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  1. Article ; Online: Immersive and interactive visualization of 3D spatio-temporal data using a space time hypercube: Application to cell division and morphogenesis analysis.

    Fouché, Gwendal / Argelaguet, Ferran / Faure, Emmanuel / Kervrann, Charles

    Frontiers in bioinformatics

    2023  Volume 3, Page(s) 998991

    Abstract: The analysis of multidimensional time-varying datasets faces challenges, notably regarding the representation of the data and the visualization of temporal variations. We propose an extension of the well-known Space-Time Cube (STC) visualization ... ...

    Abstract The analysis of multidimensional time-varying datasets faces challenges, notably regarding the representation of the data and the visualization of temporal variations. We propose an extension of the well-known Space-Time Cube (STC) visualization technique in order to visualize time-varying 3D spatial data, taking advantage of the interaction capabilities of Virtual Reality (VR). First, we propose the Space-Time Hypercube (STH) as an abstraction for 3D temporal data, extended from the STC concept. Second, through the example of embryo development imaging dataset, we detail the construction and visualization of a STC based on a user-driven projection of the spatial and temporal information. This projection yields a 3D STC visualization, which can also encode additional numerical and categorical data. Additionally, we propose a set of tools allowing the user to filter and manipulate the 3D STC which benefits the visualization, exploration and interaction possibilities offered by VR. Finally, we evaluated the proposed visualization method in the context of 3D temporal cell imaging data analysis, through a user study (n = 5) reporting the feedback from five biologists. These domain experts also accompanied the application design as consultants, providing insights on how the STC visualization could be used for the exploration of complex 3D temporal morphogenesis data.
    Language English
    Publishing date 2023-03-08
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-7647
    ISSN (online) 2673-7647
    DOI 10.3389/fbinf.2023.998991
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Taeniasis: An unexpected variceal hemorrhage trigger.

    Faure, Emmanuel / Deckmyn, Matthieu

    IDCases

    2021  Volume 24, Page(s) e01087

    Abstract: Here we report a fatal and uncommon case of esophageal variceal bleeding secondary to the presence of a Tapeworm in the upper digestive tract in a patient coming back from North Africa. ...

    Abstract Here we report a fatal and uncommon case of esophageal variceal bleeding secondary to the presence of a Tapeworm in the upper digestive tract in a patient coming back from North Africa.
    Language English
    Publishing date 2021-03-26
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2745454-X
    ISSN 2214-2509
    ISSN 2214-2509
    DOI 10.1016/j.idcr.2021.e01087
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Duodenal Microbiota in Stunted Undernourished Children with Enteropathy.

    Le Guern, Rémi / Stabler, Sarah / Faure, Emmanuel

    The New England journal of medicine

    2021  Volume 384, Issue 18, Page(s) 1777–1778

    MeSH term(s) Child ; Duodenum ; Humans ; Intestinal Diseases/complications ; Microbiota
    Language English
    Publishing date 2021-05-05
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMc2030388
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Immersive and Interactive Visualization of 3D Spatio-Temporal Data using a Space Time Hypercube

    Fouché, Gwendal / Argelaguet, Ferran / Faure, Emmanuel / Kervrann, Charles

    2022  

    Abstract: We propose an extension of the well-known Space-Time Cube (STC) visualization technique in order to visualize time-varying 3D spatial data, taking advantage of the interaction capabilities of Virtual Reality (VR). The analysis of multidimensional time- ... ...

    Abstract We propose an extension of the well-known Space-Time Cube (STC) visualization technique in order to visualize time-varying 3D spatial data, taking advantage of the interaction capabilities of Virtual Reality (VR). The analysis of multidimensional time-varying datasets, which size grows as recording and simulating techniques advance, faces challenges on the representation and visualization of dense data, as well as on the study of temporal variations. First, we propose the Space-Time Hypercube (STH) as an abstraction for 3D temporal data, extended from the STC concept. Second, through the example of embryo development imaging dataset, we detail the construction and visualization of a STC based on a user-driven projection of the spatial and temporal information. This projection yields a 3D STC visualization, which can also encode additional numerical and categorical data. Additionally, we propose a set of tools allowing the user to filter and manipulate the 3D STC which benefits from the visualization, exploration and interaction possibilities offered by VR. Finally, we evaluated the proposed visualization method in the context of the visualization of spatio-temporal biological data. Several biology experts accompanied the application design to provide insight on how the STC visualization could be used to explore such data. We report a user study (n=12) using non-expert users performing a set of exploration and query tasks to evaluate the system.

    Comment: 21 1-column pages, 7 figures
    Keywords Computer Science - Human-Computer Interaction ; Computer Science - Graphics
    Subject code 004
    Publishing date 2022-06-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Book ; Online: Timeline Design Space for Immersive Exploration of Time-Varying Spatial 3D Data

    Fouché, Gwendal / Argelaguet, Ferran / Faure, Emmanuel / Kervrann, Charles

    2022  

    Abstract: Timelines are common visualizations to represent and manipulate temporal data, from historical events storytelling to animation authoring. However, timeline visualizations rarely consider spatio-temporal 3D data (e.g. mesh or volumetric models) directly, ...

    Abstract Timelines are common visualizations to represent and manipulate temporal data, from historical events storytelling to animation authoring. However, timeline visualizations rarely consider spatio-temporal 3D data (e.g. mesh or volumetric models) directly, which are typically explored using 3D visualizers only displaying one time-step at a time. In this paper, leveraging the increased workspace and 3D interaction capabilities of virtual reality, we propose to use timelines for the visualization of 3D temporal data to support exploration and analysis. First, we propose a timeline design space for 3D temporal data extending the timeline design space proposed by Brehmer et al. The proposed design space adapts the scale, layout and representation dimensions to account for the depth dimension and how 3D temporal data can be partitioned and structured. In our approach, an additional dimension is introduced, the support, which further characterizes the 3D dimension of the visualization. To complement the design space and the interaction capabilities of VR systems, we discuss the interaction methods required for the efficient visualization of 3D timelines. Then, to evaluate the benefits of 3D timelines, we conducted a formal evaluation with two main objectives: comparing the proposed visualization with a traditional visualization method; exploring how users interact with different 3D timeline designs. Our results showed that time-related tasks can be achieved more comfortably using timelines, and more efficiently for specific tasks requiring the analysis of the surrounding temporal context. Though the comparison between the different timeline designs were inconclusive, participants reported a clear preference towards the timeline design that did not occupy the vertical space. Finally, we illustrate the use of the 3D timelines to a real use-case on the analysis of biological 3D temporal datasets.

    Comment: 11 pages, 6 figures
    Keywords Computer Science - Human-Computer Interaction ; Computer Science - Graphics
    Subject code 004
    Publishing date 2022-06-20
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Reliability of QuantiFERON®-CMV in predicting CMV recurrence in heart transplant recipients: A single-center retrospective study.

    Sermet, Kevin / Goeminne, Céline / Hantz, Sébastien / Assaf, Ady / Faure, Emmanuel / Lazrek, Mouna / Faure, Karine / Alain, Sophie / Vuotto, Fanny

    Clinical transplantation

    2023  Volume 37, Issue 12, Page(s) e15109

    Abstract: Background: Recurrence after Cytomegalovirus (CMV) infection in heart transplant recipients is difficult to predict, in spite of its high incidence. Secondary prophylaxis could reduce this burden; however, its duration remains unestablished. We ... ...

    Abstract Background: Recurrence after Cytomegalovirus (CMV) infection in heart transplant recipients is difficult to predict, in spite of its high incidence. Secondary prophylaxis could reduce this burden; however, its duration remains unestablished. We evaluated the QuantiFERON®-CMV test to see if it could predict CMV recurrence and help optimize the duration of secondary prophylaxis.
    Methods: This observational retrospective single center study included all heart transplant recipients who developed CMV infection between 2019 and 2021, with the CD8+ T-cell-mediated CMV immunity QuantiFERON®-CMV test assessed at the time of (val)ganciclovir curative treatment completion. The main outcomes were CMV recurrence and duration of secondary prophylaxis. Secondary outcomes included immunosuppressive regimen, rejection, lymphocyte count, CMV viral load, infection type, and duration as possible confounding factors for recurrence.
    Results: Among the 15 patients included, five (33%) experienced recurrence, of whom three (60%) had a positive QuantiFERON®-CMV test. The duration of secondary prophylaxis was similar regardless of QF-CMV positivity. No confounding factor was significantly associated with CMV recurrence; however, it occurred in only 1/7 (14%) of the patients receiving an everolimus-containing immunosuppressive regimen.
    Conclusion: In the population of heart transplant recipients, most of whom received ATG-based induction, the QuantiFERON®-CMV assay may not accurately predict CMV recurrence and would have not helped refining the duration of secondary prophylaxis in our patients. Other cell-mediated immunity tests and strategies in this specific population, including everolimus-containing regimens, may help predict and manage CMV recurrence.
    MeSH term(s) Humans ; Retrospective Studies ; Antiviral Agents/therapeutic use ; Cytomegalovirus ; Everolimus ; Reproducibility of Results ; Cytomegalovirus Infections/diagnosis ; Cytomegalovirus Infections/drug therapy ; Cytomegalovirus Infections/etiology ; Ganciclovir/therapeutic use ; Immunosuppressive Agents/therapeutic use ; Heart Transplantation/adverse effects ; Transplant Recipients
    Chemical Substances Antiviral Agents ; Everolimus (9HW64Q8G6G) ; Ganciclovir (P9G3CKZ4P5) ; Immunosuppressive Agents
    Language English
    Publishing date 2023-08-29
    Publishing country Denmark
    Document type Observational Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639001-8
    ISSN 1399-0012 ; 0902-0063
    ISSN (online) 1399-0012
    ISSN 0902-0063
    DOI 10.1111/ctr.15109
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2204: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  7. Article ; Online: Intracellular

    Malet, Karim / Faure, Emmanuel / Adam, Damien / Donner, Jannik / Liu, Lin / Pilon, Sarah-Jeanne / Fraser, Richard / Jorth, Peter / Newman, Dianne K / Brochiero, Emmanuelle / Rousseau, Simon / Nguyen, Dao

    American journal of respiratory and critical care medicine

    2024  

    Abstract: Rationale: Pseudomonas aeruginosa: Objectives: To detect and characterize intracellular : Methods: We sampled the lung explant tissues from CF patients undergoing lung transplantation and non-CF lung donor control. We analyzed lung tissue sections ...

    Abstract Rationale: Pseudomonas aeruginosa
    Objectives: To detect and characterize intracellular
    Methods: We sampled the lung explant tissues from CF patients undergoing lung transplantation and non-CF lung donor control. We analyzed lung tissue sections for the presence of intracellular
    Measurements and main results: P.a.
    Conclusion: This is the first study describing the presence of intracellular
    Language English
    Publishing date 2024-02-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.202308-1451OC
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  8. Article ; Online: The Brief Case: Mycoplasma hominis Extragenital Abscess.

    Stabler, Sarah / Faure, Emmanuel / Duployez, Claire / Wallet, Frédéric / Dessein, Rodrigue / Le Guern, Rémi

    Journal of clinical microbiology

    2021  Volume 59, Issue 4

    MeSH term(s) Abscess/diagnosis ; Humans ; Mycoplasma Infections/diagnosis ; Mycoplasma hominis/genetics ; Surgical Wound Infection
    Language English
    Publishing date 2021-03-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.02343-20
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    Zs.A 1188: Show issues Location:
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  9. Article ; Online: Closing the Brief Case: Mycoplasma hominis Extragenital Abscess.

    Stabler, Sarah / Faure, Emmanuel / Duployez, Claire / Wallet, Frédéric / Dessein, Rodrigue / Le Guern, Rémi

    Journal of clinical microbiology

    2021  Volume 59, Issue 4

    Language English
    Publishing date 2021-03-19
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.02344-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1188: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    ab Jg. 2022: Lesesaal (EG)

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  10. Article ; Online: Inflammasomes in Tissue Damages and Immune Disorders After Trauma.

    Bortolotti, Perrine / Faure, Emmanuel / Kipnis, Eric

    Frontiers in immunology

    2018  Volume 9, Page(s) 1900

    Abstract: Trauma remains a leading cause of death worldwide. Hemorrhagic shock and direct injury to vital organs are responsible for early mortality whereas most delayed deaths are secondary to complex pathophysiological processes. These processes result from ... ...

    Abstract Trauma remains a leading cause of death worldwide. Hemorrhagic shock and direct injury to vital organs are responsible for early mortality whereas most delayed deaths are secondary to complex pathophysiological processes. These processes result from imbalanced systemic reactions to the multiple aggressions associated with trauma. Trauma results in the uncontrolled local and systemic release of endogenous mediators acting as danger signals [damage-associated molecular patterns (DAMPs)]. Their recognition by the innate immune system triggers a pro-inflammatory immune response paradoxically associated with concomitant immunosuppression. These responses, ranging in intensity from inappropriate to overwhelming, promote the propagation of injuries to remote organs, leading to multiple organ failure and death. Some of the numerous DAMPs released after trauma trigger the assembly of intracellular multiprotein complexes named inflammasomes. Once activated by a ligand, inflammasomes lead to the activation of a caspase. Activated caspases allow the release of mature forms of interleukin-1β and interleukin-18 and trigger a specific pro-inflammatory cell death termed pyroptosis. Accumulating data suggest that inflammasomes, mainly NLRP3, NLRP1, and AIM2, are involved in the generation of tissue damage and immune dysfunction after trauma. Following trauma-induced DAMP(s) recognition, inflammasomes participate in multiple ways in the development of exaggerated systemic and organ-specific inflammatory response, contributing to organ damage. Inflammasomes are involved in the innate responses to traumatic brain injury and contribute to the development of acute respiratory distress syndrome. Inflammasomes may also play a role in post-trauma immunosuppression mediated by dysregulated monocyte functions. Characterizing the involvement of inflammasomes in the pathogenesis of post-trauma syndrome is a key issue as they may be potential therapeutic targets. This review summarizes the current knowledge on the roles of inflammasomes in trauma.
    MeSH term(s) Alarmins/metabolism ; Animals ; Blood Coagulation ; Blood Platelets/metabolism ; Endothelium, Vascular/immunology ; Endothelium, Vascular/metabolism ; Humans ; Immune System/immunology ; Immune System/metabolism ; Immune System Diseases/etiology ; Immune System Diseases/metabolism ; Immune System Diseases/pathology ; Immunity, Innate ; Inflammasomes/metabolism ; Inflammation/etiology ; Inflammation/metabolism ; Inflammation/pathology ; Wounds and Injuries/complications
    Chemical Substances Alarmins ; Inflammasomes
    Language English
    Publishing date 2018-08-16
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2018.01900
    Database MEDical Literature Analysis and Retrieval System OnLINE

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