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  1. Article ; Online: Excellence paves the way with Current Research in Toxicology.

    Knudsen, Thomas B / Vinken, Mathieu

    Current research in toxicology

    2020  Volume 1, Page(s) iv

    Language English
    Publishing date 2020-06-29
    Document type Editorial
    ISSN 2666-027X
    ISSN (online) 2666-027X
    DOI 10.1016/j.crtox.2020.06.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Identifying candidate reference chemicals for in vitro testing of the retinoid pathway for predictive developmental toxicity.

    Baker, Nancy C / Pierro, Jocylin D / Taylor, Laura W / Knudsen, Thomas B

    ALTEX

    2022  Volume 40, Issue 2, Page(s) 217–236

    Abstract: Evaluating chemicals for potential in vivo toxicity based on their in vitro bioactivity profile is an important step toward animal- free testing. A compendium of reference chemicals and data describing their bioactivity on specific molecular targets, ... ...

    Abstract Evaluating chemicals for potential in vivo toxicity based on their in vitro bioactivity profile is an important step toward animal- free testing. A compendium of reference chemicals and data describing their bioactivity on specific molecular targets, cellular pathways, and biological processes is needed to bolster confidence in the predictive value of in vitro hazard detection. Endogenous signaling by all-trans retinoic acid (ATRA) is an important pathway in developmental processes and toxicities. Employing data extraction methods and advanced literature extraction tools, we assembled a set of candidate reference chemicals with demonstrated activity on ten protein family targets in the retinoid system. The compendium was culled from Protein Data Bank, ChEMBL, ToxCast/Tox21, and the biomedical literature in PubMed. Finally, we performed a case study on one chemical in our collection, citral, an inhibitor of endogenous ATRA production, to determine whether the literature supports an adverse outcome pathway explaining the compound’s developmental toxicity initiated by disruption of the retinoid pathway. We also deliver an updated Abstract Sifter tool populated with these reference compounds and complex search terms designed to query the literature for the downstream consequences to support concordance with targeted retinoid pathway disruption.
    MeSH term(s) Animals ; Retinoids ; Animal Testing Alternatives ; In Vitro Techniques ; Adverse Outcome Pathways
    Chemical Substances Retinoids
    Language English
    Publishing date 2022-06-23
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 165707-0
    ISSN 1868-8551 ; 1018-4562 ; 0946-7785
    ISSN (online) 1868-8551
    ISSN 1018-4562 ; 0946-7785
    DOI 10.14573/altex.2202231
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book: The clinical interpretation of the MMPI-2

    Gotts, Edward Earl / Knudsen, Thomas E.

    a content cluster approach

    2005  

    Author's details Edward E. Gotts ; Thomas E. Knudsen
    Keywords MMPI ; Psychiatric Status Rating Scales ; Mental Disorders / diagnosis ; Minnesota Multiphasic Personality Inventory ; Mental illness/Diagnosis ; Psychoanalytic interpretation
    Subject code 616.89075
    Language English
    Size XXI, 279 S.
    Publisher Lawrence Erlbaum
    Publishing place Mahwah, NJ u.a.
    Publishing country United States
    Document type Book
    Note Includes bibliographical references (p. 255-266) and indexes
    HBZ-ID HT014391150
    ISBN 0-8058-5033-3 ; 978-0-8058-5033-8
    Database Catalogue ZB MED Medicine, Health

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  4. Article ; Online: Retinoid signaling in skeletal development: Scoping the system for predictive toxicology.

    Knudsen, Thomas B / Pierro, Jocylin D / Baker, Nancy C

    Reproductive toxicology (Elmsford, N.Y.)

    2020  Volume 99, Page(s) 109–130

    Abstract: All-trans retinoic acid (ATRA), the biologically active form of vitamin A, is instrumental in regulating the patterning and specification of the vertebrate embryo. Various animal models demonstrate adverse developmental phenotypes following experimental ... ...

    Abstract All-trans retinoic acid (ATRA), the biologically active form of vitamin A, is instrumental in regulating the patterning and specification of the vertebrate embryo. Various animal models demonstrate adverse developmental phenotypes following experimental retinoid depletion or excess during pregnancy. Windows of vulnerability for altered skeletal patterning coincide with early specification of the body plan (gastrulation) and regional specification of precursor cell populations forming the facial skeleton (cranial neural crest), vertebral column (somites), and limbs (lateral plate mesoderm) during organogenesis. A common theme in physiological roles of ATRA signaling is mutual antagonism with FGF signaling. Consequences of genetic errors or environmental disruption of retinoid signaling include stage- and region-specific homeotic transformations to severe deficiencies for various skeletal elements. This review derives from an annex in Detailed Review Paper (DRP) of the OECD Test Guidelines Programme (Project 4.97) to support recommendations regarding assay development for the retinoid system and the use of resulting data in a regulatory context for developmental and reproductive toxicity (DART) testing.
    MeSH term(s) Animals ; Bone Development ; Bone and Bones/abnormalities ; Bone and Bones/metabolism ; Humans ; Retinoids/metabolism ; Signal Transduction ; Teratogenesis
    Chemical Substances Retinoids
    Language English
    Publishing date 2020-11-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 639342-1
    ISSN 1873-1708 ; 0890-6238
    ISSN (online) 1873-1708
    ISSN 0890-6238
    DOI 10.1016/j.reprotox.2020.10.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Single-cell profiling for advancing birth defects research and prevention.

    Knudsen, Thomas B / Spielmann, Malte / Megason, Sean G / Faustman, Elaine M

    Birth defects research

    2021  Volume 113, Issue 7, Page(s) 546–559

    Abstract: Cellular analysis of developmental processes and toxicities has traditionally entailed bulk methods (e.g., transcriptomics) that lack single cell resolution or tissue localization methods (e.g., immunostaining) that allow only a few genes to be monitored ...

    Abstract Cellular analysis of developmental processes and toxicities has traditionally entailed bulk methods (e.g., transcriptomics) that lack single cell resolution or tissue localization methods (e.g., immunostaining) that allow only a few genes to be monitored in each experiment. Recent technological advances have enabled interrogation of genomic function at the single-cell level, providing new opportunities to unravel developmental pathways and processes with unprecedented resolution. Here, we review emerging technologies of single-cell RNA-sequencing (scRNA-seq) to globally characterize the gene expression sets of different cell types and how different cell types emerge from earlier cell states in development. Cell atlases of experimental embryology and human embryogenesis at single-cell resolution will provide an encyclopedia of genes that define key stages from gastrulation to organogenesis. This technology, combined with computational models to discover key organizational principles, was recognized by Science magazine as the "Breakthrough of the year" for 2018 due to transformative potential on the way we study how human cells mature over a lifetime, how tissues regenerate, and how cells change in diseases (e.g., patient-derived organoids to screen disease-specific targets and design precision therapy). Profiling transcriptomes at the single-cell level can fulfill the need for greater detail in the molecular progression of all cell lineages, from pluripotency to adulthood and how cell-cell signaling pathways control progression at every step. Translational opportunities emerge for elucidating pathogenesis of genetic birth defects with cellular precision and improvements for predictive toxicology of chemical teratogenesis.
    MeSH term(s) Adult ; Humans ; Sequence Analysis, RNA ; Signal Transduction ; Single-Cell Analysis ; Transcriptome/genetics
    Language English
    Publishing date 2021-01-25
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2104792-3
    ISSN 2472-1727
    ISSN (online) 2472-1727
    DOI 10.1002/bdr2.1870
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Society for birth defects research and prevention's multidisciplinary research needs workshop 2022: A call to action.

    Basu, Madhumita / Howdeshell, Kembra L / Rasmussen, Sonja A / Rychlik, Kristal A / Knudsen, Thomas B / Shuey, Dana L / Slikker, William

    Birth defects research

    2023  Volume 115, Issue 10, Page(s) 959–966

    Abstract: The Society for Birth Defects Research and Prevention (BDRP) strives to understand and protect against potential hazards to developing embryos, fetuses, children, and adults by bringing together scientific knowledge from diverse fields. The theme of 62nd ...

    Abstract The Society for Birth Defects Research and Prevention (BDRP) strives to understand and protect against potential hazards to developing embryos, fetuses, children, and adults by bringing together scientific knowledge from diverse fields. The theme of 62nd Annual Meeting of BDRP, "From Bench to Bedside and Back Again", represented the cutting-edge research areas of high relevance to public health and significance in the fields of birth defects research and surveillance. The multidisciplinary Research Needs Workshop (RNW) convened at the Annual Meeting continues to identify pressing knowledge gaps and encourage interdisciplinary research initiatives. The multidisciplinary RNW was first introduced at the 2018 annual meeting to provide an opportunity for annual meeting attendees to participate in breakout discussions on emerging topics in birth defects research and to foster collaboration between basic researchers, clinicians, epidemiologists, drug developers, industry partners, funding agencies, and regulators to discuss state-of-the-art methods and innovative projects. Initially, a list of workshop topics was compiled by the RNW planning committee and circulated among the members of BDRP to obtain the most popular topics for the Workshop discussions. Based on the pre-meeting survey results, the top three discussion topics selected were, A) Inclusion of pregnant and lactating women in clinical trials. When, why, and how? B) Building multidisciplinary teams across disciplines: What cross-training is needed? And C) Challenges in applications of Artificial Intelligence (AI) and machine learning for risk factor analysis in birth defects research. This report summarizes the key highlights of the RNW workshop and specific topic discussions.
    MeSH term(s) Pregnancy ; Child ; Female ; Humans ; Interdisciplinary Research ; Artificial Intelligence ; Lactation ; Interdisciplinary Studies ; Societies
    Language English
    Publishing date 2023-05-22
    Publishing country United States
    Document type Editorial
    ZDB-ID 2104792-3
    ISSN 2472-1727
    ISSN (online) 2472-1727
    DOI 10.1002/bdr2.2186
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Protecting Human and Animal Health: The Road from Animal Models to New Approach Methods.

    Kaplan, Barbara L F / Hoberman, Alan M / Slikker, William / Smith, Mary Alice / Corsini, Emanuela / Knudsen, Thomas B / Marty, M Sue / Sobrian, Sonya K / Fitzpatrick, Suzanne C / Ratner, Marcia H / Mendrick, Donna L

    Pharmacological reviews

    2024  Volume 76, Issue 2, Page(s) 251–266

    Abstract: Animals and animal models have been invaluable for our current understanding of human and animal biology, including physiology, pharmacology, biochemistry, and disease pathology. However, there are increasing concerns with continued use of animals in ... ...

    Abstract Animals and animal models have been invaluable for our current understanding of human and animal biology, including physiology, pharmacology, biochemistry, and disease pathology. However, there are increasing concerns with continued use of animals in basic biomedical, pharmacological, and regulatory research to provide safety assessments for drugs and chemicals. There are concerns that animals do not provide sufficient information on toxicity and/or efficacy to protect the target population, so scientists are utilizing the principles of replacement, reduction, and refinement (the 3Rs) and increasing the development and application of new approach methods (NAMs). NAMs are any technology, methodology, approach, or assay used to understand the effects and mechanisms of drugs or chemicals, with specific focus on applying the 3Rs. Although progress has been made in several areas with NAMs, complete replacement of animal models with NAMs is not yet attainable. The road to NAMs requires additional development, increased use, and, for regulatory decision making, usually formal validation. Moreover, it is likely that replacement of animal models with NAMs will require multiple assays to ensure sufficient biologic coverage. The purpose of this manuscript is to provide a balanced view of the current state of the use of animal models and NAMs as approaches to development, safety, efficacy, and toxicity testing of drugs and chemicals. Animals do not provide all needed information nor do NAMs, but each can elucidate key pieces of the puzzle of human and animal biology and contribute to the goal of protecting human and animal health. SIGNIFICANCE STATEMENT: Data from traditional animal studies have predominantly been used to inform human health safety and efficacy. Although it is unlikely that all animal studies will be able to be replaced, with the continued advancement in new approach methods (NAMs), it is possible that sometime in the future, NAMs will likely be an important component by which the discovery, efficacy, and toxicity testing of drugs and chemicals is conducted and regulatory decisions are made.
    MeSH term(s) Animals ; Humans ; Toxicity Tests/methods ; Models, Animal
    Language English
    Publishing date 2024-02-13
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 209898-2
    ISSN 1521-0081 ; 0031-6997
    ISSN (online) 1521-0081
    ISSN 0031-6997
    DOI 10.1124/pharmrev.123.000967
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Book: Comprehensive toxicology / 12

    Knudsen, Thomas / Daston, George P. / McQueen, Charlene A.

    2010  

    Author's details ed.-in-chief, Charlene A. McQueen
    Collection Comprehensive toxicology
    Language English
    Size XVII, 367 S. : Ill., graph. Darst., Kt.
    Publisher Elsevier
    Publishing place Amsterdam u.a.
    Publishing country Netherlands
    Document type Book
    HBZ-ID HT016438021
    ISBN 978-0-08-046880-8 ; 0-08-046880-2
    Database Catalogue ZB MED Medicine, Health

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  9. Article: Computational model for fetal skeletal defects potentially linked to disruption of retinoic acid signaling.

    Pierro, Jocylin D / Ahir, Bhavesh K / Baker, Nancy C / Kleinstreuer, Nicole C / Xia, Menghang / Knudsen, Thomas B

    Frontiers in pharmacology

    2022  Volume 13, Page(s) 971296

    Abstract: All-trans retinoic acid (ATRA) gradients determine skeletal patterning morphogenesis and can be disrupted by diverse genetic or environmental factors during pregnancy, leading to fetal skeleton defects. Adverse Outcome Pathway (AOP) frameworks for ATRA ... ...

    Abstract All-trans retinoic acid (ATRA) gradients determine skeletal patterning morphogenesis and can be disrupted by diverse genetic or environmental factors during pregnancy, leading to fetal skeleton defects. Adverse Outcome Pathway (AOP) frameworks for ATRA metabolism, signaling, and homeostasis allow for the development of new approach methods (NAMs) for predictive toxicology with less reliance on animal testing. Here, a data-driven model was constructed to identify chemicals associated with both ATRA pathway bioactivity and prenatal skeletal defects. The phenotype data was culled from ToxRefDB prenatal developmental toxicity studies and produced a list of 363 ToxRefDB chemicals with altered skeletal observations. Defects were classified regionally as cranial, post-cranial axial, appendicular, and other (unspecified) features based on ToxRefDB descriptors. To build a multivariate statistical model, high-throughput screening bioactivity data from >8,070 chemicals in ToxCast/Tox21 across 10
    Language English
    Publishing date 2022-09-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2022.971296
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: A cross-platform approach to characterize and screen potential neurovascular unit toxicants.

    Zurlinden, Todd J / Saili, Katerine S / Baker, Nancy C / Toimela, Tarja / Heinonen, Tuula / Knudsen, Thomas B

    Reproductive toxicology (Elmsford, N.Y.)

    2020  Volume 96, Page(s) 300–315

    Abstract: Development of the neurovascular unit (NVU) is a complex, multistage process that requires orchestrated cell signaling mechanisms across several cell types and ultimately results in formation of the blood-brain barrier. Typical high-throughput screening ( ...

    Abstract Development of the neurovascular unit (NVU) is a complex, multistage process that requires orchestrated cell signaling mechanisms across several cell types and ultimately results in formation of the blood-brain barrier. Typical high-throughput screening (HTS) assays investigate single biochemical or single cell responses following chemical insult. As the NVU comprises multiple cell types interacting at various stages of development, a methodology combining high-throughput results across pertinent cell-based assays is needed to investigate potential chemical-induced disruption to the development of this complex cell system. To this end, we implemented a novel method for screening putative NVU disruptors across diverse assay platforms to predict chemical perturbation of the developing NVU. HTS assay results measuring chemical-induced perturbations to cellular key events across angiogenic and neurogenic outcomes in vitro were combined to create a cell-based prioritization of NVU hazard. Chemicals were grouped according to similar modes of action to train a logistic regression literature model on a training set of 38 chemicals. This model utilizes the chemical-specific pairwise mutual information score for PubMed MeSH annotations to represent a quantitative measure of previously published results. Taken together, this study presents a methodology to investigate NVU developmental hazard using cell-based HTS assays and literature evidence to prioritize screening of putative NVU disruptors towards a knowledge-driven characterization of neurovascular developmental toxicity. The results from these screening efforts demonstrate that chemicals representing a range of putative vascular disrupting compound (pVDC) scores can also produce effects on neurogenic outcomes and characterizes possible modes of action for disrupting the developing NVU.
    MeSH term(s) Biological Assay ; Cells, Cultured ; Endothelial Cells/drug effects ; Endothelial Cells/physiology ; Fibroblasts/drug effects ; Hazardous Substances/toxicity ; High-Throughput Screening Assays ; Humans ; Neovascularization, Physiologic/drug effects ; Nerve Net/drug effects ; Neural Crest/drug effects ; Neural Stem Cells/drug effects ; Neurogenesis/drug effects
    Chemical Substances Hazardous Substances
    Language English
    Publishing date 2020-06-24
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 639342-1
    ISSN 1873-1708 ; 0890-6238
    ISSN (online) 1873-1708
    ISSN 0890-6238
    DOI 10.1016/j.reprotox.2020.06.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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