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Article ; 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

2021 Volume 11, Issue 1, Page(s) 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 term(s)	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
Language	English
Publishing date	2021-04-28
Publishing country	England
Document type	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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: 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.
Keywords	covid19
Language	English
Publishing date	2020-09-02
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.08.12.20173831
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; 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 Volume 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.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: 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
Language	English
Publishing date	2023-06-16
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.16.545321
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; 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.
Keywords	covid19
Language	English
Publishing date	2020-08-14
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.08.12.20173831
Database	COVID19

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Article: 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.
Keywords	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
Language	English
Dates of publication	2022-05
Size	p. 944-963.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2136367-5
ISSN	1467-7652 ; 1467-7644
ISSN (online)	1467-7652
ISSN	1467-7644
DOI	10.1111/pbi.13775
Database	NAL-Catalogue (AGRICOLA)

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Article ; 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 Volume 20, Issue 5, Page(s) 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 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 term(s)	Chromosomes ; Ecosystem ; Genome, Plant/genetics ; Molecular Sequence Annotation ; Thlaspi/genetics ; Translational Research, Biomedical
Language	English
Publishing date	2022-02-06
Publishing country	England
Document type	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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: 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
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.25.581948
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; 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 Volume 41, Issue 1, Page(s) 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 term(s)	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
Chemical Substances	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
Language	English
Publishing date	2022-12-22
Publishing country	United States
Document type	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
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Article ; 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 Volume 119, Issue 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 term(s)	Animals ; Base Sequence/genetics ; Biodiversity ; Eukaryota/genetics ; Genomics/methods ; Genomics/standards ; Humans ; Reference Standards ; Reference Values ; Sequence Analysis, DNA/methods ; Sequence Analysis, DNA/standards
Language	English
Publishing date	2022-01-18
Publishing country	United States
Document type	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
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