes with different mechanisms of action are available. Since only a limited set of dosing regimens and drug combinations can be tested in clinical trials, it is currently unclear whether common medication strategies achieve optimal bone mineral density gains or are outperformed by alternative dosing schemes and combination therapies that have not been explored so far. Here, we develop a mathematical framework of drug interventions for postmenopausal osteoporosis that unifies fundamental mechanisms of bone remodeling and the mechanisms of action of four drug classes: bisphosphonates, parathyroid hormone analogs, sclerostin inhibitors, and receptor activator of NF-κB ligand inhibitors. Using data from several clinical trials, we calibrate and validate the model, demonstrating its predictive capacity for complex medication scenarios, including sequential and parallel drug combinations. Via simulations, we reveal that there is a large potential to improve gains in bone mineral density by exploiting synergistic interactions between different drug classes, without increasing the total amount of drug administered.
    MeSH term(s) Bone Density ; Bone Density Conservation Agents/therapeutic use ; Diphosphonates/therapeutic use ; Drug Combinations ; Female ; Humans ; Osteoporosis/drug therapy ; Osteoporosis, Postmenopausal/drug therapy
    Chemical Substances Bone Density Conservation Agents ; Diphosphonates ; Drug Combinations
    Language English
    Publishing date 2022-08-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.76228
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Analysis of Lauffenburger-Kennedy bacterial infection model for tissue inflammation dynamics.

    Yang, Yu / Cherif, Alhaji / Zhang, Yuxin

    Journal of biological dynamics

    2018  Volume 12, Issue 1, Page(s) 938–960

    Abstract: In this paper, we analyze a mathematical model for an inflammatory response to bacterial infection of homogeneous tissues. Specifically, we provide a detailed analysis of the Lauffenburger-Kennedy bacterial infection model and show that the model ... ...

    Abstract In this paper, we analyze a mathematical model for an inflammatory response to bacterial infection of homogeneous tissues. Specifically, we provide a detailed analysis of the Lauffenburger-Kennedy bacterial infection model and show that the model exhibits three possible equilibria corresponding to a bacteria-free and two endemic compromised steady states. Asymptotic results of the steady states along with the existences of saddle-node connection Hopf bifurcations are shown under certain conditions of the parameters. Within the biological ranges of the parameter values, we observe that the system can exhibit both forward and backward bifurcation. In addition, in both cases, the larger compromise bacterial infection steady state can either approach an equilibrium or can oscillate around it via Hopf bifurcation depending on the value of the ratio of leukocyte mortality to phagocytosis rates. Numerical results are used to provide illustrative examples of these different dynamical patterns observed in the model.
    MeSH term(s) Bacterial Infections/complications ; Bacterial Infections/pathology ; Humans ; Inflammation/complications ; Inflammation/microbiology ; Models, Biological ; Time Factors
    Language English
    Publishing date 2018-11-26
    Publishing country England
    Document type Journal Article
    ISSN 1751-3766
    ISSN (online) 1751-3766
    DOI 10.1080/17513758.2018.1538463
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Modeling osteoporosis to design and optimize pharmacological therapies comprising multiple drug types

    David J Jörg / Doris H Fuertinger / Alhaji Cherif / David A Bushinsky / Ariella Mermelstein / Jochen G Raimann / Peter Kotanko

    eLife, Vol

    2022  Volume 11

    Abstract: For the treatment of postmenopausal osteoporosis, several drug classes with different mechanisms of action are available. Since only a limited set of dosing regimens and drug combinations can be tested in clinical trials, it is currently unclear whether ... ...

    Abstract For the treatment of postmenopausal osteoporosis, several drug classes with different mechanisms of action are available. Since only a limited set of dosing regimens and drug combinations can be tested in clinical trials, it is currently unclear whether common medication strategies achieve optimal bone mineral density gains or are outperformed by alternative dosing schemes and combination therapies that have not been explored so far. Here, we develop a mathematical framework of drug interventions for postmenopausal osteoporosis that unifies fundamental mechanisms of bone remodeling and the mechanisms of action of four drug classes: bisphosphonates, parathyroid hormone analogs, sclerostin inhibitors, and receptor activator of NF-κB ligand inhibitors. Using data from several clinical trials, we calibrate and validate the model, demonstrating its predictive capacity for complex medication scenarios, including sequential and parallel drug combinations. Via simulations, we reveal that there is a large potential to improve gains in bone mineral density by exploiting synergistic interactions between different drug classes, without increasing the total amount of drug administered.
    Keywords osteoporosis ; pharmacodynamics ; mathematical model ; combination therapy ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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