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  • Journal article
    Barnes H, Elmrayed S, Barber CM, Feary J, Lee CT, Gandhi S, Peters CE, Salisbury ML, Johannson KAet al., 2024,

    Scoping review of exposure questionnaires and surveys in interstitial lung disease.

    , BMJ Open Respir Res, Vol: 11

    BACKGROUND: Many interstitial lung diseases (ILDs) have clear causal relationships with environmental and occupational exposures. Exposure identification can assist with diagnosis, understanding disease pathogenesis, prognostication and prevention of disease progression and occurrence in others at risk. Despite the importance of exposure identification in ILD, there is no standardised assessment approach. Many questionnaires are in clinical and research use, yet their utility, applicability, relevance and performance characteristics are unknown. OBJECTIVES: This scoping review aimed to summarise the available evidence relating to ILD exposure assessment questionnaires, identify research gaps and inform the content for a future single evidence-based ILD questionnaire. METHODS: A scoping review based on Arksey and O'Malley's methodological framework was conducted. ELIGIBILITY CRITERIA: Any questionnaire that elicited exposures specific to ILD was included. A modified COSMIN Risk of Bias Framework was used to assess quality. SOURCES OF EVIDENCE: Relevant articles were identified from MEDLINE and EMBASE up to 23 July 2023. RESULTS: 22 exposure questionnaires were identified, including 15 generally pertaining to ILD, along with several disease-specific questionnaires for hypersensitivity pneumonitis (n=4), chronic beryllium disease, sarcoidosis and silicosis (1 questionnaire each). For most questionnaires, quality was low, whereby the methods used to determine exposure inclusion and questionnaire validation were not reported or not performed. Collectively the questionnaires covered 158 unique exposures and at-risk occupations, most commonly birds, mould/water damage, wood dust, asbestos, farming, automotive mechanic and miners. Only five questionnaires also provided free-text fields, and 13 queried qualifiers such as temporality or respiratory protection. CONCLUSIONS: Designing a robust ILD-specific questionnaire should include an evidence-based and relevance-based appro

  • Journal article
    Xu Y, Tang L, Nok-Iangthong C, Wagner M, Baumann G, Feist F, Bismarck A, Jiang Qet al., 2024,

    Functionally Gradient Macroporous Polymers: Emulsion Templating Offers Control over Density, Pore Morphology, and Composition.

    , ACS Appl Polym Mater, Vol: 6, Pages: 5150-5162

    Gradient macroporous polymers were produced by polymerization of emulsion templates comprising a continuous monomer phase and an internal aqueous template phase. To produce macroporous polymers with gradient composition, pore size, and foam density, we varied the template formulation, droplet size, and internal phase ratio of emulsion templates continuously and stacked those prior to polymerization. Using the outlined approach, it is possible to vary one property along the resulting macroporous polymer while retaining the other properties. The elastic moduli and crush strengths change along the gradient of the macroporous polymers; their mechanical properties are dominated by those of the weakest layers in the gradient. Macroporous polymers with gradient chemical composition and thus stiffness provide both high impact load and energy adsorption, rendering the gradient foam suitable for impact protective applications. We show that dual-dispensing and simultaneous blending of two different emulsion formulations in various ratios results in a fine, bidirectional change of the template composition, enabling the production of true gradient macroporous polymers with a high degree of design freedom.

  • Journal article
    Hernández-García J, Serrano-Mislata A, Lozano-Quiles M, Úrbez C, Nohales MA, Blanco-Touriñán N, Peng H, Ledesma-Amaro R, Blázquez MAet al., 2024,

    DELLA proteins recruit the Mediator complex subunit MED15 to coactivate transcription in land plants

    , Proceedings of the National Academy of Sciences of USA, Vol: 121, ISSN: 0027-8424

    DELLA proteins are negative regulators of the gibberellin response pathway in angiosperms, acting as central hubs that interact with hundreds of transcription factors (TFs) and regulators to modulate their activities. While the mechanism of TF sequestration by DELLAs to prevent DNA binding to downstream targets has been extensively documented, the mechanism that allows them to act as coactivators remains to be understood. Here, we demonstrate that DELLAs directly recruit the Mediator complex to specific loci in Arabidopsis, facilitating transcription. This recruitment involves DELLA amino-terminal domain and the conserved MED15 KIX domain. Accordingly, partial loss of MED15 function mainly disrupted processes known to rely on DELLA coactivation capacity, including cytokinin-dependent regulation of meristem function and skotomorphogenic response, gibberellin metabolism feedback, and flavonol production. We have also found that the single DELLA protein in the liverwort Marchantia polymorpha is capable of recruiting MpMED15 subunits, contributing to transcriptional coactivation. The conservation of Mediator-dependent transcriptional coactivation by DELLA between Arabidopsis and Marchantia implies that this mechanism is intrinsic to the emergence of DELLA in the last common ancestor of land plants.

  • Journal article
    Hassan S, Syun-Ichi U, Shabeer S, Kiran TA, Wu C-F, Moriyama H, Coutts RHA, Kotta Loizou I, Jamal Aet al., 2024,

    Molecular and biological characterization of a novel partitivirus from Talaromyces pinophilus

    , Virus Research, Vol: 343, ISSN: 0168-1702

    Talaromyces spp. have a worldwide distribution, are ecologically diverse and have been isolated from numerous different substrates. Talaromyces spp. are considered biotechnologically important due to their ability to produce a range of enzymes and pigments. Talaromyces pinophilus, belonging to genus Talaromyces and family Trichocomaceae, is known for producing several important bioactive metabolites. Here we report the isolation and characterisation of a partitivirus from T. pinophilus which we have nominated Talaromyces pinophilus partitivirus-1 (TpPV-1). TpPV-1 possesses a genome consisting of three double stranded (ds) RNA segments i.e., dsRNAs1-3, 1824 bp, 1638 bp and 1451 bp respectively, which are encapsidated in icosahedral particles 35 nm in diameter. Both dsRNA1 and dsRNA2 contain a single open reading frame (ORF) encoding respectively a 572 amino acid (aa) protein of 65 kDa and a 504 aa protein of 50 kDa. The third segment (dsRNA3) is potentially a satellite RNA. Phylogenetic analysis revealed that the TpPV-1 belongs to the family Partitiviridae in the proposed genus Zetapartitivirus. TpPV-1 infection decreases the mycelial growth rate of the host fungus and alters pigmentation as indicated by time course experiments performed on a range of different solid media comparing virus-infected and virus-free isogenic lines. This is the first report of mycovirus infection in T. pinophilus and may provide insights into understanding the effect of the mycovirus on the production of enzymes and pigments by the host fungus.

  • Journal article
    Wu Z, Smith DJF, Yazbeck L, Saunders P, Smith JA, Maher TM, Molyneaux PLet al., 2024,

    Cough Severity Visual Analog Scale Assesses Cough Burden and Predicts Survival in Idiopathic Pulmonary Fibrosis.

    , Am J Respir Crit Care Med, Vol: 209, Pages: 1165-1167
  • Journal article
    Darawshy F, Molyneaux PL, Segal LN, 2024,

    Looking Beyond the Lower Airways for Microbes Affecting Pulmonary Fibrosis.

    , Am J Respir Crit Care Med, Vol: 209, Pages: 1054-1056
  • Journal article
    Mohammed A, Mohammed C, Mautner A, Kistow M, Chaitram P, Bismarck A, Ward Ket al., 2024,

    On the performance of Sargassum-derived calcium alginate ion exchange resins for Pb2+ adsorption: batch and packed bed applications.

    , Environ Sci Pollut Res Int, Vol: 31, Pages: 31224-31239

    Driven by climate change and human activity, Sargassum blooming rates have intensified, producing copious amount of the invasive, pelagic seaweed across the Caribbean and Latin America. Battery recycling and lead-smelter wastes have heavily polluted the environment and resulted in acute lead poisoning in children through widespread heavy metal contamination particular in East Trinidad. Our study details a comprehensive investigation into the use of Sargassum (S. natans), as a potential resource-circular feedstock for the synthesis of calcium alginate beads utilized in heavy metal adsorption, both in batch and column experiments. Here, ionic cross-linking of extracted sodium alginate with calcium chloride was utilized to create functional ion-exchange beads. Given the low quality of alginates extracted from Sargassum which produce poor morphological beads, composite beads in conjunction with graphene oxide and acrylamide were used to improve fabrication. Stand-alone calcium alginate beads exhibited superior Pb2+ adsorption, with a capacity of 213 mg g-1 at 20 °C and pH 3.5, surpassing composite and commercial resins. Additives like acrylamide and graphene oxide in composite alginate resins led to a 21-40% decrease in Pb2+ adsorption due to reduced active sites. Column operations confirmed Alginate systems' practicality, with 20-24% longer operating times, 15 times lower adsorbent mass on scale-up and 206% smaller column diameters compared to commercial counterparts. Ultimately, this study advocates for Sargassum-based Alginate ion-exchange beads as a bio-based alternative in Trinidad and developing nations for dealing with heavy metal ion waste, offering superior heavy metal adsorption performance and supporting resource circularity.

  • Journal article
    Merckx VSFT, Gomes SIF, Wang D, Verbeek C, Jacquemyn H, Zahn FE, Gebauer G, Bidartondo MIet al., 2024,

    Mycoheterotrophy in the wood-wide web

    , Nature Plants, Vol: 10, Pages: 710-718, ISSN: 2055-026X

    The prevalence and potential functions of common mycorrhizal networks, or the 'wood-wide web', resulting from the simultaneous interaction of mycorrhizal fungi and roots of different neighbouring plants have been increasingly capturing the interest of science and society, sometimes leading to hyperbole and misinterpretation. Several recent reviews conclude that popular claims regarding the widespread nature of these networks in forests and their role in the transfer of resources and information between plants lack evidence. Here we argue that mycoheterotrophic plants associated with ectomycorrhizal or arbuscular mycorrhizal fungi require resource transfer through common mycorrhizal networks and thus are natural evidence for the occurrence and function of these networks, offering a largely overlooked window into this methodologically challenging underground phenomenon. The wide evolutionary and geographic distribution of mycoheterotrophs and their interactions with a broad phylogenetic range of mycorrhizal fungi indicate that common mycorrhizal networks are prevalent, particularly in forests, and result in net carbon transfer among diverse plants through shared mycorrhizal fungi. On the basis of the available scientific evidence, we propose a continuum of carbon transfer options within common mycorrhizal networks, and we discuss how knowledge on the biology of mycoheterotrophic plants can be instrumental for the study of mycorrhizal-mediated transfers between plants.

  • Journal article
    Hameed T, Motsi N, Bignell E, Tanaka Ret al., 2024,

    Inferring fungal growth rates from optical density data

    , PLoS Computational Biology, Vol: 20, ISSN: 1553-734X

    Quantifying fungal growth underpins our ability to effectively treat severe fungal infections. Current methods quantify fungal growth rates from time-course morphology-specific data, such as hyphal length data. However, automated large-scale collection of such data lies beyond the scope of most clinical microbiology laboratories. In this paper, we propose a mathematical model of fungal growth to estimate morphology-specific growth rates from easy-to-collect, but indirect, optical density (OD600) data of Aspergillus fumigatus growth (filamentous fungus). Our method accounts for OD600 being an indirect measure by explicitly including the relationship between the indirect OD600 measurements and the calibrating true fungal growth in the model. Therefore, the method does not require de novo generation of calibration data. Our model outperformed reference models at fitting to and predicting OD600 growth curves and overcame observed discrepancies between morphology-specific rates inferred from OD600 versus directly measured data in reference models that did not include calibration.

  • Journal article
    Desai SR, Sivarasan N, Johannson KA, George PM, Culver DA, Devaraj A, Lynch DA, Milne D, Renzoni E, Nunes H, Sverzellati N, Spagnolo P, Baughman RP, Yadav R, Piciucchi S, Walsh SLF, Kouranos V, Wells AU, Sarcoid Delphi Groupet al., 2024,

    High-resolution CT phenotypes in pulmonary sarcoidosis: a multinational Delphi consensus study.

    , Lancet Respir Med, Vol: 12, Pages: 409-418

    One view of sarcoidosis is that the term covers many different diseases. However, no classification framework exists for the future exploration of pathogenetic pathways, genetic or trigger predilections, patterns of lung function impairment, or treatment separations, or for the development of diagnostic algorithms or relevant outcome measures. We aimed to establish agreement on high-resolution CT (HRCT) phenotypic separations in sarcoidosis to anchor future CT research through a multinational two-round Delphi consensus process. Delphi participants included members of the Fleischner Society and the World Association of Sarcoidosis and other Granulomatous Disorders, as well as members' nominees. 146 individuals (98 chest physicians, 48 thoracic radiologists) from 28 countries took part, 144 of whom completed both Delphi rounds. After rating of 35 Delphi statements on a five-point Likert scale, consensus was achieved for 22 (63%) statements. There was 97% agreement on the existence of distinct HRCT phenotypes, with seven HRCT phenotypes that were categorised by participants as non-fibrotic or likely to be fibrotic. The international consensus reached in this Delphi exercise justifies the formulation of a CT classification as a basis for the possible definition of separate diseases. Further refinement of phenotypes with rapidly achievable CT studies is now needed to underpin the development of a formal classification of sarcoidosis.

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