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  1. AU="Jacobs, Jonathan L"
  2. AU="Massmann, Amanda K"
  3. AU="Shah, Rohan R"
  4. AU="Coppin, Peter"
  5. AU="Kun, Lyubomyra"
  6. AU="Grauvogel, Tanja Daniela"
  7. AU="Serafim, Ricardo A M"
  8. AU="Urzainqui, Ana"
  9. AU="Navarro, Elisa"
  10. AU="Ibrahim, Tawheeda"
  11. AU="Sonntag, William E"
  12. AU="Tamagawa, Masumi"
  13. AU="Subhan, Fazli"
  14. AU="Parisi, A"
  15. AU="Calisher, C H"
  16. AU="Altaş, İrem"

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  1. Artikel ; Online: Myeloid madness: assessing diagnostic inconsistency between the new WHO and ICC schemes for myelodysplastic/myeloproliferative neoplasms.

    Benton, Leah G / Kallen, Michael Edward / Jacobs, Jonathan L / McCool, Isaac E / Ning, Yi / Duong, Vu H / Koka, Rima / Singh, Zeba N

    Journal of clinical pathology

    2023  Band 77, Heft 1, Seite(n) 68–72

    Abstract: The classification of haematological neoplasms recently underwent revision, generating two separate schemes-the International Consensus Classification and the fifth edition of the WHO classification. The new division into separate classification systems ... ...

    Abstract The classification of haematological neoplasms recently underwent revision, generating two separate schemes-the International Consensus Classification and the fifth edition of the WHO classification. The new division into separate classification systems presents challenges for haematopathologists, haematologists/oncologists and patients. While it is too early to assess the full clinical impact, we sought to identify diagnostic discordance which may arise from applying separate classification schemes in myeloid neoplasia, and particularly in the challenging category of myelodysplastic syndrome/myeloproliferative neoplasms. A review of 64 such cases found 1 case with a significant discrepancy between the WHO and International Consensus Classification systems, and 9 cases with nominal discrepancies. Confusion from the use of conflicting diagnostic terms represents a potential source of patient harm, increased pathologist workload and burnout and erosion of clinician and patient trust.
    Mesh-Begriff(e) Humans ; Myelodysplastic Syndromes/diagnosis ; Myeloproliferative Disorders/diagnosis ; Hematologic Neoplasms/diagnosis ; World Health Organization
    Sprache Englisch
    Erscheinungsdatum 2023-12-14
    Erscheinungsland England
    Dokumenttyp Review ; Journal Article
    ZDB-ID 80261-x
    ISSN 1472-4146 ; 0021-9746
    ISSN (online) 1472-4146
    ISSN 0021-9746
    DOI 10.1136/jcp-2023-209009
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: EGR1 Upregulation during Encephalitic Viral Infections Contributes to Inflammation and Cell Death

    Lehman, Caitlin W. / Smith, Amy / Kelly, Jamie / Jacobs, Jonathan L. / Dinman, Jonathan D. / Kehn-Hall, Kylene

    Viruses. 2022 June 02, v. 14, no. 6

    2022  

    Abstract: Early growth response 1 (EGR1) is an immediate early gene and transcription factor previously found to be significantly upregulated in human astrocytoma cells infected with Venezuelan equine encephalitis virus (VEEV). The loss of EGR1 resulted in ... ...

    Abstract Early growth response 1 (EGR1) is an immediate early gene and transcription factor previously found to be significantly upregulated in human astrocytoma cells infected with Venezuelan equine encephalitis virus (VEEV). The loss of EGR1 resulted in decreased cell death but had no significant impact on viral replication. Here, we extend these studies to determine the impacts of EGR1 on gene expression following viral infection. Inflammatory genes CXCL3, CXCL8, CXCL10, TNF, and PTGS2 were upregulated in VEEV-infected cells, which was partially dependent on EGR1. Additionally, transcription factors, including EGR1 itself, as well as ATF3, FOS, JUN, KLF4, EGR2, and EGR4 were found to be partially transcriptionally dependent on EGR1. We also examined the role of EGR1 and the changes in gene expression in response to infection with other alphaviruses, including eastern equine encephalitis virus (EEEV), Sindbis virus (SINV), and chikungunya virus (CHIKV), as well as Zika virus (ZIKV) and Rift Valley fever virus (RVFV), members of the Flaviviridae and Phenuiviridae families, respectively. EGR1 was significantly upregulated to varying degrees in EEEV-, CHIKV-, RVFV-, SINV-, and ZIKV-infected astrocytoma cells. Genes that were identified as being partially transcriptionally dependent on EGR1 in infected cells included ATF3 (EEEV, CHIKV, ZIKV), JUN (EEEV), KLF4 (SINV, ZIKV, RVFV), CXCL3 (EEEV, CHIKV, ZIKV), CXCL8 (EEEV, CHIKV, ZIKV, RVFV), CXCL10 (EEEV, RVFV), TNF-α (EEEV, ZIKV, RVFV), and PTGS2 (EEEV, CHIKV, ZIKV). Additionally, inhibition of the inflammatory gene PTGS2 with Celecoxib, a small molecule inhibitor, rescued astrocytoma cells from VEEV-induced cell death but had no impact on viral titers. Collectively, these results suggest that EGR1 induction following viral infection stimulates multiple inflammatory mediators. Managing inflammation and cell death in response to viral infection is of utmost importance, especially during VEEV infection where survivors are at-risk for neurological sequalae.
    Schlagwörter Chikungunya virus ; Eastern equine encephalitis virus ; Rift Valley fever phlebovirus ; Sindbis virus ; Venezuelan equine encephalitis virus ; Zika virus ; astrocytoma ; cell death ; gene expression ; genes ; humans ; inflammation ; transcription (genetics) ; transcription factors ; virus replication
    Sprache Englisch
    Erscheinungsverlauf 2022-0602
    Erscheinungsort Multidisciplinary Digital Publishing Institute
    Dokumenttyp Artikel
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14061210
    Datenquelle NAL Katalog (AGRICOLA)

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  3. Artikel ; Online: FAIR Header Reference genome: a TRUSTworthy standard.

    Wright, Adam / Wilkinson, Mark D / Mungall, Christopher / Cain, Scott / Richards, Stephen / Sternberg, Paul / Provin, Ellen / Jacobs, Jonathan L / Geib, Scott / Raciti, Daniela / Yook, Karen / Stein, Lincoln / Molik, David C

    Briefings in bioinformatics

    2024  Band 25, Heft 3

    Abstract: The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard ... ...

    Abstract The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
    Mesh-Begriff(e) Humans ; Genome ; Genomics ; Information Dissemination ; Software
    Sprache Englisch
    Erscheinungsdatum 2024-03-28
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbae122
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: EGR1 Upregulation during Encephalitic Viral Infections Contributes to Inflammation and Cell Death.

    Lehman, Caitlin W / Smith, Amy / Kelly, Jamie / Jacobs, Jonathan L / Dinman, Jonathan D / Kehn-Hall, Kylene

    Viruses

    2022  Band 14, Heft 6

    Abstract: Early growth response 1 (EGR1) is an immediate early gene and transcription factor previously found to be significantly upregulated in human astrocytoma cells infected with Venezuelan equine encephalitis virus (VEEV). The loss of EGR1 resulted in ... ...

    Abstract Early growth response 1 (EGR1) is an immediate early gene and transcription factor previously found to be significantly upregulated in human astrocytoma cells infected with Venezuelan equine encephalitis virus (VEEV). The loss of EGR1 resulted in decreased cell death but had no significant impact on viral replication. Here, we extend these studies to determine the impacts of EGR1 on gene expression following viral infection. Inflammatory genes CXCL3, CXCL8, CXCL10, TNF, and PTGS2 were upregulated in VEEV-infected cells, which was partially dependent on EGR1. Additionally, transcription factors, including EGR1 itself, as well as ATF3, FOS, JUN, KLF4, EGR2, and EGR4 were found to be partially transcriptionally dependent on EGR1. We also examined the role of EGR1 and the changes in gene expression in response to infection with other alphaviruses, including eastern equine encephalitis virus (EEEV), Sindbis virus (SINV), and chikungunya virus (CHIKV), as well as Zika virus (ZIKV) and Rift Valley fever virus (RVFV), members of the
    Mesh-Begriff(e) Astrocytoma ; Cell Death ; Cyclooxygenase 2/genetics ; Early Growth Response Protein 1 ; Encephalitis Virus, Venezuelan Equine/genetics ; Encephalomyelitis, Equine ; Humans ; Inflammation ; Sindbis Virus ; Up-Regulation ; Zika Virus ; Zika Virus Infection
    Chemische Substanzen EGR1 protein, human ; Early Growth Response Protein 1 ; Cyclooxygenase 2 (EC 1.14.99.1)
    Sprache Englisch
    Erscheinungsdatum 2022-06-02
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14061210
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: The ATCC genome portal: 3,938 authenticated microbial reference genomes.

    Nguyen, Scott V / Puthuveetil, Nikhita P / Petrone, Joseph R / Kirkland, Jade L / Gaffney, Kaitlyn / Tabron, Corina L / Wax, Noah / Duncan, James / King, Stephen / Marlow, Robert / Reese, Amy L / Yarmosh, David A / McConnell, Hannah H / Fernandes, Ana S / Bagnoli, John / Benton, Briana / Jacobs, Jonathan L

    Microbiology resource announcements

    2024  Band 13, Heft 2, Seite(n) e0104523

    Abstract: The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC's biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO 9000 by ATCC. Here, ...

    Abstract The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC's biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO 9000 by ATCC. Here, we present new features and content added to the AGP for the research community.
    Sprache Englisch
    Erscheinungsdatum 2024-01-30
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.01045-23
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Pan-resistant Candida auris: New York subcluster susceptible to antifungal combinations.

    O'Brien, Brittany / Liang, Jiali / Chaturvedi, Sudha / Jacobs, Jonathan L / Chaturvedi, Vishnu

    The Lancet. Microbe

    2020  Band 1, Heft 5, Seite(n) e193–e194

    Sprache Englisch
    Erscheinungsdatum 2020-08-03
    Erscheinungsland England
    Dokumenttyp Letter
    ISSN 2666-5247
    ISSN (online) 2666-5247
    DOI 10.1016/S2666-5247(20)30090-2
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel: DATA RESOURCES AND ANALYSES FAIR Header Reference genome: A TRUSTworthy standard.

    Wright, Adam / Wilkinson, Mark D / Mungall, Chris / Cain, Scott / Richards, Stephen / Sternberg, Paul / Provin, Ellen / Jacobs, Jonathan L / Geib, Scott / Raciti, Daniela / Yook, Karen / Stein, Lincoln / Molik, David C

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard ... ...

    Abstract The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability, and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST). The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility, and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
    Sprache Englisch
    Erscheinungsdatum 2023-12-20
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.11.29.569306
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel: PERK Is Critical for Alphavirus Nonstructural Protein Translation

    Dahal, Bibha / Lehman, Caitlin W / Akhrymuk, Ivan / Bracci, Nicole R / Panny, Lauren / Barrera, Michael D / Bhalla, Nishank / Jacobs, Jonathan L / Dinman, Jonathan D / Kehn-Hall, Kylene

    Viruses. 2021 May 12, v. 13, no. 5

    2021  

    Abstract: Venezuelan equine encephalitis virus (VEEV) is an alphavirus that causes encephalitis. Previous work indicated that VEEV infection induced early growth response 1 (EGR1) expression, leading to cell death via the protein kinase R (PKR)-like endoplasmic ... ...

    Abstract Venezuelan equine encephalitis virus (VEEV) is an alphavirus that causes encephalitis. Previous work indicated that VEEV infection induced early growth response 1 (EGR1) expression, leading to cell death via the protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK) arm of the unfolded protein response (UPR) pathway. Loss of PERK prevented EGR1 induction and decreased VEEV-induced death. The results presented within show that loss of PERK in human primary astrocytes dramatically reduced VEEV and eastern equine encephalitis virus (EEEV) infectious titers by 4–5 log₁₀. Loss of PERK also suppressed VEEV replication in primary human pericytes and human umbilical vein endothelial cells, but it had no impact on VEEV replication in transformed U87MG and 293T cells. A significant reduction in VEEV RNA levels was observed as early as 3 h post-infection, but viral entry assays indicated that the loss of PERK minimally impacted VEEV entry. In contrast, the loss of PERK resulted in a dramatic reduction in viral nonstructural protein translation and negative-strand viral RNA production. The loss of PERK also reduced the production of Rift Valley fever virus and Zika virus infectious titers. These data indicate that PERK is an essential factor for the translation of alphavirus nonstructural proteins and impacts multiple RNA viruses, making it an exciting target for antiviral development.
    Schlagwörter Eastern equine encephalitis virus ; RNA ; Rift Valley fever phlebovirus ; Venezuelan equine encephalitis virus ; Zika virus ; astrocytes ; cell death ; death ; encephalitis ; endoplasmic reticulum ; humans ; protein kinases ; unfolded protein response ; viral nonstructural proteins
    Sprache Englisch
    Erscheinungsverlauf 2021-0512
    Erscheinungsort Multidisciplinary Digital Publishing Institute
    Dokumenttyp Artikel
    Anmerkung NAL-AP-2-clean
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13050892
    Datenquelle NAL Katalog (AGRICOLA)

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  9. Artikel ; Online: Standardized In Vitro Models of Human Adipose Tissue Reveal Metabolic Flexibility in Brown Adipocyte Thermogenesis.

    Cero, Cheryl / Shu, Weiguo / Reese, Amy L / Douglas, Diana / Maddox, Michael / Singh, Ajeet P / Ali, Sahara L / Zhu, Alexander R / Katz, Jacqueline M / Pierce, Anne E / Long, Kelly T / Nilubol, Naris / Cypess, Raymond H / Jacobs, Jonathan L / Tian, Fang / Cypess, Aaron M

    Endocrinology

    2023  Band 164, Heft 12

    Abstract: Functional human brown and white adipose tissue (BAT and WAT) are vital for thermoregulation and nutritional homeostasis, while obesity and other stressors lead, respectively, to cold intolerance and metabolic disease. Understanding BAT and WAT ... ...

    Abstract Functional human brown and white adipose tissue (BAT and WAT) are vital for thermoregulation and nutritional homeostasis, while obesity and other stressors lead, respectively, to cold intolerance and metabolic disease. Understanding BAT and WAT physiology and dysfunction necessitates clinical trials complemented by mechanistic experiments at the cellular level. These require standardized in vitro models, currently lacking, that establish references for gene expression and function. We generated and characterized a pair of immortalized, clonal human brown (hBA) and white (hWA) preadipocytes derived from the perirenal and subcutaneous depots, respectively, of a 40-year-old male individual. Cells were immortalized with hTERT and confirmed to be of a mesenchymal, nonhematopoietic lineage based on fluorescence-activated cell sorting and DNA barcoding. Functional assessments showed that the hWA and hBA phenocopied primary adipocytes in terms of adrenergic signaling, lipolysis, and thermogenesis. Compared to hWA, hBA were metabolically distinct, with higher rates of glucose uptake and lactate metabolism, and greater basal, maximal, and nonmitochondrial respiration, providing a mechanistic explanation for the association between obesity and BAT dysfunction. The hBA also responded to the stress of maximal respiration by using both endogenous and exogenous fatty acids. In contrast to certain mouse models, hBA adrenergic thermogenesis was mediated by several mechanisms, not principally via uncoupling protein 1 (UCP1). Transcriptomics via RNA-seq were consistent with the functional studies and established a molecular signature for each cell type before and after differentiation. These standardized cells are anticipated to become a common resource for future physiological, pharmacological, and genetic studies of human adipocytes.
    Mesh-Begriff(e) Male ; Mice ; Animals ; Humans ; Adult ; Adipocytes, Brown/metabolism ; Adipose Tissue, Brown/metabolism ; Obesity/metabolism ; Adipose Tissue, White/metabolism ; Thermogenesis/genetics ; Adrenergic Agents/metabolism ; Uncoupling Protein 1/genetics ; Uncoupling Protein 1/metabolism
    Chemische Substanzen Adrenergic Agents ; Uncoupling Protein 1
    Sprache Englisch
    Erscheinungsdatum 2023-11-09
    Erscheinungsland United States
    Dokumenttyp Case Reports ; Journal Article
    ZDB-ID 427856-2
    ISSN 1945-7170 ; 0013-7227
    ISSN (online) 1945-7170
    ISSN 0013-7227
    DOI 10.1210/endocr/bqad161
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies.

    Yarmosh, David A / Lopera, Juan G / Puthuveetil, Nikhita P / Combs, Patrick Ford / Reese, Amy L / Tabron, Corina / Pierola, Amanda E / Duncan, James / Greenfield, Samuel R / Marlow, Robert / King, Stephen / Riojas, Marco A / Bagnoli, John / Benton, Briana / Jacobs, Jonathan L

    mSphere

    2022  Band 7, Heft 3, Seite(n) e0007722

    Abstract: The availability of public genomics data has become essential for modern life sciences research, yet the quality, traceability, and curation of these data have significant impacts on a broad range of microbial genomics research. While microbial genome ... ...

    Abstract The availability of public genomics data has become essential for modern life sciences research, yet the quality, traceability, and curation of these data have significant impacts on a broad range of microbial genomics research. While microbial genome databases such as NCBI's RefSeq database leverage the scalability of crowd sourcing for growth, genomics data provenance and authenticity of the source materials used to produce data are not strict requirements. Here, we describe the
    Mesh-Begriff(e) Databases, Genetic ; Genome, Bacterial ; Genome, Microbial ; Genomics ; Reproducibility of Results
    Sprache Englisch
    Erscheinungsdatum 2022-05-02
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2379-5042
    ISSN (online) 2379-5042
    DOI 10.1128/msphere.00077-22
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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