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Journal articleThillai M, Oldham JM, Ruggiero A, et al., 2024,
Deep Learning-based Segmentation of CT Scans Predicts Disease Progression and Mortality in IPF.
, Am J Respir Crit Care MedRATIONALE: Despite evidence demonstrating a prognostic role for CT scans in IPF, image-based biomarkers are not routinely used in clinical practice or trials. OBJECTIVES: Develop automated imaging biomarkers using deep learning based segmentation of CT scans. METHODS: We developed segmentation processes for four anatomical biomarkers which were applied to a unique cohort of treatment-naive IPF patients enrolled in the PROFILE study and tested against a further UK cohort. The relationship between CT biomarkers, lung function, disease progression and mortality were assessed. MEASUREMENTS AND MAIN RESULTS: Data was analysed from 446 PROFILE patients. Median follow-up was 39.1 months (IQR 18.1-66.4) with cumulative incidence of death of 277 over 5 years (62.1%). Segmentation was successful on 97.8% of all scans, across multiple imaging vendors at slice thicknesses 0.5-5mm. Of 4 segmentations, lung volume showed strongest correlation with FVC (r=0.82, p<0.001). Lung, vascular and fibrosis volumes were consistently associated across cohorts with differential five-year survival, which persisted after adjustment for baseline GAP score. Lower lung volume (HR 0.98, CI 0.96-0.99, p=0.001), increased vascular volume (HR 1.30, CI 1.12-1.51, p=0.001) and increased fibrosis volume (HR 1.17, CI 1.12-1.22, p=<0.001) were associated with reduced two-year progression-free survival in the pooled PROFILE cohort. Longitudinally, decreasing lung volume (HR 3.41; 95% CI 1.36-8.54; p=0.009) and increasing fibrosis volume (HR 2.23; 95% CI 1.22-4.08; p=0.009) were associated with differential survival. CONCLUSIONS: Automated models can rapidly segment IPF CT scans, providing prognostic near and long-term information, which could be used in routine clinical practice or as key trial endpoints. This article is open access and distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).
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Journal articleBrandfellner L, Muratspahić E, Bismarck A, et al., 2024,
Quantitative description of polymer drag reduction: Effect of polyacrylamide molecular weight distributions
, Journal of Non-Newtonian Fluid Mechanics, Vol: 325, ISSN: 0377-0257The effect of molecular weight distribution of polyacrylamide (PAAm) on drag reduction was studied in two flow geometries. Commercial PAAm with different weight averaged molecular weights (Mw = 5 × 105 to 1.8 × 107 g/mol) were investigated in turbulent pipe and rotational flows. Comparison of PAAm with different molecular weight distributions showed that drag reduction is not only a function of the averaged molecular weight. Broader polymer molecular weight distributions provided increased drag reduction over polymers of same average molecular weight but with a more narrow distribution. The role of distribution widths is of significance as polymer degradation in turbulent flows causes narrowing of the molecular weight distributions. Multiple linear regression was employed to connect weight fractions of polyacrylamide with drag reduction. Multiple linear regression was successfully applied to describe drag reduction in turbulent pipe and rotational flows indicating that drag reduction can be quantitatively derived from the molecular weight distribution of PAAm.
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Journal articleSole A, Davies JC, Quintana-Gallego E, 2024,
Cystic Fibrosis: From Salty Malediction to Possible Cure.
, Arch Bronconeumol, Vol: 60, Pages: 129-130 -
Journal articleGrover M, Gang SS, Troemel ER, et al., 2024,
Proteasome inhibition triggers tissue-specific immune responses against different pathogens in C. elegans
, PLoS Biology, Vol: 22, Pages: 1-21, ISSN: 1544-9173Protein quality control pathways play important roles in resistance against pathogen infection. For example, the conserved transcription factor SKN-1/NRF up-regulates proteostasis capacity after blockade of the proteasome and also promotes resistance against bacterial infection in the nematode Caenorhabditis elegans. SKN-1/NRF has 3 isoforms, and the SKN-1A/NRF1 isoform, in particular, regulates proteasomal gene expression upon proteasome dysfunction as part of a conserved bounce-back response. We report here that, in contrast to the previously reported role of SKN-1 in promoting resistance against bacterial infection, loss-of-function mutants in skn-1a and its activating enzymes ddi-1 and png-1 show constitutive expression of immune response programs against natural eukaryotic pathogens of C. elegans. These programs are the oomycete recognition response (ORR), which promotes resistance against oomycetes that infect through the epidermis, and the intracellular pathogen response (IPR), which promotes resistance against intestine-infecting microsporidia. Consequently, skn-1a mutants show increased resistance to both oomycete and microsporidia infections. We also report that almost all ORR/IPR genes induced in common between these programs are regulated by the proteasome and interestingly, specific ORR/IPR genes can be induced in distinct tissues depending on the exact trigger. Furthermore, we show that increasing proteasome function significantly reduces oomycete-mediated induction of multiple ORR markers. Altogether, our findings demonstrate that proteasome regulation keeps innate immune responses in check in a tissue-specific manner against natural eukaryotic pathogens of the C. elegans epidermis and intestine.
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Journal articleMak J, Feary J, Amaral AFS, et al., 2024,
Occupational exposure to particulate matter and staff sickness absence on the London underground
, Environment International, Vol: 185, ISSN: 0160-4120The London Underground (LU) employs over 19,000 staff, some of whom are exposed to elevated concentrations of particulate matter (PM) within the network. This study quantified the occupational exposure of LU staff to subway PM and investigated the possible association with sickness absence (SA). A job exposure matrix to quantify subway PM2.5 staff exposure was developed by undertaking measurement campaigns across the LU network. The association between exposure and SA was evaluated using zero-inflated mixed-effects negative binomial models. Staff PM2.5 exposure varied by job grade and tasks undertaken. Drivers had the highest exposure over a work shift (mean: 261 µg/m3), but concentrations varied significantly by LU line and time the train spent subway. Office staff work in office buildings separate to the LU network and are unexposed to occupational subway PM2.5. They were found to have lower rates of all-cause and respiratory infection SA compared to non-office staff, those who work across the LU network and are occupational exposed to subway PM2.5. Train drivers on five out of eight lines showed higher rates of all-cause SA, but no dose-response relationship was seen. Only drivers from one line showed higher rates of SAs from respiratory infections (incidence rate ratio: 1.24, 95% confidence interval 1.10-1.39). Lower-grade customer service (CS) staff showed higher rates of all-cause and respiratory infection SA compared to higher grade CS staff. Doctor-certified chronic respiratory and cardiovascular SAs were associated with occupational PM2.5 exposure in CS staff and drivers. While some groups with higher occupational exposure to subway PM reported higher rates of SA, no evidence suggests that subway PM is the main contributing factor to SA. This is the largest subway study on health effects of occupational PM2.5 exposure and may have wider implications for subway workers, contributing to safer working environments.
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Journal articlePeng H, Darlington APS, South EJ, et al., 2024,
A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities
, Nature Reviews Microbiology, Vol: 9, Pages: 848-863, ISSN: 1740-1526Engineered microbial consortia often have enhanced system performance and robustness compared with single-strain biomanufacturing production platforms. However, few tools are available for generating co-cultures of the model and key industrial host Saccharomyces cerevisiae. Here we engineer auxotrophic and overexpression yeast strains that can be used to create co-cultures through exchange of essential metabolites. Using these strains as modules, we engineered two- and three-member consortia using different cross-feeding architectures. Through a combination of ensemble modelling and experimentation, we explored how cellular (for example, metabolite production strength) and environmental (for example, initial population ratio, population density and extracellular supplementation) factors govern population dynamics in these systems. We tested the use of the toolkit in a division of labour biomanufacturing case study and show that it enables enhanced and tuneable antioxidant resveratrol production. We expect this toolkit to become a useful resource for a variety of applications in synthetic ecology and biomanufacturing.
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Journal articleDavies J, Mossop M, Jonathan I-H, et al., 2024,
Chronicity Counts: The Impact of P. aeruginosa, S. aureus, and Co-Infection in Cystic Fibrosis
, American Journal of Respiratory and Critical Care Medicine, ISSN: 1073-449X -
Journal articleEder T, Mautner A, Xu Y, et al., 2024,
Transparent PDMS Surfaces with Covalently Attached Lubricants for Enhanced Anti-adhesion Performance.
, ACS Appl Mater Interfaces, Vol: 16, Pages: 10942-10952Liquid-like surfaces featuring slippery, omniphobic, covalently attached liquids (SOCALs) reduce unwanted adhesion by providing a molecularly smooth and slippery surface arising from the high mobility of the liquid chains. Such SOCALs are commonly prepared on hard substrates, such as glass, wafers, or metal oxides, despite the importance of nonpolar elastomeric substrates, such as polydimethylsiloxane (PDMS) in anti-fouling or nonstick applications. Compared to polar elastomers, hydrophobic PDMS elastomer activation and covalent functionalization are significantly more challenging, as PDMS tends to display fast hydrophobic recovery upon activation as well as superficial cracking. Through the extraction of excess PDMS oligomers and fine-tuning of plasma activation parameters, homogeneously functionalized PDMS with fluorinated polysiloxane brushes could be obtained while at the same time reducing crack formation. Polymer brush mobility was increased through the addition of a smaller molecular silane linker to exhibit enhanced dewetting properties and reduced substrate swelling compared to functionalizations featuring hydrocarbon functionalities. Linear polymer brushes were verified by thermogravimetric analysis. The optical properties of PDMS remained unaffected by the activation in high-frequency plasma but were impacted by low-frequency plasma. Drastic decreases in solid adhesion of not just complex contaminants but even ice could be shown in horizontal push tests, demonstrating the potential of SOCAL-functionalized PDMS surfaces for improved nonstick applications.
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Journal articleYoon S, Bae HE, Hariharan P, et al., 2024,
Rational approach to improve detergent efficacy for membrane protein stabilization
, Bioconjugate Chemistry, Vol: 35, Pages: 223-231, ISSN: 1043-1802Membrane protein structures are essential for the molecular understanding of diverse cellular processes and drug discovery. Detergents are not only widely used to extract membrane proteins from membranes but also utilized to preserve native protein structures in aqueous solution. However, micelles formed by conventional detergents are suboptimal for membrane protein stabilization, necessitating the development of novel amphiphilic molecules with enhanced protein stabilization efficacy. In this study, we prepared two sets of tandem malonate-derived glucoside (TMG) variants, both of which were designed to increase the alkyl chain density in micelle interiors. The alkyl chain density was modulated either by reducing the spacer length (TMG-Ms) or by introducing an additional alkyl chain between the two alkyl chains of the original TMGs (TMG-Ps). When evaluated with a few membrane proteins including a G protein-coupled receptor, TMG-P10,8 was found to be substantially more efficient at extracting membrane proteins and also effective at preserving protein integrity in the long term compared to the previously described TMG-A13. This result reveals that inserting an additional alkyl chain between the two existing alkyl chains is an effective way to optimize detergent properties for membrane protein study. This new biochemical tool and the design principle described have the potential to facilitate membrane protein structure determination.
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Journal articleMurphy RA, Pizzato J, Cuthbertson L, et al., 2024,
Antimicrobial peptide glatiramer acetate targets Pseudomonas aeruginosa lipopolysaccharides to breach membranes without altering lipopolysaccharide modification
, npj Antimicrobials and Resistance, Vol: 2, ISSN: 2731-8745Antimicrobial peptides (AMPs) are key components of innate immunity across all domains of life. Natural and synthetic AMPs are receiving renewed attention in efforts to combat the antimicrobial resistance (AMR) crisis and the loss of antibiotic efficacy. The gram-negative pathogen Pseudomonas aeruginosa is one of the most concerning infecting bacteria in AMR, particularly in people with cystic fibrosis (CF) where respiratory infections are difficult to eradicate and associated with increased morbidity and mortality. Cationic AMPs exploit the negatively charged lipopolysaccharides (LPS) on P. aeruginosa to bind and disrupt bacterial membrane(s), causing lethal damage. P. aeruginosa modifies its LPS to evade AMP killing. Free-LPS is also a component of CF sputum and feeds pro-inflammatory cycles. Glatiramer acetate (GA) is a random peptide co-polymer—of glycine, lysine, alanine, tyrosine—used as a drug in treatment of multiple sclerosis (MS); we have previously shown GA to be an AMP which synergises with tobramycin against CF P. aeruginosa, functioning via bacterial membrane disruption. Here, we demonstrate GA’s direct binding and sequestration/neutralisation of P. aeruginosa LPS, in keeping with GA’s ability to disrupt the outer membrane. At CF-relevant LPS concentrations, however, membrane disruption by GA was not strongly inhibited. Furthermore, exposure to GA did not result in increased Lipid A modification of LPS or in increased gene expression of systems involved in AMP sensing and LPS modification. Therefore, despite the electrostatic targeting of LPS by GA as part of its activity, P. aeruginosa does not demonstrate LPS modification in its defence.
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