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  1. Article: CVRanalysis

    Pichot, Vincent / Corbier, Christophe / Chouchou, Florian / Barthélémy, Jean-Claude / Roche, Frédéric

    Frontiers in physiology

    2024  Volume 14, Page(s) 1224440

    Abstract: Introduction: ...

    Abstract Introduction:
    Language English
    Publishing date 2024-01-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564217-0
    ISSN 1664-042X
    ISSN 1664-042X
    DOI 10.3389/fphys.2023.1224440
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Elucidation of bioinformatic-guided high-prospect drug repositioning candidates for DMD via Swanson linking of target-focused latent knowledge from text-mined categorical metadata.

    Ulm, J Wes / Barthélémy, Florian / Nelson, Stanley F

    Frontiers in cell and developmental biology

    2023  Volume 11, Page(s) 1226707

    Abstract: Duchenne Muscular Dystrophy (DMD)'s complex multi-system pathophysiology, coupled with the cost-prohibitive logistics of multi-year drug screening and follow-up, has hampered the pursuit of new therapeutic approaches. Here we conducted a systematic ... ...

    Abstract Duchenne Muscular Dystrophy (DMD)'s complex multi-system pathophysiology, coupled with the cost-prohibitive logistics of multi-year drug screening and follow-up, has hampered the pursuit of new therapeutic approaches. Here we conducted a systematic historical and text mining-based pilot feasibility study to explore the potential of established or previously tested drugs as prospective DMD therapeutic agents. Our approach utilized a Swanson linking-inspired method to uncover meaningful yet largely hidden deep semantic connections between pharmacologically significant DMD targets and drugs developed for unrelated diseases. Specifically, we focused on molecular target-based MeSH terms and categories as high-yield bioinformatic proxies, effectively tagging relevant literature with categorical metadata. To identify promising leads, we comprehensively assembled published reports from 2011 and sampling from subsequent years. We then determined the earliest year when distinct MeSH terms or category labels of the relevant cellular target were referenced in conjunction with the drug, as well as when the pertinent target itself was first conclusively identified as holding therapeutic value for DMD. By comparing the earliest year when the drug was identifiable as a DMD treatment candidate with that of the first actual report confirming this, we computed an Index of Delayed Discovery (IDD), which serves as a metric of Swanson-linked latent knowledge. Using these findings, we identified data from previously unlinked articles subsetted via MeSH-derived Swanson linking or from target classes within the DrugBank repository. This enabled us to identify new but untested high-prospect small-molecule candidates that are of particular interest in repurposing for DMD and warrant further investigations.
    Language English
    Publishing date 2023-08-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2023.1226707
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Editorial: Personalized medicine for neuromuscular disorders.

    Bartoli, Marc / Bailey, Rachel M / Meyer, Kathrin / Barthélémy, Florian

    Frontiers in cell and developmental biology

    2023  Volume 11, Page(s) 1329048

    Language English
    Publishing date 2023-11-16
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2023.1329048
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Elucidation of bioinformatic-guided high-prospect drug repositioning candidates for DMD via Swanson linking of target-focused latent knowledge from text-mined categorical metadata

    J. Wes Ulm / Florian Barthélémy / Stanley F. Nelson

    Frontiers in Cell and Developmental Biology, Vol

    2023  Volume 11

    Abstract: Duchenne Muscular Dystrophy (DMD)’s complex multi-system pathophysiology, coupled with the cost-prohibitive logistics of multi-year drug screening and follow-up, has hampered the pursuit of new therapeutic approaches. Here we conducted a systematic ... ...

    Abstract Duchenne Muscular Dystrophy (DMD)’s complex multi-system pathophysiology, coupled with the cost-prohibitive logistics of multi-year drug screening and follow-up, has hampered the pursuit of new therapeutic approaches. Here we conducted a systematic historical and text mining-based pilot feasibility study to explore the potential of established or previously tested drugs as prospective DMD therapeutic agents. Our approach utilized a Swanson linking-inspired method to uncover meaningful yet largely hidden deep semantic connections between pharmacologically significant DMD targets and drugs developed for unrelated diseases. Specifically, we focused on molecular target-based MeSH terms and categories as high-yield bioinformatic proxies, effectively tagging relevant literature with categorical metadata. To identify promising leads, we comprehensively assembled published reports from 2011 and sampling from subsequent years. We then determined the earliest year when distinct MeSH terms or category labels of the relevant cellular target were referenced in conjunction with the drug, as well as when the pertinent target itself was first conclusively identified as holding therapeutic value for DMD. By comparing the earliest year when the drug was identifiable as a DMD treatment candidate with that of the first actual report confirming this, we computed an Index of Delayed Discovery (IDD), which serves as a metric of Swanson-linked latent knowledge. Using these findings, we identified data from previously unlinked articles subsetted via MeSH-derived Swanson linking or from target classes within the DrugBank repository. This enabled us to identify new but untested high-prospect small-molecule candidates that are of particular interest in repurposing for DMD and warrant further investigations.
    Keywords data mining ; drug repositioning ; Swanson linking ; MeSH ; DMD ; drug repurposing ; Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2023-08-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Optimization of glass separating funnels to facilitate microplastic extraction from sediments

    Mohammad Wazne / Florian Mermillod-Blondin / Manon Vallier / Stefan Krause / Nans Barthélémy / Laurent Simon

    MethodsX, Vol 12, Iss , Pp 102540- (2024)

    2024  

    Abstract: Recent studies on the distribution of microplastics in aquatic sediments have deployed different methods and devices for density separation of microplastics from sediments. However, instrument specific limitations have been noted, including their high ... ...

    Abstract Recent studies on the distribution of microplastics in aquatic sediments have deployed different methods and devices for density separation of microplastics from sediments. However, instrument specific limitations have been noted, including their high cost, difficulty in handling, or/and the potential for elevated contamination risk due to their plastic composition. This study improves existing sediment microplastic separation techniques by modifying the commonly used conical shape glass separating funnels. The modification consists in connecting a silicone tube at the base of the funnel, whose opening and closure was manually controlled by a Mohr clamp. This adjustment made to the funnels have effectively mitigated critical clogging problems frequently encountered in density separation units. An experiment was conducted using sand-based sediment spiked with polyamide fragments to validate this method modification. Following a complete extraction protocol with the modification of separating funnels, the microplastic extraction efficiency from sediments was high with a 90% recovery rate. Based on these promising results, future studies should consider naturally diverse substrates, as recovery efficiency may be sediment-dependent.Two key adjustments to the glass separation funnels: • Removal of stopcocks • Use of silicone tubes and Mohr clamps to control sediment release
    Keywords Glass separation funnels adapted with Mohr clamps ; Science ; Q
    Subject code 550
    Language English
    Publishing date 2024-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  6. Article: Optimization of glass separating funnels to facilitate microplastic extraction from sediments.

    Wazne, Mohammad / Mermillod-Blondin, Florian / Vallier, Manon / Krause, Stefan / Barthélémy, Nans / Simon, Laurent

    MethodsX

    2023  Volume 12, Page(s) 102540

    Abstract: Recent studies on the distribution of microplastics in aquatic sediments have deployed different methods and devices for density separation of microplastics from sediments. However, instrument specific limitations have been noted, including their high ... ...

    Abstract Recent studies on the distribution of microplastics in aquatic sediments have deployed different methods and devices for density separation of microplastics from sediments. However, instrument specific limitations have been noted, including their high cost, difficulty in handling, or/and the potential for elevated contamination risk due to their plastic composition. This study improves existing sediment microplastic separation techniques by modifying the commonly used conical shape glass separating funnels. The modification consists in connecting a silicone tube at the base of the funnel, whose opening and closure was manually controlled by a Mohr clamp. This adjustment made to the funnels have effectively mitigated critical clogging problems frequently encountered in density separation units. An experiment was conducted using sand-based sediment spiked with polyamide fragments to validate this method modification. Following a complete extraction protocol with the modification of separating funnels, the microplastic extraction efficiency from sediments was high with a 90% recovery rate. Based on these promising results, future studies should consider naturally diverse substrates, as recovery efficiency may be sediment-dependent. Two key adjustments to the glass separation funnels:•Removal of stopcocks•Use of silicone tubes and Mohr clamps to control sediment release.
    Language English
    Publishing date 2023-12-27
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2830212-6
    ISSN 2215-0161
    ISSN 2215-0161
    DOI 10.1016/j.mex.2023.102540
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Personalized gene and cell therapy for Duchenne Muscular Dystrophy.

    Barthélémy, Florian / Wein, Nicolas

    Neuromuscular disorders : NMD

    2018  Volume 28, Issue 10, Page(s) 803–824

    Abstract: Dystrophinopathies are diseases caused by mutations in the Duchenne Muscular Dystrophy gene (DMD) encoding the dystrophin protein. Depending on the type of mutation, patients develop either the severe DMD or the milder Becker Muscular Dystrophy. Although ...

    Abstract Dystrophinopathies are diseases caused by mutations in the Duchenne Muscular Dystrophy gene (DMD) encoding the dystrophin protein. Depending on the type of mutation, patients develop either the severe DMD or the milder Becker Muscular Dystrophy. Although substantial effort was made, the pathophysiology and variation in disease severity are still poorly understood. During the last two decades, relentless efforts were made to develop therapeutic strategies. Among these, gene therapy and cell replacement therapy appear very promising. These approaches are based on the replacement and/or repair of the mutated DMD gene or transcript at the molecular level, or at the cellular level via replacement of the damaged muscle cells. While highly successful in animal models, these therapies showed only modest efficacy in human clinical trials. More importantly, variable effects were observed in patients carrying the same mutation, suggesting that several factors (e.g., genetic modifiers, environmental factors) can affect treatment outcomes. In this review, we will describe recent advancements and new approaches of gene and cell therapies for dystrophinopathies that pave the way for a medicine "à la carte".
    MeSH term(s) Animals ; Cell- and Tissue-Based Therapy ; Genetic Therapy ; Humans ; Muscular Dystrophy, Duchenne/genetics ; Muscular Dystrophy, Duchenne/therapy ; Precision Medicine
    Language English
    Publishing date 2018-07-26
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1077681-3
    ISSN 1873-2364 ; 0960-8966
    ISSN (online) 1873-2364
    ISSN 0960-8966
    DOI 10.1016/j.nmd.2018.06.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3258: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  8. Article: Modeling Patient-Specific Muscular Dystrophy Phenotypes and Therapeutic Responses in Reprogrammed Myotubes Engineered on Micromolded Gelatin Hydrogels.

    Barthélémy, Florian / Santoso, Jeffrey W / Rabichow, Laura / Jin, Rongcheng / Little, Isaiah / Nelson, Stanley F / McCain, Megan L / Miceli, M Carrie

    Frontiers in cell and developmental biology

    2022  Volume 10, Page(s) 830415

    Abstract: ... In ... ...

    Abstract In vitro
    Language English
    Publishing date 2022-04-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2022.830415
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Severe odontogenic infections drastically dropped during the COVID19-confinement: because hospitals became sanctuaries or because of the massive interruption in the consumption of NSAIDs?

    Pham Dang, Nathalie / Kappes, Florian / Pereira, Bruno / Barthélémy, Isabelle / Devoize, Laurent

    Journal of stomatology, oral and maxillofacial surgery

    2020  Volume 122, Issue 2, Page(s) 125–126

    MeSH term(s) Anti-Inflammatory Agents, Non-Steroidal ; COVID-19 ; Hospitals ; Humans ; SARS-CoV-2
    Chemical Substances Anti-Inflammatory Agents, Non-Steroidal
    Keywords covid19
    Language English
    Publishing date 2020-10-29
    Publishing country France
    Document type Editorial
    ZDB-ID 2916276-2
    ISSN 2468-7855 ; 2468-8509
    ISSN (online) 2468-7855
    ISSN 2468-8509
    DOI 10.1016/j.jormas.2020.10.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Transcriptomic analysis of paired healthy human skeletal muscles to identify modulators of disease severity in DMD.

    Nieves-Rodriguez, Shirley / Barthélémy, Florian / Woods, Jeremy D / Douine, Emilie D / Wang, Richard T / Scripture-Adams, Deirdre D / Chesmore, Kevin N / Galasso, Francesca / Miceli, M Carrie / Nelson, Stanley F

    Frontiers in genetics

    2023  Volume 14, Page(s) 1216066

    Abstract: Muscle damage and fibro-fatty replacement of skeletal muscles is a main pathologic feature of Duchenne muscular dystrophy (DMD) with more proximal muscles affected earlier and more distal affected later in the disease course, suggesting that different ... ...

    Abstract Muscle damage and fibro-fatty replacement of skeletal muscles is a main pathologic feature of Duchenne muscular dystrophy (DMD) with more proximal muscles affected earlier and more distal affected later in the disease course, suggesting that different skeletal muscle groups possess distinctive characteristics that influence their susceptibility to disease. To explore transcriptomic factors driving differential gene expression and modulating DMD skeletal muscle severity, we characterized the transcriptome of vastus lateralis (VL), a more proximal and susceptible muscle, relative to tibialis anterior (TA), a more distal and protected muscle, in 15 healthy individuals using bulk RNA sequencing to identify gene expression differences that may mediate their relative susceptibility to damage with loss of dystrophin. Matching single nuclei RNA sequencing data was generated for 3 of the healthy individuals, to infer cell composition in the bulk RNA sequencing dataset and to improve mapping of differentially expressed genes to their cell source of expression. A total of 3,410 differentially expressed genes were identified and mapped to cell type using single nuclei RNA sequencing of muscle, including long non-coding RNAs and protein coding genes. There was an enrichment of genes involved in calcium release from the sarcoplasmic reticulum, particularly in the myofibers and these myofiber genes were higher in the VL. There was an enrichment of genes in "Collagen-Containing Extracellular Matrix" expressed by fibroblasts, endothelial, smooth muscle and pericytes, with most genes higher in the TA, as well as genes in "Regulation Of Apoptotic Process" expressed across all cell types. Previously reported genetic modifiers were also enriched within the differentially expressed genes. We also identify 6 genes with differential isoform usage between the VL and TA. Lastly, we integrate our findings with DMD RNA sequencing data from the TA, and identify "Collagen-Containing Extracellular Matrix" and "Negative Regulation Of Apoptotic Process" as differentially expressed between DMD compared to healthy. Collectively, these findings propose novel candidate mechanisms that may mediate differential muscle susceptibility in muscular dystrophies and provide new insight into potential therapeutic targets.
    Language English
    Publishing date 2023-07-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1216066
    Database MEDical Literature Analysis and Retrieval System OnLINE

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