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  1. Book ; Online ; E-Book: The Applied Genomic Epidemiology Handbook

    Black, Allison / Dudas, Gytis

    A Practical Guide to Leveraging Pathogen Genomic Data in Public Health

    (Chapman and Hall/CRC Computational Biology Series)

    2024  

    Abstract: An Applied Genomic Epidemiology Handbook: A Practical Guide to Leveraging Pathogen Genomic Data in Public Health provides rationale, theory, and implementation guidance to help public health practitioners incorporate pathogen genomic data analysis into ... ...

    Series title Chapman and Hall/CRC Computational Biology Series
    Abstract An Applied Genomic Epidemiology Handbook: A Practical Guide to Leveraging Pathogen Genomic Data in Public Health provides rationale, theory, and implementation guidance to help public health practitioners incorporate pathogen genomic data analysis into their investigations.
    Language English
    Size 1 online resource (165 pages)
    Edition 1st ed.
    Publisher CRC Press LLC
    Publishing place Milton
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 1-003-85384-6 ; 9781032530260 ; 978-1-003-85384-8 ; 103253026X
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Invited Commentary: Computational Flow Dynamics: The Future of Fontan Conduit Selection and Operative Planning?

    Black, Allison K / Alsoufi, Bahaaldin

    World journal for pediatric & congenital heart surgery

    2022  Volume 13, Issue 3, Page(s) 302–303

    MeSH term(s) Fontan Procedure ; Heart Defects, Congenital/surgery ; Hemodynamics ; Humans
    Language English
    Publishing date 2022-04-20
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2550261-X
    ISSN 2150-136X ; 2150-1351
    ISSN (online) 2150-136X
    ISSN 2150-1351
    DOI 10.1177/21501351221091341
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2

    Nanduri, Sravani / Black, Allison / Bedford, Trevor / Huddleston, John

    bioRxiv

    Abstract: Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic ... ...

    Abstract Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge. For example, pairwise distances between sequences can be enough to identify clusters of related samples or assign new samples to existing phylogenetic clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic viruses that cause substantial human morbidity and mortality and frequently reassort or recombine, respectively: seasonal influenza A/H3N2 and SARS-CoV-2. We applied principal component analysis (PCA), multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP) to sequences with well-defined phylogenetic clades and either reassortment (H3N2) or recombination (SARS-CoV-2). For each low-dimensional embedding of sequences, we calculated the correlation between pairwise genetic and Euclidean distances in the embedding and applied a hierarchical clustering method to identify clusters in the embedding. We measured the accuracy of clusters compared to previously defined phylogenetic clades, reassortment clusters, or recombinant lineages. We found that MDS maintained the strongest correlation between pairwise genetic and Euclidean distances between sequences and best captured the intermediate placement of recombinant lineages between parental lineages. Clusters from t-SNE most accurately recapitulated known phylogenetic clades and recombinant lineages. Both MDS and t-SNE accurately identified reassortment groups. We show that simple statistical methods without a biological model can accurately represent known genetic relationships for relevant human pathogenic viruses. Our open source implementation of these methods for analysis of viral genome sequences can be easily applied when phylogenetic methods are either unnecessary or inappropriate.
    Keywords covid19
    Language English
    Publishing date 2024-02-08
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.02.07.579374
    Database COVID19

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  4. Article ; Online: Changing genomic epidemiology of COVID-19 in long-term care facilities during the 2020-2022 pandemic, Washington State.

    Oltean, Hanna N / Black, Allison / Lunn, Stephanie M / Smith, Nailah / Templeton, Allison / Bevers, Elyse / Kibiger, Lynae / Sixberry, Melissa / Bickel, Josina B / Hughes, James P / Lindquist, Scott / Baseman, Janet G / Bedford, Trevor

    BMC public health

    2024  Volume 24, Issue 1, Page(s) 182

    Abstract: Background: Long-term care facilities (LTCFs) are vulnerable to disease outbreaks. Here, we jointly analyze SARS-CoV-2 genomic and paired epidemiologic data from LTCFs and surrounding communities in Washington state (WA) to assess transmission patterns ... ...

    Abstract Background: Long-term care facilities (LTCFs) are vulnerable to disease outbreaks. Here, we jointly analyze SARS-CoV-2 genomic and paired epidemiologic data from LTCFs and surrounding communities in Washington state (WA) to assess transmission patterns during 2020-2022, in a setting of changing policy. We describe sequencing efforts and genomic epidemiologic findings across LTCFs and perform in-depth analysis in a single county.
    Methods: We assessed genomic data representativeness, built phylogenetic trees, and conducted discrete trait analysis to estimate introduction sizes over time, and explored selected outbreaks to further characterize transmission events.
    Results: We found that transmission dynamics among cases associated with LTCFs in WA changed over the course of the COVID-19 pandemic, with variable introduction rates into LTCFs, but decreasing amplification within LTCFs. SARS-CoV-2 lineages circulating in LTCFs were similar to those circulating in communities at the same time. Transmission between staff and residents was bi-directional.
    Conclusions: Understanding transmission dynamics within and between LTCFs using genomic epidemiology on a broad scale can assist in targeting policies and prevention efforts. Tracking facility-level outbreaks can help differentiate intra-facility outbreaks from high community transmission with repeated introduction events. Based on our study findings, methods for routine tree building and overlay of epidemiologic data for hypothesis generation by public health practitioners are recommended. Discrete trait analysis added valuable insight and can be considered when representative sequencing is performed. Cluster detection tools, especially those that rely on distance thresholds, may be of more limited use given current data capture and timeliness. Importantly, we noted a decrease in data capture from LTCFs over time. Depending on goals for use of genomic data, sentinel surveillance should be increased or targeted surveillance implemented to ensure available data for analysis.
    MeSH term(s) Humans ; COVID-19/epidemiology ; Pandemics/prevention & control ; SARS-CoV-2/genetics ; Washington/epidemiology ; Long-Term Care/methods ; Phylogeny ; Genomics
    Language English
    Publishing date 2024-01-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2041338-5
    ISSN 1471-2458 ; 1471-2458
    ISSN (online) 1471-2458
    ISSN 1471-2458
    DOI 10.1186/s12889-023-17461-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition.

    Lee, Jover / Hadfield, James / Black, Allison / Sibley, Thomas R / Neher, Richard A / Bedford, Trevor / Huddleston, John

    Frontiers in bioinformatics

    2023  Volume 3, Page(s) 1069487

    Abstract: Seasonal influenza vaccines must be updated regularly to account for mutations that allow influenza viruses to escape our existing immunity. A successful vaccine should represent the genetic diversity of recently circulating viruses and induce antibodies ...

    Abstract Seasonal influenza vaccines must be updated regularly to account for mutations that allow influenza viruses to escape our existing immunity. A successful vaccine should represent the genetic diversity of recently circulating viruses and induce antibodies that effectively prevent infection by those recent viruses. Thus, linking the genetic composition of circulating viruses and the serological experimental results measuring antibody efficacy is crucial to the vaccine design decision. Historically, genetic and serological data have been presented separately in the form of static visualizations of phylogenetic trees and tabular serological results to identify vaccine candidates. To simplify this decision-making process, we have created an interactive tool for visualizing serological data that has been integrated into Nextstrain's real-time phylogenetic visualization framework, Auspice. We show how the combined interactive visualizations may be used by decision makers to explore the relationships between complex data sets for both prospective vaccine virus selection and retrospectively exploring the performance of vaccine viruses.
    Language English
    Publishing date 2023-03-22
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-7647
    ISSN (online) 2673-7647
    DOI 10.3389/fbinf.2023.1069487
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Hunger in the household: Food insecurity and associations with maternal eating and toddler feeding.

    Armstrong, Bridget / Hepworth, Allison D / Black, Maureen M

    Pediatric obesity

    2020  Volume 15, Issue 10, Page(s) e12637

    Abstract: Background: Research is needed to identify how food insecurity affects maternal eating behavior and child feeding practices, factors that may pose intergenerational risks for obesity.: Objectives: This longitudinal study investigated whether maternal ...

    Abstract Background: Research is needed to identify how food insecurity affects maternal eating behavior and child feeding practices, factors that may pose intergenerational risks for obesity.
    Objectives: This longitudinal study investigated whether maternal restrained eating mediated the association between household food insecurity and feeding practices.
    Methods: Participants included 277 WIC-eligible mothers (69% below the poverty line, 70% African American) and their toddlers (M
    Results: Forty percent of mothers reported some degree of household food insecurity over 12 months. Within-person analyses showed that relative increases in household food insecurity were indirectly related to increases in restrictive and decreases in responsive child feeding practices, mediated through increases in mothers' own restrained eating.
    Conclusions: Relative change in household food insecurity (rather than overall severity) appears to have indirect effects on toddler feeding practices, through mothers' own eating. Stable household food security without transient food insecurity may improve health and wellbeing for both mothers and children.
    MeSH term(s) Adult ; Child, Preschool ; Feeding Behavior ; Female ; Food Insecurity ; Humans ; Hunger ; Infant ; Longitudinal Studies ; Male ; Maternal Behavior ; Pediatric Obesity/prevention & control ; Poverty
    Language English
    Publishing date 2020-04-15
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2655527-X
    ISSN 2047-6310 ; 2047-6302
    ISSN (online) 2047-6310
    ISSN 2047-6302
    DOI 10.1111/ijpo.12637
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Parent Website Engagement and Health Equity Implications in a Child Care-Based Wellness Intervention.

    Ezran, Marie / Trude, Angela C B / Hepworth, Allison D / Black, Maureen M

    Journal of nutrition education and behavior

    2021  Volume 53, Issue 8, Page(s) 654–662

    Abstract: Objective: To evaluate demographic differences in parent website engagement in a child care-based wellness intervention.: Design: Parent-reported demographic characteristics and observed website engagement were averaged by child care centers ... ...

    Abstract Objective: To evaluate demographic differences in parent website engagement in a child care-based wellness intervention.
    Design: Parent-reported demographic characteristics and observed website engagement were averaged by child care centers participating in the web-based intervention arm of a cluster randomized controlled trial of wellness interventions.
    Setting and participants: Parents of preschoolers in 17 Maryland child care centers.
    Main outcome measures: Website engagement: (1) webpage views, (2) average time on webpage, and (3) intervention activity completion.
    Intervention: Parents received access to a website containing content on wellness-promoting topics (eg, parenting, nutrition, physical activity) and their child care center's activities.
    Analysis: Cross-sectional differences in website engagement by demographic characteristics were assessed using ANOVA.
    Results: Centers with a high proportion of parents who identified as other than non-Hispanic White and had less than a bachelor's degree had significantly fewer webpage views, and completed significantly fewer intervention activities compared with centers with parents who were predominantly non-Hispanic White and had more than a bachelor's degree.
    Conclusions and implications: Demographic differences in parents' child care center website engagement represent disparities that could contribute to health inequities in parents' access to wellness-promoting material. Future efforts could identify factors that eliminate demographic disparities in parent engagement in web-based interventions.
    MeSH term(s) Child ; Child Care ; Cross-Sectional Studies ; Health Equity ; Humans ; Parenting ; Parents
    Language English
    Publishing date 2021-05-01
    Publishing country United States
    Document type Journal Article ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural
    ISSN 1878-2620
    ISSN (online) 1878-2620
    DOI 10.1016/j.jneb.2021.03.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Identifying Food Insecurity in Cardiology Clinic and Connecting Families to Resources.

    Black, Allison K / Pantalone, Julia / Marrone, Anna-Claire / Morell, Evonne / Telles, Robin / DeBrunner, Mark

    Pediatrics

    2022  Volume 149, Issue 5

    Abstract: ... including screening discomfort. FI families were more likely to identify as Black or multiple or ...

    Abstract Background: Food insecurity (FI) increases children's risk for illness and developmental and behavioral problems, which are ongoing concerns for congenital heart disease (CHD) patients. In 2020, 14.8% of households with children suffered from FI. The Hunger Vital Signs (HVS) asks 2 questions to assess FI. The global aim of the project is to implement HVS and connect FI families to resources.
    Methods: Stakeholders identified 6 critical drivers in implementing FI screening at an outpatient cardiology clinic and conducted plan-do-study-act (PDSA) cycles to implement HVS. Over the 13-month study period, time series analyses were performed to assess our process measure (FI screening) and outcome measure (connection of FI families to resources). Demographics and severity of CHD were analyzed for FI families.
    Results: Screening rates increased from 0% to >85%, screening 5064 families. Process evaluations revealed roadblocks including screening discomfort. FI families were more likely to identify as Black or multiple or other ethnicity. Severe CHD patients were at higher risk for FI (n = 106, odds ratio [OR] 1.67 [1.21-2.29], P = .002). Face-to-face meetings with social work and community partnerships reduced loss to follow-up and our ability to offer all FI families individualized FI resources.
    Conclusion: HVS screening can be implemented in a cardiology clinic to improve identification of FI families. A written tool can combat screening discomfort and improve identification of FI families. Children with severe CHD may be at increased risk for FI. A multidisciplinary team and community partnerships can improve individualized resource distribution.
    MeSH term(s) Ambulatory Care Facilities ; Cardiology ; Child ; Food Insecurity ; Food Supply ; Humans ; Mass Screening
    Language English
    Publishing date 2022-04-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 207677-9
    ISSN 1098-4275 ; 0031-4005
    ISSN (online) 1098-4275
    ISSN 0031-4005
    DOI 10.1542/peds.2020-011718
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Use of abatacept in steroid refractory, immune checkpoint-induced myocarditis.

    Kalapurackal Mathai, Vinod / Black, Allison / Lovibond, Sam / Binny, Simon / Lipton, Jonathan / Moldovan, Cristina

    Internal medicine journal

    2021  Volume 51, Issue 11, Page(s) 1971–1972

    MeSH term(s) Abatacept ; Humans ; Myocarditis/chemically induced ; Myocarditis/drug therapy ; Nivolumab ; Steroids
    Chemical Substances Steroids ; Nivolumab (31YO63LBSN) ; Abatacept (7D0YB67S97)
    Language English
    Publishing date 2021-11-19
    Publishing country Australia
    Document type Letter
    ZDB-ID 2045436-3
    ISSN 1445-5994 ; 1444-0903
    ISSN (online) 1445-5994
    ISSN 1444-0903
    DOI 10.1111/imj.15566
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Trends in Maternal Outcomes During the COVID-19 Pandemic in Alabama From 2016 to 2021.

    Shukla, Vivek V / Rahman, Akm Fazlur / Shen, Xuejun / Black, Allison / Nakhmani, Arie / Ambalavanan, Namasivayam / Carlo, Waldemar A

    JAMA network open

    2022  Volume 5, Issue 4, Page(s) e222681

    MeSH term(s) Alabama/epidemiology ; COVID-19/epidemiology ; Humans ; Pandemics ; SARS-CoV-2
    Language English
    Publishing date 2022-04-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2574-3805
    ISSN (online) 2574-3805
    DOI 10.1001/jamanetworkopen.2022.2681
    Database MEDical Literature Analysis and Retrieval System OnLINE

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