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  1. Artikel ; Online: Temporal dynamics of viral load and false negative rate influence the levels of testing necessary to combat COVID-19 spread.

    Jarvis, Katherine F / Kelley, Joshua B

    Scientific reports

    2021  Band 11, Heft 1, Seite(n) 9221

    Abstract: Colleges and other organizations are considering testing plans to return to operation as the COVID-19 pandemic continues. Pre-symptomatic spread and high false negative rates for testing may make it difficult to stop viral spread. Here, we develop a ... ...

    Abstract Colleges and other organizations are considering testing plans to return to operation as the COVID-19 pandemic continues. Pre-symptomatic spread and high false negative rates for testing may make it difficult to stop viral spread. Here, we develop a stochastic agent-based model of COVID-19 in a university sized population, considering the dynamics of both viral load and false negative rate of tests on the ability of testing to combat viral spread. Reported dynamics of SARS-CoV-2 can lead to an apparent false negative rate from ~ 17 to ~ 48%. Nonuniform distributions of viral load and false negative rate lead to higher requirements for frequency and fraction of population tested in order to bring the apparent Reproduction number (Rt) below 1. Thus, it is important to consider non-uniform dynamics of viral spread and false negative rate in order to model effective testing plans.
    Mesh-Begriff(e) COVID-19/diagnosis ; COVID-19/etiology ; COVID-19/transmission ; COVID-19/virology ; COVID-19 Serological Testing/methods ; Carrier State ; Contact Tracing ; False Negative Reactions ; Humans ; Models, Biological ; Models, Statistical ; Stochastic Processes ; Viral Load
    Sprache Englisch
    Erscheinungsdatum 2021-04-28
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-88498-9
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: Temporal Dynamics of Viral Load and False negative Rate Influence the Levels of Testing Necessary to Combat COVID19 Spread.

    Jarvis, Katherine F / Kelley, Joshua B

    medRxiv : the preprint server for health sciences

    2020  

    Abstract: Colleges and other organizations are considering testing plans to return to operation as the COVID19 pandemic continues. Pre-symptomatic spread and high false negative rates for testing may make it difficult to stop viral spread. Here, we develop a ... ...

    Abstract Colleges and other organizations are considering testing plans to return to operation as the COVID19 pandemic continues. Pre-symptomatic spread and high false negative rates for testing may make it difficult to stop viral spread. Here, we develop a stochastic agent-based model of COVID19 in a university sized population, considering the dynamics of both viral load and false negative rate of tests on the ability of testing to combat viral spread. Reported dynamics of SARS-CoV-2 can lead to an apparent false negative rate from ~17% to ~48%. Nonuniform distributions of viral load and false negative rate lead to higher requirements for frequency and fraction of population tested in order to bring the apparent Reproduction number (Rt) below 1. Thus, it is important to consider non-uniform dynamics of viral spread and false negative rate in order to model effective testing plans.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2020-09-02
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2020.08.12.20173831
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Temporal dynamics of viral load and false negative rate influence the levels of testing necessary to combat COVID-19 spread

    Katherine F. Jarvis / Joshua B. Kelley

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Band 12

    Abstract: Abstract Colleges and other organizations are considering testing plans to return to operation as the COVID-19 pandemic continues. Pre-symptomatic spread and high false negative rates for testing may make it difficult to stop viral spread. Here, we ... ...

    Abstract Abstract Colleges and other organizations are considering testing plans to return to operation as the COVID-19 pandemic continues. Pre-symptomatic spread and high false negative rates for testing may make it difficult to stop viral spread. Here, we develop a stochastic agent-based model of COVID-19 in a university sized population, considering the dynamics of both viral load and false negative rate of tests on the ability of testing to combat viral spread. Reported dynamics of SARS-CoV-2 can lead to an apparent false negative rate from ~ 17 to ~ 48%. Nonuniform distributions of viral load and false negative rate lead to higher requirements for frequency and fraction of population tested in order to bring the apparent Reproduction number (Rt) below 1. Thus, it is important to consider non-uniform dynamics of viral spread and false negative rate in order to model effective testing plans.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2021-04-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel: The G-alpha Gpa1 directs septin localization in the mating projection of

    Johnson, Cory P / Hart, Andrew / Jarvis, Katherine F / Latario, Sarah G / Shrestha, Sudati / Leclerc, Nicholas / Khalil, André / Kelley, Joshua B

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The yeast mating response uses a G-protein coupled receptor (GPCR), Ste2, to detect mating pheromone and initiate mating projection morphogenesis. The septin cytoskeleton plays a key role in the formation of the mating projection, forming structures at ... ...

    Abstract The yeast mating response uses a G-protein coupled receptor (GPCR), Ste2, to detect mating pheromone and initiate mating projection morphogenesis. The septin cytoskeleton plays a key role in the formation of the mating projection, forming structures at the base of the projection. Desensitization of the Gα, Gpa1, by the Regulator of G-protein Signaling (RGS), Sst2, is required for proper septin organization and morphogenesis. In cells where the Gα is hyperactive, septins are mislocalized to the site of polarity, and the cells are unable to track a pheromone gradient. We set out to identify the proteins that mediate Gα control of septins during the
    Sprache Englisch
    Erscheinungsdatum 2023-06-16
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.06.16.545321
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Temporal Dynamics of Viral Load and False Negative Rate Influence the Levels of Testing Necessary to Combat COVID19 Spread

    Jarvis, Katherine F / Kelley, Joshua B

    medRxiv

    Abstract: Many colleges and other organizations are considering testing plans to return to operation as the COVID19 pandemic continues. The temporal dynamics of viral load and test false negative rate have the potential to alter the apparent efficacy of testing, ... ...

    Abstract Many colleges and other organizations are considering testing plans to return to operation as the COVID19 pandemic continues. The temporal dynamics of viral load and test false negative rate have the potential to alter the apparent efficacy of testing, as testing must identify a sick individual prior to that person transmitting the virus to one or more people and isolate them. High levels of pre-symptomatic spread and high false negative rates for testing would therefore be likely to make it difficult to successfully test an individual in the time frame necessary to stop viral spread. Here, we develop a stochastic agent-based model of COVID19 in a university sized population, considering the dynamics of both viral load and false negative rate of tests on the ability of testing to combat viral spread. We find that the undetectable period of SARS-CoV-2 can lead to an apparent false negative rate of ~17% in the presence of a hypothetical perfect test, while full implementation of dynamic false negative rates reported in the literature leads to an overall false negative rate of ~48%. We then compare testing while varying fraction of the population and the frequency of testing. We find that these assumptions about viral load and false negative rate lead to a requirement for high levels of both frequency and fraction of population tested in order to bring the apparent R0 below 1. We conclude that models that do not consider the non-uniform dynamics of viral spread and false negative rate may come up with unrealistic testing plans that will not lead to the desired reduction in apparent R0.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2020-08-14
    Verlag Cold Spring Harbor Laboratory Press
    Dokumenttyp Artikel ; Online
    DOI 10.1101/2020.08.12.20173831
    Datenquelle COVID19

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  6. Artikel: Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

    Nunn, Adam / Rodríguez‐Arévalo, Isaac / Tandukar, Zenith / Frels, Katherine / Contreras‐Garrido, Adrián / Carbonell‐Bejerano, Pablo / Zhang, Panpan / Ramos Cruz, Daniela / Jandrasits, Katharina / Lanz, Christa / Brusa, Anthony / Mirouze, Marie / Dorn, Kevin / Galbraith, David W / Jarvis, Brice A. / Sedbrook, John C. / Wyse, Donald L. / Otto, Christian / Langenberger, David /
    Stadler, Peter F. / Weigel, Detlef / Marks, M. David / Anderson, James A. / Becker, Claude / Chopra, Ratan

    Plant biotechnology journal. 2022 May, v. 20, no. 5

    2022  

    Abstract: Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is ... ...

    Abstract Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field‐based model species for genetics and epigenetics. The availability of a high‐quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome‐level genome assembly of var. MN106‐Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32‐10) that are highly amenable to genetic transformation. We describe non‐coding RNAs, pseudogenes and transposable elements, and highlight tissue‐specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome‐wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
    Schlagwörter Thlaspi arvense ; agricultural productivity ; biotechnology ; color ; cover crops ; diploidy ; epigenetics ; genetic transformation ; genetic variation ; genome assembly ; land use ; methylation ; oilseed crops ; phenotype ; pseudogenes ; seedlings ; selfing
    Sprache Englisch
    Erscheinungsverlauf 2022-05
    Umfang p. 944-963.
    Erscheinungsort John Wiley & Sons, Ltd
    Dokumenttyp Artikel
    Anmerkung JOURNAL ARTICLE
    ZDB-ID 2136367-5
    ISSN 1467-7652 ; 1467-7644
    ISSN (online) 1467-7652
    ISSN 1467-7644
    DOI 10.1111/pbi.13775
    Datenquelle NAL Katalog (AGRICOLA)

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  7. Artikel ; Online: Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates.

    Nunn, Adam / Rodríguez-Arévalo, Isaac / Tandukar, Zenith / Frels, Katherine / Contreras-Garrido, Adrián / Carbonell-Bejerano, Pablo / Zhang, Panpan / Ramos Cruz, Daniela / Jandrasits, Katharina / Lanz, Christa / Brusa, Anthony / Mirouze, Marie / Dorn, Kevin / Galbraith, David W / Jarvis, Brice A / Sedbrook, John C / Wyse, Donald L / Otto, Christian / Langenberger, David /
    Stadler, Peter F / Weigel, Detlef / Marks, M David / Anderson, James A / Becker, Claude / Chopra, Ratan

    Plant biotechnology journal

    2022  Band 20, Heft 5, Seite(n) 944–963

    Abstract: Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is ... ...

    Abstract Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
    Mesh-Begriff(e) Chromosomes ; Ecosystem ; Genome, Plant/genetics ; Molecular Sequence Annotation ; Thlaspi/genetics ; Translational Research, Biomedical
    Sprache Englisch
    Erscheinungsdatum 2022-02-06
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2136367-5
    ISSN 1467-7652 ; 1467-7652
    ISSN (online) 1467-7652
    ISSN 1467-7652
    DOI 10.1111/pbi.13775
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel: Oncogenic GNAS drives a gastric pylorus program in intraductal papillary mucinous neoplasms of the pancreas.

    Trinh, Vincent Quoc-Huy / Ankenbauer, Katherine E / Liu, Jiayue / Batardiere, Maelle / Maurer, H Carlo / Copeland, Celina / Wong, Jahg / Ben-Levy, Olivia / Torbit, Sabrina M / Jarvis, Brenda / Revetta, Frank / Ivanov, Sergey / Jyotsana, Nidhi / Makino, Yuki / Ruelas, Amanda M / Means, Anna L / Maitra, Anirban / Tan, Marcus C B / DelGiorno, Kathleen E

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Objective: Intraductal Papillary Mucinous Neoplasms (IPMNs) are cystic lesions and bona fide precursors for pancreatic ductal adenocarcinoma (PDAC). Recently, we showed that acinar to ductal metaplasia, an injury repair program, is characterized by a ... ...

    Abstract Objective: Intraductal Papillary Mucinous Neoplasms (IPMNs) are cystic lesions and bona fide precursors for pancreatic ductal adenocarcinoma (PDAC). Recently, we showed that acinar to ductal metaplasia, an injury repair program, is characterized by a transcriptomic program similar to gastric spasmolytic polypeptide expressing metaplasia (SPEM), suggesting common mechanisms of reprogramming between the stomach and pancreas. The aims of this study were to assay IPMN for pyloric markers and to identify molecular drivers of this program.
    Design: We analyzed RNA-seq studies of IPMN for pyloric markers, which were validated by immunostaining in patient samples. Cell lines expressing
    Results: Pyloric markers were identified in human IPMN.
    Conclusion: De novo
    Sprache Englisch
    Erscheinungsdatum 2024-02-28
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2024.02.25.581948
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia.

    Wang, Eric / Pineda, Jose Mario Bello / Kim, Won Jun / Chen, Sisi / Bourcier, Jessie / Stahl, Maximilian / Hogg, Simon J / Bewersdorf, Jan Phillipp / Han, Cuijuan / Singer, Michael E / Cui, Daniel / Erickson, Caroline E / Tittley, Steven M / Penson, Alexander V / Knorr, Katherine / Stanley, Robert F / Rahman, Jahan / Krishnamoorthy, Gnana / Fagin, James A /
    Creger, Emily / McMillan, Elizabeth / Mak, Chi-Ching / Jarvis, Matthew / Bossard, Carine / Beaupre, Darrin M / Bradley, Robert K / Abdel-Wahab, Omar

    Cancer cell

    2022  Band 41, Heft 1, Seite(n) 164–180.e8

    Abstract: Therapy resistance is a major challenge in the treatment of cancer. Here, we performed CRISPR-Cas9 screens across a broad range of therapies used in acute myeloid leukemia to identify genomic determinants of drug response. Our screens uncover a selective ...

    Abstract Therapy resistance is a major challenge in the treatment of cancer. Here, we performed CRISPR-Cas9 screens across a broad range of therapies used in acute myeloid leukemia to identify genomic determinants of drug response. Our screens uncover a selective dependency on RNA splicing factors whose loss preferentially enhances response to the BCL2 inhibitor venetoclax. Loss of the splicing factor RBM10 augments response to venetoclax in leukemia yet is completely dispensable for normal hematopoiesis. Combined RBM10 and BCL2 inhibition leads to mis-splicing and inactivation of the inhibitor of apoptosis XIAP and downregulation of BCL2A1, an anti-apoptotic protein implicated in venetoclax resistance. Inhibition of splicing kinase families CLKs (CDC-like kinases) and DYRKs (dual-specificity tyrosine-regulated kinases) leads to aberrant splicing of key splicing and apoptotic factors that synergize with venetoclax, and overcomes resistance to BCL2 inhibition. Our findings underscore the importance of splicing in modulating response to therapies and provide a strategy to improve venetoclax-based treatments.
    Mesh-Begriff(e) Humans ; Proto-Oncogene Proteins c-bcl-2 ; Myeloid Cell Leukemia Sequence 1 Protein/metabolism ; Cell Line, Tumor ; Bridged Bicyclo Compounds, Heterocyclic/pharmacology ; Bridged Bicyclo Compounds, Heterocyclic/therapeutic use ; RNA Splicing/genetics ; Leukemia, Myeloid, Acute/genetics ; Protein-Tyrosine Kinases ; Apoptosis/genetics ; RNA-Binding Proteins/genetics
    Chemische Substanzen venetoclax (N54AIC43PW) ; Proto-Oncogene Proteins c-bcl-2 ; Myeloid Cell Leukemia Sequence 1 Protein ; Bridged Bicyclo Compounds, Heterocyclic ; Protein-Tyrosine Kinases (EC 2.7.10.1) ; RBM10 protein, human ; RNA-Binding Proteins ; BCL2 protein, human
    Sprache Englisch
    Erscheinungsdatum 2022-12-22
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2078448-X
    ISSN 1878-3686 ; 1535-6108
    ISSN (online) 1878-3686
    ISSN 1535-6108
    DOI 10.1016/j.ccell.2022.12.002
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: Standards recommendations for the Earth BioGenome Project.

    Lawniczak, Mara K N / Durbin, Richard / Flicek, Paul / Lindblad-Toh, Kerstin / Wei, Xiaofeng / Archibald, John M / Baker, William J / Belov, Katherine / Blaxter, Mark L / Marques Bonet, Tomas / Childers, Anna K / Coddington, Jonathan A / Crandall, Keith A / Crawford, Andrew J / Davey, Robert P / Di Palma, Federica / Fang, Qi / Haerty, Wilfried / Hall, Neil /
    Hoff, Katharina J / Howe, Kerstin / Jarvis, Erich D / Johnson, Warren E / Johnson, Rebecca N / Kersey, Paul J / Liu, Xin / Lopez, Jose Victor / Myers, Eugene W / Pettersson, Olga Vinnere / Phillippy, Adam M / Poelchau, Monica F / Pruitt, Kim D / Rhie, Arang / Castilla-Rubio, Juan Carlos / Sahu, Sunil Kumar / Salmon, Nicholas A / Soltis, Pamela S / Swarbreck, David / Thibaud-Nissen, Françoise / Wang, Sibo / Wegrzyn, Jill L / Zhang, Guojie / Zhang, He / Lewin, Harris A / Richards, Stephen

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Band 119, Heft 4

    Abstract: A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five ... ...

    Abstract A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
    Mesh-Begriff(e) Animals ; Base Sequence/genetics ; Biodiversity ; Eukaryota/genetics ; Genomics/methods ; Genomics/standards ; Humans ; Reference Standards ; Reference Values ; Sequence Analysis, DNA/methods ; Sequence Analysis, DNA/standards
    Sprache Englisch
    Erscheinungsdatum 2022-01-18
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2115639118
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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