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  • Conference paper
    Santofimio VQ, Knox-Brown B, Potts J, Bartlett-Pestell S, Feary J, Amaral AFSet al., 2024,

    Small airways obstruction and mortality in the UK Biobank

    , European-Respiratory-Society Congress (ERS), Publisher: EUROPEAN RESPIRATORY SOC JOURNALS LTD, ISSN: 0903-1936
  • Conference paper
    Fiorenzo E, Kumar K, Kebadze T, Losa F, Mallia P, Singanayagam A, Edwards M, Johnston Set al., 2024,

    <i>β</i> 2-agonists induce and augment rhinovirus-induction of pro-inflammatory mediators in bronchial epithelial cells.

    , European-Respiratory-Society Congress (ERS), Publisher: EUROPEAN RESPIRATORY SOC JOURNALS LTD, ISSN: 0903-1936
  • Conference paper
    Tanaka A, Filippidis FT, El Asma ML, Reed A, Gerovasili Vet al., 2024,

    Pregnancy Outcomes and Management in Lung and Heart Transplant Recipients: A Systematic Review

    , Publisher: EUROPEAN RESPIRATORY SOC JOURNALS LTD, ISSN: 0903-1936
  • Conference paper
    Johnson E, Crichton M, Gilmour A, Long M, Shuttleworth M, Cant E, De Soyza A, Dimakou K, Shteinberg M, Spinou A, Ringshausen F, Lorent N, Goeminne P, Loebinger M, Chotirmall S, Dhar R, Hawort C, Altenburg J, Blasi F, Welte T, Sibila O, Aliberti S, Shoemark A, Mallia P, Footit J, Johnston S, Singanayagam A, Chalmers Jet al., 2024,

    Sputum Azurocidin-1 is a marker of disease severity and microbiome dysbiosis in adult bronchiectasis, and increases in response to Rhinovirus challenge in COPD.

    , European-Respiratory-Society Congress (ERS), Publisher: EUROPEAN RESPIRATORY SOC JOURNALS LTD, ISSN: 0903-1936
  • Journal article
    Moratto E, Tang Z, Bozkurt T, Sena Get al., 2024,

    Reduction of Phytophthora palmivora plant root infection in weak electric fields

    , Scientific Reports, Vol: 14, ISSN: 2045-2322

    The global food security crisis is partly caused by significant crop losses due to pests and pathogens, leading to economic burdens. Phytophthora palmivora, an oomycete pathogen, affects many plantation crops and costs over USD 1 billion each year. Unfortunately, there is currently no prevention plan in place, highlighting the urgent need for an effective solution. P. palmivora produces motile zoospores that respond to weak electric fields. Here, we show that external electric fields can be used to reduce root infection in two plant species. We developed two original essays to study the effects of weak electric fields on the interaction between P. palmivora’s zoospores and roots of Arabidopsis thaliana and Medicago truncatula. In the first configuration, a global artificial electric field is set up to induce ionic currents engulfing the plant roots while, in the second configuration, ionic currents are induced only locally and at a distance from the roots. In both cases, we found that weak ionic currents (250–550 μA) are sufficient to reduce zoospore attachment to Arabidopsis and Medicago roots, without affecting plant health. Moreover, we show that the same configurations decrease P. palmivora mycelial growth in Medicago roots after 24 h. We conclude that ionic currents can reduce more than one stage of P. palmivora root infection in hydroponics. Overall, our findings suggest that weak external electric fields can be used as a sustainable strategy for preventing P. palmivora infection, providing innovative prospects for agricultural crop protection.

  • Journal article
    Liu C, Cheng S, Shi M, Shah A, Bai W, Arcucci Ret al., 2024,

    IMITATE: Clinical Prior Guided Hierarchical Vision-Language Pre-training.

    , IEEE Trans Med Imaging, Vol: PP

    In the field of medical Vision-Language Pretraining (VLP), significant efforts have been devoted to deriving text and image features from both clinical reports and associated medical images. However, most existing methods may have overlooked the opportunity in leveraging the inherent hierarchical structure of clinical reports, which are generally split into 'findings' for descriptive content and 'impressions' for conclusive observation. Instead of utilizing this rich, structured format, current medical VLP approaches often simplify the report into either a unified entity or fragmented tokens. In this work, we propose a novel clinical prior guided VLP framework named IMITATE to learn the structure information from medical reports with hierarchical vision-language alignment. The framework derives multi-level visual features from the chest X-ray (CXR) images and separately aligns these features with the descriptive and the conclusive text encoded in the hierarchical medical report. Furthermore, a new clinical-informed contrastive loss is introduced for cross-modal learning, which accounts for clinical prior knowledge in formulating sample correlations in contrastive learning. The proposed model, IMITATE, outperforms baseline VLP methods across six different datasets, spanning five medical imaging downstream tasks. Comprehensive experimental results highlight the advantages of integrating the hierarchical structure of medical reports for vision-language alignment.

  • Journal article
    sun M, Xiong Gao A, Liu X, Ledesma Amaro R, Bai Zet al., 2024,

    Microbial conversion of ethanol to high-value products: progress and challenges

    , Biotechnology for Biofuels and Bioproducts, Vol: 17, ISSN: 2731-3654

    Industrial biotechnology heavily relies on the microbial conversion of carbohydrate substrates derived from sugar- or starch-rich crops. This dependency poses significant challenges in the face of a rising population and food scarcity. Consequently, exploring renewable, non-competing carbon sources for sustainable bioprocessing becomes increasingly important. Ethanol, a key C2 feedstock, presents a promising alternative, especially for producing acetyl-CoA derivatives. In this review, we offer an in-depth analysis of ethanol's potential as an alternative carbon source, summarizing its distinctive characteristics when utilized by microbes, microbial ethanol metabolism pathway, and microbial responses and tolerance mechanisms to ethanol stress. We provide an update on recent progress in ethanol-based biomanufacturing and ethanol biosynthesis, discuss current challenges, and outline potential research directions to guide future advancements in this field. The insights presented here could serve as valuable theoretical support for researchers and industry professionals seeking to harness ethanol's potential for the production of high-value products.

  • Journal article
    Dobra R, Carroll S, Davies JC, Dowdall F, Duff A, Elderton A, Georgiopoulos AM, Massey-Chase R, McNally P, Puckey M, Madge Set al., 2024,

    Exploring the complexity of cystic fibrosis (CF) and psychosocial wellbeing in the 2020s: current and future challenges

    , Paediatric Respiratory Reviews, ISSN: 1526-0542

    Cystic fibrosis (CF) is traditionally associated with considerable and progressive multisystem pathology, onerous treatment burden, complex psychosocial challenges, and reduced life-expectancy [1], [2], [3], [4], [5], [6], [7], [8], [9].This decade has seen transformative change in management for many, but not all, people with CF. The most notable change comes from Cystic Fibrosis Transmembrane Receptor (CFTR) modulators, which bring significant benefits for people who are eligible for, and able to access, them [10]. However alongside, or perhaps because of, this exciting progress, the past few years have also brought important novel challenges to the psychosocial wellbeing of people with CF.This article, written as a collaboration between CF psychologists, social workers, physicians and nurses aims to provide an accessible overview of the novel psychosocial challenges now faced by children, their families, and adults with CF, and to invite consideration of their changing psychosocial requirements to inform future holistic care. Themes include geopolitical stressors such as the pandemic and its wake, a growing divide between those able or unable to access CFTR modulators, potential rapid changes in life expectancy secondary to these drugs and the inevitable associated challenges this brings; evolving body image, mental health side effects of CFTR modulators, the challenges of adherence in apparently well children and young adults, as well as the diagnostic conundrum and associated anxiety of the cystic fibrosis screen positive inconclusive diagnosis (CFSPID) label. It also highlights some unmet research and service delivery needs in the area.

  • Journal article
    Thillai M, Oldham JM, Ruggiero A, Kanavati F, McLellan T, Saini G, Johnson SR, Ble F-X, Azim A, Ostridge K, Platt A, Belvisi M, Maher TM, Molyneaux PLet al., 2024,

    Deep Learning-based Segmentation of Computed Tomography Scans Predicts Disease Progression and Mortality in Idiopathic Pulmonary Fibrosis

    , AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, Vol: 210, Pages: 465-472, ISSN: 1073-449X
  • Conference paper
    Huang Y, Ma S-F, Oldham JM, Adegunsoye A, Zhu D, Murray S, Kim JS, Bonham C, Strickland E, Linderholm AL, Lee CT, Paul T, Mannem H, Maher TM, Molyneaux PL, Strek ME, Martinez FJ, Noth Iet al., 2024,

    Machine Learning of Plasma Proteomics Classifies Diagnosis of Interstitial Lung Disease

    , International Conference of the American-Thoracic-Society (ATS), Publisher: AMER THORACIC SOC, Pages: 444-454, ISSN: 1073-449X

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