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  1. Article ; Online: How does the microbiota control systemic innate immunity?

    Jordan, Christine K I / Clarke, Thomas B

    Trends in immunology

    2024  Volume 45, Issue 2, Page(s) 94–102

    Abstract: The intestinal microbiota has a pervasive influence on mammalian innate immunity fortifying defenses to infection in tissues throughout the host. How intestinal microbes control innate defenses in systemic tissues is, however, poorly defined. In our ... ...

    Abstract The intestinal microbiota has a pervasive influence on mammalian innate immunity fortifying defenses to infection in tissues throughout the host. How intestinal microbes control innate defenses in systemic tissues is, however, poorly defined. In our opinion, there are three core challenges that need addressing to advance our understanding of how the intestinal microbiota controls innate immunity systemically: first, deciphering how signals from intestinal microbes are transmitted to distal tissues; second, unraveling how intestinal microbes prime systemic innate immunity without inducing widespread immunopathology; and third, identifying which intestinal microbes control systemic immunity. Here, we propose answers to these problems which provide a framework for understanding how microbes in the intestine can regulate innate immunity systemically.
    MeSH term(s) Animals ; Humans ; Immunity, Innate ; Intestines ; Microbiota ; Gastrointestinal Microbiome ; Intestinal Mucosa ; Mammals
    Language English
    Publishing date 2024-01-11
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2036831-8
    ISSN 1471-4981 ; 1471-4906
    ISSN (online) 1471-4981
    ISSN 1471-4906
    DOI 10.1016/j.it.2023.12.002
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  2. Article: Correction: Abiotic microcompartments form when neighbouring droplets fuse: an electrochemiluminescence investigation.

    Voci, Silvia / Clarke, Thomas B / Dick, Jeffrey E

    Chemical science

    2023  Volume 14, Issue 27, Page(s) 7595

    Abstract: This corrects the article DOI: 10.1039/D2SC06553C.]. ...

    Abstract [This corrects the article DOI: 10.1039/D2SC06553C.].
    Language English
    Publishing date 2023-06-29
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2559110-1
    ISSN 2041-6539 ; 2041-6520
    ISSN (online) 2041-6539
    ISSN 2041-6520
    DOI 10.1039/d3sc90104a
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  3. Article ; Online: Preferential Electroreduction at the Oil|Water|Conductor Interface.

    Clarke, Thomas B / Dick, Jeffrey E

    The journal of physical chemistry letters

    2022  Volume 13, Issue 15, Page(s) 3338–3341

    Abstract: Chemistry in confined volumes, such as aqueous droplets, is different from bulk, continuous water. However, few techniques are available to probe interfacial reactivity in complex, multiphase environments. Here, we demonstrate preferential ... ...

    Abstract Chemistry in confined volumes, such as aqueous droplets, is different from bulk, continuous water. However, few techniques are available to probe interfacial reactivity in complex, multiphase environments. Here, we demonstrate preferential electroreduction at the oil|water|conductor (three-phase) interface. Electrodeposition of cobalt and nickel results in ringlike structures that can be characterized with tens of nanometers precision in scanning electron microscopy and energy dispersive X-ray spectroscopy. To demonstrate the generalizability of these observations, we show that electroreduction of resazurin to fluorescent resorufin occurs preferentially at the three-phase boundary. The preferential electroreduction does not depend on droplet geometry. These results, grounded in three-phase boundary reactivity, are highly important across all fields of chemistry and biology because they highlight how the interface can change chemistry in unexpected ways.
    MeSH term(s) Water/chemistry
    Chemical Substances Water (059QF0KO0R)
    Language English
    Publishing date 2022-04-08
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.2c00545
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  4. Article ; Online: Interfacial solute flux promotes emulsification at the water|oil interface.

    Colón-Quintana, Guillermo S / Clarke, Thomas B / Dick, Jeffrey E

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 705

    Abstract: Emulsions are critical across a broad spectrum of industries. Unfortunately, emulsification requires a significant driving force for droplet dispersion. Here, we demonstrate a mechanism of spontaneous droplet formation (emulsification), where the ... ...

    Abstract Emulsions are critical across a broad spectrum of industries. Unfortunately, emulsification requires a significant driving force for droplet dispersion. Here, we demonstrate a mechanism of spontaneous droplet formation (emulsification), where the interfacial solute flux promotes droplet formation at the liquid-liquid interface when a phase transfer agent is present. We have termed this phenomenon fluxification. For example, when HAuCl
    Language English
    Publishing date 2023-02-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-35964-9
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  5. Conference proceedings ; Online: Re-evaluation of GRACE Groundwater Drought Index (GGDI)

    Akl, M. / Thomas, B. / Clarke, P.

    XXVIII General Assembly of the International Union of Geodesy and Geophysics (IUGG)

    Precise accounting of surface water changes

    2023  

    Abstract: ... drought. Thomas et al., (2017) developed a framework to evaluate groundwater drought occurrence across ...

    Abstract Groundwater is a crucial resource for drinking water, agricultural irrigation, and industry, and its sustainable management is essential for maintaining economic development and healthy ecosystems. Climate change (e.g., droughts) and human interventions (e.g., land use change, and water withdrawals) increase global reliance on groundwater, leading to more pressure on already depleted aquifers. A lack of direct groundwater observations presents many challenges to assess groundwater stores, especially when under stress caused by groundwater drought. Thomas et al., (2017) developed a framework to evaluate groundwater drought occurrence across California Central Valley (CCV), based on observations from NASA's Gravity Recovery and Climate Experiment (GRACE) satellite mission. The GRACE Groundwater Drought Index (GGDI), a normalized GRACE-groundwater time series, was shown to quantify groundwater storage deficits attributed to groundwater drought. The GGDI demonstrated a good agreement with in-situ groundwater drought timeseries, capturing the characteristics of groundwater drought in the CCV. As applied for the CCV, in-situ records of surface water storage changes were used to derive GRACE-groundwater. However, many follow-on studies have applied GGDI without strict accounting for surface water storage change. Accurate extraction of GRACE-groundwater requires robust estimation of water budget components; thus, it stands to reason that accounting for surface water stores within GGDI would result in a more robust estimate of groundwater drought. The aim of this project is to investigate the influence of accounting for surface water changes within GGDI on capturing groundwater storage deficits. Our findings indicated that a strict accounting of changes in surface water stores improved GGDI’s ability to identify groundwater drought characteristics across large-scale basins.
    Language English
    Publishing country de
    Document type Conference proceedings ; Online
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  6. Article ; Online: Automated extraction of clinical measures from videos of oculofacial disorders using machine learning: feasibility, validity and reliability.

    Schulz, Christopher B / Clarke, Holly / Makuloluwe, Sarith / Thomas, Peter B / Kang, Swan

    Eye (London, England)

    2023  Volume 37, Issue 13, Page(s) 2810–2816

    Abstract: Objectives: To determine the feasibility, validity and reliability of automatically extracting clinically meaningful eyelid measurements from consumer-grade videos of individuals with oculofacial disorders.: Methods: A custom computer program was ... ...

    Abstract Objectives: To determine the feasibility, validity and reliability of automatically extracting clinically meaningful eyelid measurements from consumer-grade videos of individuals with oculofacial disorders.
    Methods: A custom computer program was designed to automatically extract clinical measures from consumer-grade videos. This program was applied to publicly available videos of individuals with oculofacial disorders, and age-matched controls. The primary outcomes were margin reflex distance 1 (MRD1) and 2 (MRD2), blink lagophthalmos, and ocular surface area exposure. Test-retest reliability was evaluated using Bland-Altman analysis to compare the agreement in obtained measures between separate videos of the same individual taken within 48 h of each other.
    Results: MRD1 was reduced in individuals with ptosis versus controls (2.2 mm versus 3.4 mm, p < 0.001), and increased in individuals with facial nerve palsy (FNP) (3.9 mm, p = 0.049) and thyroid eye disease (TED) (4.1 mm; p = 0.038). Blink lagophthalmos was increased in individuals with FNP (3.7 mm); p < 0.001) and those with TED (0.1 mm, p = 0.003) versus controls (0.0 mm). Ocular surface exposure was reduced in individuals with ptosis compared with controls (12.2 mm
    Conclusions: The presented program is capable of taking consumer grade videos of patients with oculofacial disease and providing clinically meaningful and reliable eyelid measurements that show promising validity.
    MeSH term(s) Humans ; Reproducibility of Results ; Feasibility Studies ; Eyelids ; Blepharoptosis/diagnosis ; Facial Paralysis ; Graves Ophthalmopathy ; Machine Learning ; Retrospective Studies
    Language English
    Publishing date 2023-02-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 91001-6
    ISSN 1476-5454 ; 0950-222X
    ISSN (online) 1476-5454
    ISSN 0950-222X
    DOI 10.1038/s41433-023-02424-z
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  7. Article ; Online: Rapid SABRE Catalyst Scavenging Using Functionalized Silicas.

    Robertson, Thomas B R / Clarke, Leon J / Mewis, Ryan E

    Molecules (Basel, Switzerland)

    2022  Volume 27, Issue 2

    Abstract: In recent years the NMR hyperpolarisation method signal amplification by reversible exchange (SABRE) has been applied to multiple substrates of potential interest for in vivo investigation. Unfortunately, SABRE commonly requires an iridium-containing ... ...

    Abstract In recent years the NMR hyperpolarisation method signal amplification by reversible exchange (SABRE) has been applied to multiple substrates of potential interest for in vivo investigation. Unfortunately, SABRE commonly requires an iridium-containing catalyst that is unsuitable for biomedical applications. This report utilizes inductively coupled plasma-optical emission spectroscopy (ICP-OES) to investigate the potential use of metal scavengers to remove the iridium catalytic species from the solution. The most sensitive iridium emission line at 224.268 nm was used in the analysis. We report the effects of varying functionality, chain length, and scavenger support identity on iridium scavenging efficiency. The impact of varying the quantity of scavenger utilized is reported for the three scavengers with the highest iridium removed from initial investigations: 3-aminopropyl (
    Language English
    Publishing date 2022-01-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules27020332
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  8. Article: Abiotic microcompartments form when neighbouring droplets fuse: an electrochemiluminescence investigation.

    Voci, Silvia / Clarke, Thomas B / Dick, Jeffrey E

    Chemical science

    2022  Volume 14, Issue 9, Page(s) 2336–2341

    Abstract: Many studies have shown chemistry proceeds differently in small volumes compared to bulk phases. However, few studies exist elucidating spontaneous means by which small volumes can form in Nature. Such studies are critical in understanding the formation ... ...

    Abstract Many studies have shown chemistry proceeds differently in small volumes compared to bulk phases. However, few studies exist elucidating spontaneous means by which small volumes can form in Nature. Such studies are critical in understanding the formation of life in microcompartments. In this study, we track in real-time the coalescence of two or more water microdroplets adsorbed on an electrified surface in a 1,2-dichloroethane continuous phase by electrogenerated chemiluminescence (ECL) imaging, uncovering the spontaneous generation of multiple emulsions inside the resulting water droplets. During the fusion of adsorbed water droplets with each other on the electrode surface, volumes of organic and water phases are entrapped in between and detected respectively as ECL not-emitting and emitting regions. The diameter of those confined environments inside the water droplets can be less than a micrometer, as described by scanning electron microscopy data. This study adds a new mechanism for the generation of micro- and nano-emulsions and provides insight into confinement techniques under abiotic conditions as well as new potential strategies in microfluidic devices.
    Language English
    Publishing date 2022-12-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2559110-1
    ISSN 2041-6539 ; 2041-6520
    ISSN (online) 2041-6539
    ISSN 2041-6520
    DOI 10.1039/d2sc06553c
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  9. Article ; Online: Interfacial solute flux promotes emulsification at the water|oil interface

    Guillermo S. Colón-Quintana / Thomas B. Clarke / Jeffrey E. Dick

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 9

    Abstract: Emulsions are critical across a broad spectrum of industries. Here authors demonstrate a mechanism of spontaneous droplet formation, where the interfacial solute flux promotes droplet formation at the liquid-liquid interface when a phase transfer agent ... ...

    Abstract Emulsions are critical across a broad spectrum of industries. Here authors demonstrate a mechanism of spontaneous droplet formation, where the interfacial solute flux promotes droplet formation at the liquid-liquid interface when a phase transfer agent is present.
    Keywords Science ; Q
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
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  10. Article ; Online: Microbiota-mediated protection against antibiotic-resistant pathogens.

    Panwar, Rekha B / Sequeira, Richard P / Clarke, Thomas B

    Genes and immunity

    2021  Volume 22, Issue 5-6, Page(s) 255–267

    Abstract: Colonization by the microbiota provides one of our most effective barriers against infection by pathogenic microbes. The microbiota protects against infection by priming immune defenses, by metabolic exclusion of pathogens from their preferred niches, ... ...

    Abstract Colonization by the microbiota provides one of our most effective barriers against infection by pathogenic microbes. The microbiota protects against infection by priming immune defenses, by metabolic exclusion of pathogens from their preferred niches, and through direct antimicrobial antagonism. Disruption of the microbiota, especially by antibiotics, is a major risk factor for bacterial pathogen colonization. Restoration of the microbiota through microbiota transplantation has been shown to be an effective way to reduce pathogen burden in the intestine but comes with a number of drawbacks, including the possibility of transferring other pathogens into the host, lack of standardization, and potential disruption to host metabolism. More refined methods to exploit the power of the microbiota would allow us to utilize its protective power without the drawbacks of fecal microbiota transplantation. To achieve this requires detailed understanding of which members of the microbiota protect against specific pathogens and the mechanistic basis for their effects. In this review, we will discuss the clinical and experimental evidence that has begun to reveal which members of the microbiota protect against some of the most troublesome antibiotic-resistant pathogens: Klebsiella pneumoniae, vancomycin-resistant enterococci, and Clostridioides difficile.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Clostridioides difficile ; Klebsiella pneumoniae ; Microbiota
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2021-05-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2060566-3
    ISSN 1476-5470 ; 1466-4879
    ISSN (online) 1476-5470
    ISSN 1466-4879
    DOI 10.1038/s41435-021-00129-5
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